AB351700
 

Information on mRNA AB351700

Description: Mus musculus non-coding RNA, oocyte_piRNA2516, complete sequence.
Gene: n/a
Product: n/a
Author: Watanabe,T., Totoki,Y., Toyoda,A., Kaneda,M., Kuramochi-Miyagawa,S., Obata,Y., Chiba,H., Kohara,Y., Kono,T., Nakano,T., Surani,M.A., Sakaki,Y. and Sasaki,H.
Organism: Mus musculus
Tissue: ovary
Development stage: p8
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2008-04-24
Version: 1
mRNA sequence: AB351700
Position: chr12:57049408-57049431

mRNA/Genomic Alignments

The alignment you clicked on is first in the table below.
BROWSER | SIZE IDENTITY CHROMOSOME  STRAND    START     END              QUERY      START  END  TOTAL
-----------------------------------------------------------------------------------------------------
browser |    24  100.0%         12     -  57049408  57049431              AB351700     1    24    26
browser |    24  100.0%          1     -   7622963   7622986              AB351700     1    24    26
browser |    26  100.0%          1     +  12119986  12120011              AB351700     1    26    26
browser |    25  100.0%          1     -  27976752  27976776              AB351700     1    25    26
browser |    24  100.0%          1     +  30926719  30926742              AB351700     1    24    26
browser |    24  100.0%          1     -  31108755  31108778              AB351700     1    24    26
browser |    26  100.0%          1     -  35175937  35175962              AB351700     1    26    26
browser |    25  100.0%          1     +  37751730  37751754              AB351700     1    25    26
browser |    25  100.0%          1     -  38643411  38643435              AB351700     1    25    26
browser |    25  100.0%          1     -  39153559  39153583              AB351700     1    25    26
browser |    25  100.0%          1     -  45885252  45885276              AB351700     1    25    26
browser |    24  100.0%          1     +  50524116  50524139              AB351700     1    24    26
browser |    24  100.0%          1     +  72661416  72661439              AB351700     1    24    26
browser |    26  100.0%          1     +  75767505  75767530              AB351700     1    26    26
browser |    26  100.0%          1     +  78501421  78501446              AB351700     1    26    26
browser |    25  100.0%          1     +  92126281  92126305              AB351700     1    25    26
browser |    26  100.0%          1     - 100528527 100528552              AB351700     1    26    26
browser |    25  100.0%          1     - 103916632 103916656              AB351700     1    25    26
browser |    25  100.0%          1     + 111928499 111928523              AB351700     1    25    26
browser |    26  100.0%          1     + 122295341 122295366              AB351700     1    26    26
browser |    25  100.0%          1     + 125694041 125694065              AB351700     1    25    26
browser |    25  100.0%          1     + 132179275 132179299              AB351700     1    25    26
browser |    26  100.0%          1     - 146297076 146297101              AB351700     1    26    26
browser |    25  100.0%          1     + 164559945 164559969              AB351700     1    25    26
browser |    25  100.0%          1     + 176361118 176361142              AB351700     1    25    26
browser |    25  100.0%          1     - 178085619 178085643              AB351700     1    25    26
browser |    26  100.0%         10     +   3580119   3580144              AB351700     1    26    26
browser |    26  100.0%         10     +   5722503   5722528              AB351700     1    26    26
browser |    25  100.0%         10     -  17558347  17558371              AB351700     1    25    26
browser |    26  100.0%         10     -  20500470  20500495              AB351700     1    26    26
browser |    26  100.0%         10     +  38769487  38769512              AB351700     1    26    26
browser |    26  100.0%         10     +  57462973  57462998              AB351700     1    26    26
browser |    24  100.0%         10     +  57711281  57711304              AB351700     2    25    26
browser |    26  100.0%         10     +  57726123  57726148              AB351700     1    26    26
browser |    26  100.0%         10     +  73544669  73544694              AB351700     1    26    26
browser |    25  100.0%         10     -  79949412  79949436              AB351700     1    25    26
browser |    25  100.0%         10     +  80604715  80604739              AB351700     1    25    26
browser |    26  100.0%         10     +  83267272  83267297              AB351700     1    26    26
browser |    24  100.0%         10     -  84452801  84452824              AB351700     2    25    26
