AK209157
 

Information on mRNA AK209157

Description: Mus musculus cDNA, clone:Y2G0114C23, strand:unspecified.
Gene: n/a
Product: n/a
Author: Watahiki,A., Waki,K., Hayatsu,N., Shiraki,T., Kondo,S., Nakamura,M., Sasaki,D., Arakawa,T., Kawai,J., Harbers,M., Hayashizaki,Y. and Carninci,P.
Organism: Mus musculus
Tissue: n/a
Development stage: n/a
Cell line: mixture of B16-F10Y and melan-c
Sex: n/a
Library: Alternative Splicing Library L3
Clone: Y2G0114C23
CDS: n/a
Date: 2008-08-19
Version: 1
mRNA sequence: AK209157
Position: chr12:56797149-56797266

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 |   118   99.2%         12     -  56797149  56797266              AK209157     3   120   120
browser |   118   99.2%          1     -   6505863   6505980              AK209157     3   120   120
browser |   117   99.2%          1     -   8730875   8730991              AK209157     3   119   120
browser |   118   99.2%          1     +  16810179  16810296              AK209157     3   120   120
browser |   118   99.2%          1     +  19694387  19694504              AK209157     3   120   120
browser |   118   99.2%          1     +  27220943  27221060              AK209157     3   120   120
browser |   118   99.2%          1     +  34388276  34388393              AK209157     3   120   120
browser |   118   99.2%          1     +  35829272  35829389              AK209157     3   120   120
browser |   118   99.2%          1     +  55819225  55819342              AK209157     3   120   120
browser |   118   99.2%          1     +  56813079  56813196              AK209157     3   120   120
browser |   118   99.2%          1     -  58367789  58367906              AK209157     3   120   120
browser |   118   99.2%          1     -  60769283  60769400              AK209157     3   120   120
browser |   118   99.2%          1     -  65004745  65004862              AK209157     3   120   120
browser |   118   99.2%          1     -  66062052  66062169              AK209157     3   120   120
browser |   118   99.2%          1     -  67795857  67795974              AK209157     3   120   120
browser |   118   99.2%          1     +  70277961  70278078              AK209157     3   120   120
browser |   118   99.2%          1     -  74697865  74697982              AK209157     3   120   120
browser |   118   99.2%          1     +  79916486  79916603              AK209157     3   120   120
browser |   118   99.2%          1     -  87066640  87066757              AK209157     3   120   120
browser |   118   99.2%          1     -  91404213  91404330              AK209157     3   120   120
browser |   118   99.2%          1     +  93886009  93886126              AK209157     3   120   120
browser |   118   99.2%          1     + 109542852 109542969              AK209157     3   120   120
browser |   118   99.2%          1     + 112945527 112945644              AK209157     3   120   120
browser |   118   99.2%          1     - 117634940 117635057              AK209157     3   120   120
browser |   118   99.2%          1     - 125276383 125276500              AK209157     3   120   120
browser |   118   99.2%          1     - 127491276 127491393              AK209157     3   120   120
browser |   118   99.2%          1     - 127808075 127808192              AK209157     3   120   120
browser |   118   99.2%          1     + 130463774 130463891              AK209157     3   120   120
browser |   118   99.2%          1     - 137204182 137204299              AK209157     3   120   120
browser |   118   99.2%          1     + 140964868 140964985              AK209157     3   120   120
browser |   118   99.2%          1     - 144735705 144735822              AK209157     3   120   120
browser |   118   99.2%          1     + 145998394 145998511              AK209157     3   120   120
browser |   118   99.2%          1     - 146278218 146278335              AK209157     3   120   120
browser |   118   99.2%          1     + 149270717 149270834              AK209157     3   120   120
browser |   118   99.2%          1     + 149459027 149459144              AK209157     3   120   120
browser |   118   99.2%          1     - 154779975 154780092              AK209157     3   120   120
browser |   118   99.2%          1     - 159802608 159802725              AK209157     3   120   120
browser |   118   99.2%          1     - 176375907 176376024              AK209157     3   120   120
browser |   118   99.2%          1     - 181096364 181096481              AK209157     3   120   120
browser |   118   99.2%         10     -  19419917  19420034              AK209157     3   120   120
browser |   118   99.2%         10     -  24980563  24980680              AK209157     3   120   120
browser |   118   99.2%         10     -  34623094  34623211              AK209157     3   120   120
browser |   118   99.2%         10     +  41718259  41718376              AK209157     3   120   120
browser |   117   99.2%         10     -  43648204  43648320              AK209157     3   119   120
browser |   118   99.2%         10     +  51760817  51760934              AK209157     3   120   120
browser |   118   99.2%         10     +  56598565  56598682              AK209157     3   120   120