browser |    26  100.0%         10     -  85699261  85699286              AB351700     1    26    26
browser |    25  100.0%         10     +  88836718  88836742              AB351700     1    25    26
browser |    25  100.0%         10     +  95117780  95117804              AB351700     1    25    26
browser |    24  100.0%         10     - 110948045 110948068              AB351700     2    25    26
browser |    24  100.0%         10     + 122460406 122460429              AB351700     1    24    26
browser |    26  100.0%         11     +   9744497   9744522              AB351700     1    26    26
browser |    25  100.0%         11     -  17245291  17245315              AB351700     1    25    26
browser |    26  100.0%         11     -  20052858  20052883              AB351700     1    26    26
browser |    25  100.0%         11     +  20142510  20142534              AB351700     1    25    26
browser |    26  100.0%         11     +  21243754  21243779              AB351700     1    26    26
browser |    25  100.0%         11     +  59945491  59945515              AB351700     1    25    26
browser |    25  100.0%         11     - 110953519 110953543              AB351700     1    25    26
browser |    26  100.0%         12     +   3601966   3601991              AB351700     1    26    26
browser |    24  100.0%         12     -  11876875  11876898              AB351700     1    24    26
browser |    26  100.0%         12     -  28986221  28986246              AB351700     1    26    26
browser |    25  100.0%         12     +  40050555  40050579              AB351700     1    25    26
browser |    26  100.0%         12     -  44268229  44268254              AB351700     1    26    26
browser |    25  100.0%         12     +  51275504  51275528              AB351700     1    25    26
browser |    26  100.0%         12     -  58713520  58713545              AB351700     1    26    26
browser |    24  100.0%         12     -  61496028  61496051              AB351700     3    26    26
browser |    26  100.0%         12     -  63970638  63970663              AB351700     1    26    26
browser |    25  100.0%         12     -  63970919  63970943              AB351700     1    25    26
browser |    26  100.0%         12     -  66111331  66111356              AB351700     1    26    26
browser |    25  100.0%         12     +  82547346  82547370              AB351700     1    25    26
browser |    26  100.0%         12     +  86293537  86293562              AB351700     1    26    26
browser |    25  100.0%         12     - 117398843 117398867              AB351700     2    26    26
browser |    26  100.0%         13     -   3355205   3355230              AB351700     1    26    26
browser |    26  100.0%         13     -  10237049  10237074              AB351700     1    26    26
browser |    26  100.0%         13     +  16510910  16510935              AB351700     1    26    26
browser |    26  100.0%         13     +  16510966  16510991              AB351700     1    26    26
browser |    24  100.0%         13     -  17862334  17862357              AB351700     1    24    26
browser |    25  100.0%         13     +  26678053  26678077              AB351700     1    25    26
browser |    25  100.0%         13     -  49914152  49914176              AB351700     1    25    26
browser |    25  100.0%         13     +  57455296  57455320              AB351700     1    25    26
browser |    25  100.0%         13     +  57543701  57543725              AB351700     1    25    26
browser |    25  100.0%         13     -  96800149  96800173              AB351700     1    25    26
browser |    26  100.0%         13     - 119105661 119105686              AB351700     1    26    26
browser |    26  100.0%         14     -   9092214   9092239              AB351700     1    26    26
browser |    26  100.0%         14     +  12878002  12878027              AB351700     1    26    26
browser |    25  100.0%         14     -  14368458  14368482              AB351700     1    25    26
browser |    26  100.0%         14     -  28512721  28512746              AB351700     1    26    26
browser |    26  100.0%         14     -  51486330  51486355              AB351700     1    26    26
browser |    26  100.0%         14     -  56389678  56389703              AB351700     1    26    26
browser |    25  100.0%         14     -  64303890  64303914              AB351700     1    25    26
browser |    26  100.0%         14     -  71678015  71678040              AB351700     1    26    26
browser |    25  100.0%         14     +  81855738  81855762              AB351700     1    25    26
browser |    26  100.0%         14     - 110532636 110532661              AB351700     1    26    26
browser |    25  100.0%         14     - 114198928 114198952              AB351700     1    25    26
browser |    26  100.0%         14     + 115700825 115700850              AB351700     1    26    26
browser |    26  100.0%         14     - 121009232 121009257              AB351700     1    26    26
browser |    26  100.0%         14     - 122405803 122405828              AB351700     1    26    26
browser |    26  100.0%         15     +  17471169  17471194              AB351700     1    26    26
browser |    26  100.0%         15     -  19362071  19362096              AB351700     1    26    26
browser |    26  100.0%         15     -  19378169  19378194              AB351700     1    26    26
browser |    26  100.0%         15     -  29898551  29898576              AB351700     1    26    26
browser |    26  100.0%         15     -  61827933  61827958              AB351700     1    26    26
browser |    25  100.0%         15     +  67028939  67028963              AB351700     1    25    26
browser |    26  100.0%         15     +  72350302  72350327              AB351700     1    26    26
browser |    25  100.0%         15     +  75472759  75472783              AB351700     1    25    26
browser |    26  100.0%         15     +  77324257  77324282              AB351700     1    26    26
browser |    25  100.0%         15     +  77362856  77362880              AB351700     1    25    26
browser |    25  100.0%         15     -  77542407  77542431              AB351700     1    25    26
browser |    26  100.0%         15     -  77590482  77590507              AB351700     1    26    26
browser |    26  100.0%         15     +  85315539  85315564              AB351700     1    26    26
browser |    26  100.0%         16     +   3697754   3697779              AB351700     1    26    26
browser |    26  100.0%         16     -   4000106   4000131              AB351700     1    26    26
browser |    26  100.0%         16     +   4675261   4675286              AB351700     1    26    26
browser |    26  100.0%         16     +  18315036  18315061              AB351700     1    26    26
browser |    25  100.0%         16     -  31047186  31047210              AB351700     1    25    26
browser |    26  100.0%         16     +  58769283  58769308              AB351700     1    26    26
browser |    26  100.0%         16     -  64626444  64626469              AB351700     1    26    26
browser |    26  100.0%         16     -  71018150  71018175              AB351700     1    26    26
browser |    26  100.0%         16     +  85084177  85084202              AB351700     1    26    26
browser |    25  100.0%         16     -  91852198  91852222              AB351700     1    25    26
browser |    25  100.0%         16     +  91904610  91904634              AB351700     1    25    26
browser |    25  100.0%         17     -   4161222   4161246              AB351700     1    25    26
browser |    25  100.0%         17     -  33829297  33829321              AB351700     1    25    26
browser |    25  100.0%         17     -  53391159  53391183              AB351700     1    25    26
browser |    25  100.0%         17     +  56529032  56529056              AB351700     1    25    26
browser |    25  100.0%         17     -  64059299  64059323              AB351700     1    25    26
browser |    25  100.0%         17     -  66278865  66278889              AB351700     1    25    26
browser |    24  100.0%         17     -  68248805  68248828              AB351700     2    25    26
browser |    25  100.0%         17     -  83897350  83897374              AB351700     1    25    26
browser |    25  100.0%         17     -  87394458  87394482              AB351700     1    25    26
browser |    25  100.0%         17     +  87454979  87455003              AB351700     1    25    26
browser |    26  100.0%         18     +   6850753   6850778              AB351700     1    26    26
browser |    24  100.0%         18     +  31536835  31536858              AB351700     1    24    26
browser |    25  100.0%         18     +  71116940  71116964              AB351700     1    25    26
browser |    25  100.0%         18     -  82361088  82361112              AB351700     1    25    26
browser |    25  100.0%         19     -  11113818  11113842              AB351700     1    25    26
browser |    26  100.0%         19     +  15879569  15879594              AB351700     1    26    26
browser |    25  100.0%         19     -  31065860  31065884              AB351700     1    25    26
browser |    25  100.0%         19     -  31071758  31071782              AB351700     1    25    26
browser |    25  100.0%         19     -  36360051  36360075              AB351700     1    25    26