browser |   118   99.2%         10     -  66563512  66563629              AK209157     3   120   120
browser |   118   99.2%         10     +  71528975  71529092              AK209157     3   120   120
browser |   118   99.2%         10     -  83512057  83512174              AK209157     3   120   120
browser |   118   99.2%         10     -  96033665  96033782              AK209157     3   120   120
browser |   118   99.2%         10     + 104673153 104673270              AK209157     3   120   120
browser |   118   99.2%         10     + 105014672 105014789              AK209157     3   120   120
browser |   118   99.2%         10     - 109156351 109156468              AK209157     3   120   120
browser |   118   99.2%         10     - 116447438 116447555              AK209157     3   120   120
browser |   118   99.2%         10     - 122205047 122205164              AK209157     3   120   120
browser |   118   99.2%         10     + 124413948 124414065              AK209157     3   120   120
browser |   118   99.2%         10     - 124520118 124520235              AK209157     3   120   120
browser |   118   99.2%         11     -   9663256   9663373              AK209157     3   120   120
browser |   118   99.2%         11     +  12513659  12513776              AK209157     3   120   120
browser |   118   99.2%         11     +  15179429  15179546              AK209157     3   120   120
browser |   118   99.2%         11     -  19518698  19518815              AK209157     3   120   120
browser |   117   99.2%         11     +  20468115  20468231              AK209157     3   119   120
browser |   118   99.2%         11     -  23173856  23173973              AK209157     3   120   120
browser |   118   99.2%         11     -  27905242  27905359              AK209157     3   120   120
browser |   118   99.2%         11     +  51330247  51330364              AK209157     3   120   120
browser |   118   99.2%         11     -  55137036  55137153              AK209157     3   120   120
browser |   118   99.2%         11     +  63360289  63360406              AK209157     3   120   120
browser |   118   99.2%         11     +  81438103  81438220              AK209157     3   120   120
browser |   118   99.2%         11     -  82227346  82227463              AK209157     3   120   120
browser |   118   99.2%         11     +  86738175  86738292              AK209157     3   120   120
browser |   118   99.2%         11     -  90856273  90856390              AK209157     3   120   120
browser |   118   99.2%         11     +  98505826  98505943              AK209157     3   120   120
browser |   118   99.2%         11     -  99606219  99606336              AK209157     3   120   120
browser |   118   99.2%         11     + 111075068 111075185              AK209157     3   120   120
browser |   118   99.2%         11     - 115650999 115651116              AK209157     3   120   120
browser |   118   99.2%         11     + 117392420 117392537              AK209157     3   120   120
browser |   118   99.2%         11     + 120962471 120962588              AK209157     3   120   120
browser |   118   99.2%         12     +   6568274   6568391              AK209157     3   120   120
browser |   118   99.2%         12     -  11158930  11159047              AK209157     3   120   120
browser |   118   99.2%         12     +  17173953  17174070              AK209157     3   120   120
browser |   118   99.2%         12     +  24447209  24447326              AK209157     3   120   120
browser |   118   99.2%         12     -  31413421  31413538              AK209157     3   120   120
browser |   118   99.2%         12     +  32079733  32079850              AK209157     3   120   120
browser |   118   99.2%         12     +  40453823  40453940              AK209157     3   120   120
browser |   118   99.2%         12     +  41415240  41415357              AK209157     3   120   120
browser |   118   99.2%         12     +  49043305  49043422              AK209157     3   120   120
browser |   118   99.2%         12     +  59488897  59489014              AK209157     3   120   120
browser |   118   99.2%         12     -  61338615  61338732              AK209157     3   120   120
browser |   118   99.2%         12     +  62583352  62583469              AK209157     3   120   120
browser |   118   99.2%         12     -  65079217  65079334              AK209157     3   120   120
browser |   118   99.2%         12     -  68673828  68673945              AK209157     3   120   120
browser |   118   99.2%         12     + 109870086 109870203              AK209157     3   120   120
browser |   118   99.2%         12     + 119556258 119556375              AK209157     3   120   120
browser |   118   99.2%         13     +   4390183   4390300              AK209157     3   120   120
browser |   118   99.2%         13     -   7325247   7325364              AK209157     3   120   120
browser |   118   99.2%         13     -   7327735   7327852              AK209157     3   120   120
browser |   118   99.2%         13     -   8004450   8004567              AK209157     3   120   120