browser |    26  100.0%         19     +  39915763  39915788              AB351700     1    26    26
browser |    26  100.0%         19     -  46666786  46666811              AB351700     1    26    26
browser |    25  100.0%         19     +  49547705  49547729              AB351700     1    25    26
browser |    26  100.0%         19     +  49897850  49897875              AB351700     1    26    26
browser |    26  100.0%         19     +  58555844  58555869              AB351700     1    26    26
browser |    26  100.0%          2     +   4108390   4108415              AB351700     1    26    26
browser |    26  100.0%          2     -   4669224   4669249              AB351700     1    26    26
browser |    26  100.0%          2     -   5225911   5225936              AB351700     1    26    26
browser |    25  100.0%          2     +  11074035  11074059              AB351700     1    25    26
browser |    26  100.0%          2     -  11410594  11410619              AB351700     1    26    26
browser |    26  100.0%          2     +  19988175  19988200              AB351700     1    26    26
browser |    25  100.0%          2     +  23956470  23956494              AB351700     1    25    26
browser |    25  100.0%          2     -  25041260  25041284              AB351700     1    25    26
browser |    26  100.0%          2     -  29003195  29003220              AB351700     1    26    26
browser |    24  100.0%          2     +  44752954  44752977              AB351700     3    26    26
browser |    24  100.0%          2     +  57765197  57765220              AB351700     3    26    26
browser |    25  100.0%          2     -  72735505  72735529              AB351700     1    25    26
browser |    25  100.0%          2     +  95925527  95925551              AB351700     1    25    26
browser |    25  100.0%          2     - 108115388 108115412              AB351700     1    25    26
browser |    25  100.0%          2     - 108169076 108169100              AB351700     1    25    26
browser |    25  100.0%          2     - 148505098 148505122              AB351700     1    25    26
browser |    25  100.0%          2     - 150391274 150391298              AB351700     1    25    26
browser |    26  100.0%          2     - 157024871 157024896              AB351700     1    26    26
browser |    26  100.0%          2     - 167368109 167368134              AB351700     1    26    26
browser |    25  100.0%          2     + 170830721 170830745              AB351700     1    25    26
browser |    26  100.0%          3     -  10510894  10510919              AB351700     1    26    26
browser |    26  100.0%          3     +  22012347  22012372              AB351700     1    26    26
browser |    25  100.0%          3     -  33765241  33765265              AB351700     1    25    26
browser |    26  100.0%          3     -  35687274  35687299              AB351700     1    26    26
browser |    25  100.0%          3     -  48474879  48474903              AB351700     1    25    26
browser |    25  100.0%          3     +  50029734  50029758              AB351700     1    25    26
browser |    25  100.0%          3     -  53477942  53477966              AB351700     1    25    26
browser |    25  100.0%          3     +  53526472  53526496              AB351700     1    25    26
browser |    25  100.0%          3     +  54548990  54549014              AB351700     1    25    26
browser |    25  100.0%          3     -  62425412  62425436              AB351700     1    25    26
browser |    25  100.0%          3     -  66325415  66325439              AB351700     1    25    26
browser |    26  100.0%          3     -  69836820  69836845              AB351700     1    26    26
browser |    25  100.0%          3     + 115012500 115012524              AB351700     1    25    26
browser |    26  100.0%          3     - 118073861 118073886              AB351700     1    26    26
browser |    25  100.0%          3     + 124897063 124897087              AB351700     1    25    26
browser |    25  100.0%          3     + 139555223 139555247              AB351700     1    25    26
browser |    26  100.0%          3     - 144664617 144664642              AB351700     1    26    26
browser |    26  100.0%          4     +  16209951  16209976              AB351700     1    26    26
browser |    26  100.0%          4     -  21839850  21839875              AB351700     1    26    26
browser |    26  100.0%          4     +  21989274  21989299              AB351700     1    26    26
browser |    25  100.0%          4     +  49929742  49929766              AB351700     1    25    26
browser |    26  100.0%          4     +  98711924  98711949              AB351700     1    26    26
browser |    25  100.0%          4     - 101844131 101844155              AB351700     1    25    26
browser |    26  100.0%          4     + 123780493 123780518              AB351700     1    26    26
browser |    26  100.0%          4     - 127858890 127858915              AB351700     1    26    26
browser |    26  100.0%          4     - 143785783 143785808              AB351700     1    26    26
browser |    25  100.0%          4     + 145093595 145093619              AB351700     1    25    26
browser |    26  100.0%          4     + 150566079 150566104              AB351700     1    26    26
browser |    26  100.0%          5     -   3357108   3357133              AB351700     1    26    26
browser |    25  100.0%          5     -   6885187   6885211              AB351700     1    25    26
browser |    25  100.0%          5     +  14044258  14044282              AB351700     1    25    26
browser |    26  100.0%          5     -  17181796  17181821              AB351700     1    26    26
browser |    25  100.0%          5     +  17795740  17795764              AB351700     1    25    26
browser |    26  100.0%          5     +  24427215  24427240              AB351700     1    26    26
browser |    26  100.0%          5     -  25089012  25089037              AB351700     1    26    26
browser |    26  100.0%          5     +  29894992  29895017              AB351700     1    26    26
browser |    25  100.0%          5     +  34560916  34560940              AB351700     1    25    26
browser |    26  100.0%          5     +  46998638  46998663              AB351700     1    26    26
browser |    26  100.0%          5     -  49713439  49713464              AB351700     1    26    26
browser |    24  100.0%          5     -  65902021  65902044              AB351700     2    25    26
browser |    26  100.0%          5     -  67306285  67306310              AB351700     1    26    26
browser |    26  100.0%          5     +  68241599  68241624              AB351700     1    26    26
browser |    26  100.0%          5     +  93688900  93688925              AB351700     1    26    26
browser |    26  100.0%          5     -  93938110  93938135              AB351700     1    26    26
browser |    26  100.0%          5     -  94019058  94019083              AB351700     1    26    26
browser |    26  100.0%          5     -  94303569  94303594              AB351700     1    26    26
browser |    26  100.0%          5     -  94391912  94391937              AB351700     1    26    26
browser |    26  100.0%          5     -  95040710  95040735              AB351700     1    26    26
browser |    26  100.0%          5     -  95282395  95282420              AB351700     1    26    26
browser |    26  100.0%          5     -  95357966  95357991              AB351700     1    26    26
browser |    26  100.0%          5     -  95599990  95600015              AB351700     1    26    26
browser |    26  100.0%          5     -  95684903  95684928              AB351700     1    26    26
browser |    26  100.0%          5     -  95919175  95919200              AB351700     1    26    26
browser |    25  100.0%          5     - 103452132 103452156              AB351700     1    25    26
browser |    25  100.0%          5     + 117107039 117107063              AB351700     1    25    26
browser |    25  100.0%          5     + 121685959 121685983              AB351700     1    25    26
browser |    25  100.0%          5     + 122053018 122053042              AB351700     1    25    26
browser |    26  100.0%          5     + 125680473 125680498              AB351700     1    26    26
browser |    25  100.0%          5     + 127409912 127409936              AB351700     1    25    26
browser |    25  100.0%          5     - 136885877 136885901              AB351700     1    25    26
browser |    26  100.0%          5     + 138225230 138225255              AB351700     1    26    26
browser |    26  100.0%  5_GL456354v1_random     +     67911     67936              AB351700     1    26    26
browser |    26  100.0%  5_GL456354v1_random     +    115434    115459              AB351700     1    26    26
browser |    26  100.0%  5_JH584296v1_random     +     25362     25387              AB351700     1    26    26
browser |    26  100.0%  5_JH584296v1_random     +    105944    105969              AB351700     1    26    26
browser |    26  100.0%  5_JH584297v1_random     +     92340     92365              AB351700     1    26    26
browser |    26  100.0%  5_JH584297v1_random     +    172877    172902              AB351700     1    26    26
browser |    26  100.0%  5_JH584298v1_random     -     28157     28182              AB351700     1    26    26