browser |   118   99.2%         13     -  21819252  21819369              AK209157     3   120   120
browser |   118   99.2%         13     -  33125458  33125575              AK209157     3   120   120
browser |   118   99.2%         13     -  33136840  33136957              AK209157     3   120   120
browser |   118   99.2%         13     +  33623356  33623473              AK209157     3   120   120
browser |   118   99.2%         13     +  34047718  34047835              AK209157     3   120   120
browser |   118   99.2%         13     +  39692612  39692729              AK209157     3   120   120
browser |   118   99.2%         13     +  43432768  43432885              AK209157     3   120   120
browser |   118   99.2%         13     +  44419562  44419679              AK209157     3   120   120
browser |   118   99.2%         13     -  46534929  46535046              AK209157     3   120   120
browser |   118   99.2%         13     +  55928577  55928694              AK209157     3   120   120
browser |   118   99.2%         13     -  60174691  60174808              AK209157     3   120   120
browser |   117   99.2%         13     -  61097600  61097716              AK209157     3   119   120
browser |   118   99.2%         13     -  62626107  62626224              AK209157     3   120   120
browser |   118   99.2%         13     -  63309670  63309787              AK209157     3   120   120
browser |   118   99.2%         13     +  66161834  66161951              AK209157     3   120   120
browser |   118   99.2%         13     +  66378761  66378878              AK209157     3   120   120
browser |   118   99.2%         13     +  82040795  82040912              AK209157     3   120   120
browser |   118   99.2%         13     +  83568848  83568965              AK209157     3   120   120
browser |   118   99.2%         13     +  86862642  86862759              AK209157     3   120   120
browser |   118   99.2%         13     -  87320759  87320876              AK209157     3   120   120
browser |   118   99.2%         13     +  87706135  87706252              AK209157     3   120   120
browser |   118   99.2%         13     -  98465097  98465214              AK209157     3   120   120
browser |   118   99.2%         13     + 109989979 109990096              AK209157     3   120   120
browser |   118   99.2%         13     + 111638089 111638206              AK209157     3   120   120
browser |   118   99.2%         13     + 113411225 113411342              AK209157     3   120   120
browser |   118   99.2%         13     + 116103435 116103552              AK209157     3   120   120
browser |   118   99.2%         14     +  12285623  12285740              AK209157     3   120   120
browser |   118   99.2%         14     +  13339964  13340081              AK209157     3   120   120
browser |   118   99.2%         14     -  13423002  13423119              AK209157     3   120   120
browser |   118   99.2%         14     +  18032175  18032292              AK209157     3   120   120
browser |   118   99.2%         14     +  19592976  19593093              AK209157     3   120   120
browser |   118   99.2%         14     +  20331754  20331871              AK209157     3   120   120
browser |   117   99.2%         14     +  21412331  21412447              AK209157     3   119   120
browser |   118   99.2%         14     -  24432303  24432420              AK209157     3   120   120
browser |   118   99.2%         14     -  32120501  32120618              AK209157     3   120   120
browser |   118   99.2%         14     +  35615562  35615679              AK209157     3   120   120
browser |   118   99.2%         14     -  37346754  37346871              AK209157     3   120   120
browser |   118   99.2%         14     +  39455174  39455291              AK209157     3   120   120
browser |   118   99.2%         14     +  58291736  58291853              AK209157     3   120   120
browser |   118   99.2%         14     -  60805469  60805586              AK209157     3   120   120
browser |   118   99.2%         14     +  66701868  66701985              AK209157     3   120   120
browser |   118   99.2%         14     -  68249557  68249674              AK209157     3   120   120
browser |   118   99.2%         14     +  81327075  81327192              AK209157     3   120   120
browser |   118   99.2%         14     +  82417366  82417483              AK209157     3   120   120
browser |   118   99.2%         14     +  86128248  86128365              AK209157     3   120   120
browser |   118   99.2%         14     - 104347535 104347652              AK209157     3   120   120
browser |   118   99.2%         14     - 104825327 104825444              AK209157     3   120   120
browser |   118   99.2%         14     - 110598587 110598704              AK209157     3   120   120
browser |   118   99.2%         14     - 112870448 112870565              AK209157     3   120   120
browser |   118   99.2%         14     - 114446319 114446436              AK209157     3   120   120
browser |   118   99.2%         14     + 114745028 114745145              AK209157     3   120   120