browser |    26  100.0%  5_JH584298v1_random     -    109582    109607              AB351700     1    26    26
browser |    26  100.0%  5_JH584299v1_random     -    116603    116628              AB351700     1    26    26
browser |    26  100.0%  5_JH584299v1_random     -    192103    192128              AB351700     1    26    26
browser |    26  100.0%  5_JH584299v1_random     -    496390    496415              AB351700     1    26    26
browser |    26  100.0%  5_JH584299v1_random     -    743881    743906              AB351700     1    26    26
browser |    26  100.0%  5_JH584299v1_random     -    856420    856445              AB351700     1    26    26
browser |    26  100.0%          6     -  16261125  16261150              AB351700     1    26    26
browser |    25  100.0%          6     +  34070010  34070034              AB351700     1    25    26
browser |    26  100.0%          6     -  37787007  37787032              AB351700     1    26    26
browser |    25  100.0%          6     -  40082553  40082577              AB351700     1    25    26
browser |    26  100.0%          6     +  60483221  60483246              AB351700     1    26    26
browser |    26  100.0%          6     +  60494167  60494192              AB351700     1    26    26
browser |    24  100.0%          6     -  71151506  71151529              AB351700     2    25    26
browser |    26  100.0%          6     -  71429063  71429088              AB351700     1    26    26
browser |    26  100.0%          6     -  85557101  85557126              AB351700     1    26    26
browser |    26  100.0%          6     -  85944934  85944959              AB351700     1    26    26
browser |    26  100.0%          6     +  96459760  96459785              AB351700     1    26    26
browser |    24  100.0%          6     - 101641582 101641605              AB351700     1    24    26
browser |    25  100.0%          6     - 124398258 124398282              AB351700     1    25    26
browser |    26  100.0%          6     + 131638315 131638340              AB351700     1    26    26
browser |    25  100.0%          6     - 136517578 136517602              AB351700     1    25    26
browser |    26  100.0%          6     - 148547588 148547613              AB351700     1    26    26
browser |    26  100.0%          6     - 148783187 148783212              AB351700     1    26    26
browser |    26  100.0%          6     + 149341679 149341704              AB351700     1    26    26
browser |    26  100.0%          7     -   3188973   3188998              AB351700     1    26    26
browser |    25  100.0%          7     -   5343641   5343665              AB351700     1    25    26
browser |    25  100.0%          7     +   6421196   6421220              AB351700     1    25    26
browser |    24  100.0%          7     -  10146641  10146664              AB351700     1    24    26
browser |    26  100.0%          7     +  16027686  16027711              AB351700     1    26    26
browser |    25  100.0%          7     +  29357655  29357679              AB351700     1    25    26
browser |    24  100.0%          7     +  30867359  30867382              AB351700     2    25    26
browser |    26  100.0%          7     +  35332582  35332607              AB351700     1    26    26
browser |    26  100.0%          7     -  39559859  39559884              AB351700     1    26    26
browser |    26  100.0%          7     -  62722502  62722527              AB351700     1    26    26
browser |    25  100.0%          7     +  63108435  63108459              AB351700     1    25    26
browser |    24  100.0%          7     -  77229916  77229939              AB351700     3    26    26
browser |    25  100.0%          7     + 118072427 118072451              AB351700     1    25    26
browser |    25  100.0%          7     + 127556945 127556969              AB351700     1    25    26
browser |    26  100.0%          7     + 141197389 141197414              AB351700     1    26    26
browser |    24  100.0%          8     +   4752678   4752701              AB351700     1    24    26
browser |    25  100.0%          8     +  14378096  14378120              AB351700     1    25    26
browser |    25  100.0%          8     -  25006152  25006176              AB351700     1    25    26
browser |    25  100.0%          8     -  25906105  25906130              AB351700     1    25    26
browser |    26  100.0%          8     +  32199943  32199968              AB351700     1    26    26
browser |    26  100.0%          8     +  32235259  32235284              AB351700     1    26    26
browser |    24  100.0%          8     -  50768929  50768952              AB351700     1    24    26
browser |    26  100.0%          8     +  53597746  53597771              AB351700     1    26    26
browser |    25  100.0%          8     -  54188374  54188398              AB351700     1    25    26
browser |    25  100.0%          8     -  59678974  59678998              AB351700     1    25    26
browser |    24  100.0%          8     +  60701364  60701387              AB351700     3    26    26
browser |    25  100.0%          8     -  62866136  62866160              AB351700     1    25    26
browser |    25  100.0%          8     -  65365634  65365658              AB351700     1    25    26
browser |    26  100.0%          8     -  75177006  75177031              AB351700     1    26    26
browser |    26  100.0%          8     +  96862044  96862069              AB351700     1    26    26
browser |    26  100.0%          8     - 110421958 110421983              AB351700     1    26    26
browser |    26  100.0%          8     + 122892653 122892678              AB351700     1    26    26
browser |    26  100.0%          8     - 126970615 126970640              AB351700     1    26    26
browser |    25  100.0%          9     -  18869505  18869529              AB351700     1    25    26
browser |    25  100.0%          9     +  19862605  19862629              AB351700     1    25    26
browser |    26  100.0%          9     +  21383117  21383142              AB351700     1    26    26
browser |    25  100.0%          9     +  21998882  21998906              AB351700     1    25    26
browser |    26  100.0%          9     +  35708701  35708726              AB351700     1    26    26
browser |    24  100.0%          9     -  38151732  38151755              AB351700     1    24    26
browser |    24  100.0%          9     +  49264080  49264103              AB351700     1    24    26
browser |    25  100.0%          9     -  52180751  52180775              AB351700     1    25    26
browser |    26  100.0%          9     -  75625499  75625524              AB351700     1    26    26
browser |    25  100.0%          9     +  76488835  76488859              AB351700     1    25    26
browser |    25  100.0%          9     -  79968530  79968554              AB351700     1    25    26
browser |    25  100.0%          9     +  94975912  94975936              AB351700     1    25    26
browser |    25  100.0%          9     + 120114843 120114867              AB351700     1    25    26
browser |    25  100.0%          X     +  13253250  13253274              AB351700     1    25    26
browser |    26  100.0%          X     +  16020801  16020826              AB351700     1    26    26
browser |    25  100.0%          X     +  16473187  16473211              AB351700     1    25    26
browser |    25  100.0%          X     -  17961148  17961172              AB351700     1    25    26
browser |    26  100.0%          X     +  20468790  20468815              AB351700     1    26    26
browser |    26  100.0%          X     +  22588848  22588873              AB351700     1    26    26
browser |    26  100.0%          X     +  23479722  23479747              AB351700     1    26    26
browser |    25  100.0%          X     -  44816611  44816635              AB351700     1    25    26
browser |    25  100.0%          X     +  64265549  64265573              AB351700     1    25    26
browser |    25  100.0%          X     +  64269748  64269772              AB351700     1    25    26
browser |    26  100.0%          X     +  77881294  77881319              AB351700     1    26    26
browser |    25  100.0%          X     +  79001690  79001714              AB351700     1    25    26
browser |    26  100.0%          X     +  91766613  91766638              AB351700     1    26    26
browser |    25  100.0%          X     + 100520774 100520798              AB351700     1    25    26
browser |    26  100.0%          X     - 104473448 104473473              AB351700     1    26    26
browser |    26  100.0%          X     + 104511399 104511424              AB351700     1    26    26
browser |    26  100.0%          X     - 110597302 110597327              AB351700     1    26    26
browser |    25  100.0%          X     + 128983285 128983309              AB351700     1    25    26
browser |    25  100.0%          X     - 145677941 145677965              AB351700     1    25    26
browser |    25  100.0%          X     + 161946917 161946941              AB351700     1    25    26
browser |    25  100.0%  X_GL456233v2_random     +    104300    104324              AB351700     1    25    26
browser |    24  100.0%          Y     +   1373983   1374006              AB351700     3    26    26
browser |    26  100.0%          Y     +   1379966   1379991              AB351700     1    26    26

View details of parts of alignment within browser window
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Go to Mouse mRNAs track controls

Data last updated at UCSC: 2020-08-18

Description

The mRNA track shows alignments between mouse mRNAs in GenBank and the genome.

Display Conventions and Configuration

This track follows the display conventions for PSL alignment tracks. In dense display mode, the items that are more darkly shaded indicate matches of better quality.

The description page for this track has a filter that can be used to change the display mode, alter the color, and include/exclude a subset of items within the track. This may be helpful when many items are shown in the track display, especially when only some are relevant to the current task.

To use the filter:

  1. Type a term in one or more of the text boxes to filter the mRNA display. For example, to apply the filter to all mRNAs expressed in a specific organ, type the name of the organ in the tissue box. To view the list of valid terms for each text box, consult the table in the Table Browser that corresponds to the factor on which you wish to filter. For example, the "tissue" table contains all the types of tissues that can be entered into the tissue text box. Multiple terms may be entered at once, separated by a space. Wildcards may also be used in the filter.
  2. If filtering on more than one value, choose the desired combination logic. If "and" is selected, only mRNAs that match all filter criteria will be highlighted. If "or" is selected, mRNAs that match any one of the filter criteria will be highlighted.
  3. Choose the color or display characteristic that should be used to highlight or include/exclude the filtered items. If "exclude" is chosen, the browser will not display mRNAs that match the filter criteria. If "include" is selected, the browser will display only those mRNAs that match the filter criteria.

This track may also be configured to display codon coloring, a feature that allows the user to quickly compare mRNAs against the genomic sequence. For more information about this option, go to the Codon and Base Coloring for Alignment Tracks page. Several types of alignment gap may also be colored; for more information, go to the Alignment Insertion/Deletion Display Options page.

Methods

GenBank mouse mRNAs were aligned against the genome using the blat program. When a single mRNA aligned in multiple places, the alignment having the highest base identity was found. Only alignments having a base identity level within 0.5% of the best and at least 96% base identity with the genomic sequence were kept.

Credits

The mRNA track was produced at UCSC from mRNA sequence data submitted to the international public sequence databases by scientists worldwide.

References

Benson DA, Cavanaugh M, Clark K, Karsch-Mizrachi I, Lipman DJ, Ostell J, Sayers EW. GenBank. Nucleic Acids Res. 2013 Jan;41(Database issue):D36-42. PMID: 23193287; PMC: PMC3531190

Benson DA, Karsch-Mizrachi I, Lipman DJ, Ostell J, Wheeler DL. GenBank: update. Nucleic Acids Res. 2004 Jan 1;32(Database issue):D23-6. PMID: 14681350; PMC: PMC308779

Kent WJ. BLAT - the BLAST-like alignment tool. Genome Res. 2002 Apr;12(4):656-64. PMID: 11932250; PMC: PMC187518