browser |   118   99.2%         14     + 117418119 117418236              AK209157     3   120   120
browser |   118   99.2%         14     - 120198849 120198966              AK209157     3   120   120
browser |   118   99.2%         14     + 123963605 123963722              AK209157     3   120   120
browser |   118   99.2%         15     -   4886843   4886960              AK209157     3   120   120
browser |   118   99.2%         15     +   7942110   7942227              AK209157     3   120   120
browser |   118   99.2%         15     +  19050974  19051091              AK209157     3   120   120
browser |   118   99.2%         15     -  23245735  23245852              AK209157     3   120   120
browser |   118   99.2%         15     +  24323057  24323174              AK209157     3   120   120
browser |   118   99.2%         15     +  25053248  25053365              AK209157     3   120   120
browser |   118   99.2%         15     -  26908139  26908256              AK209157     3   120   120
browser |   118   99.2%         15     +  38480784  38480901              AK209157     3   120   120
browser |   118   99.2%         15     +  44588207  44588324              AK209157     3   120   120
browser |   118   99.2%         15     -  54049520  54049637              AK209157     3   120   120
browser |   118   99.2%         15     +  56041026  56041143              AK209157     3   120   120
browser |   118   99.2%         15     +  65540208  65540325              AK209157     3   120   120
browser |   118   99.2%         15     -  71107569  71107686              AK209157     3   120   120
browser |   118   99.2%         15     -  72957977  72958094              AK209157     3   120   120
browser |   118   99.2%         15     -  92371124  92371241              AK209157     3   120   120
browser |   118   99.2%         15     -  92514174  92514291              AK209157     3   120   120
browser |   118   99.2%         15     +  96877716  96877833              AK209157     3   120   120
browser |   118   99.2%         16     +  32399814  32399931              AK209157     3   120   120
browser |   118   99.2%         16     -  36118674  36118791              AK209157     3   120   120
browser |   118   99.2%         16     +  36146447  36146564              AK209157     3   120   120
browser |   118   99.2%         16     +  41312967  41313084              AK209157     3   120   120
browser |   118   99.2%         16     +  49907078  49907195              AK209157     3   120   120
browser |   118   99.2%         16     +  50909226  50909343              AK209157     3   120   120
browser |   118   99.2%         16     -  51771542  51771659              AK209157     3   120   120
browser |   118   99.2%         16     +  51797938  51798055              AK209157     3   120   120
browser |   118   99.2%         16     -  52836485  52836602              AK209157     3   120   120
browser |   118   99.2%         16     -  55500038  55500155              AK209157     3   120   120
browser |   118   99.2%         16     -  58947540  58947657              AK209157     3   120   120
browser |   118   99.2%         16     -  60751377  60751494              AK209157     3   120   120
browser |   118   99.2%         16     -  64999871  64999988              AK209157     3   120   120
browser |   118   99.2%         16     -  65586847  65586964              AK209157     3   120   120
browser |   118   99.2%         16     -  70434716  70434833              AK209157     3   120   120
browser |   118   99.2%         16     -  87086359  87086476              AK209157     3   120   120
browser |   118   99.2%         16     -  88592804  88592921              AK209157     3   120   120
browser |   118   99.2%         16     +  88943864  88943981              AK209157     3   120   120
browser |   118   99.2%         16     +  94077446  94077563              AK209157     3   120   120
browser |   118   99.2%         17     -  10004767  10004884              AK209157     3   120   120
browser |   118   99.2%         17     -  11322027  11322144              AK209157     3   120   120
browser |   118   99.2%         17     -  13377299  13377416              AK209157     3   120   120
browser |   118   99.2%         17     -  13639471  13639588              AK209157     3   120   120
browser |   118   99.2%         17     +  17694770  17694887              AK209157     3   120   120
browser |   118   99.2%         17     +  19215744  19215861              AK209157     3   120   120
browser |   118   99.2%         17     +  22708228  22708345              AK209157     3   120   120
browser |   118   99.2%         17     -  23719536  23719653              AK209157     3   120   120
browser |   118   99.2%         17     -  33842493  33842610              AK209157     3   120   120
browser |   118   99.2%         17     +  35588034  35588151              AK209157     3   120   120
browser |   118   99.2%         17     +  36319768  36319885              AK209157     3   120   120
browser |   118   99.2%         17     +  38266585  38266702              AK209157     3   120   120
browser |   118   99.2%         17     -  47394264  47394381              AK209157     3   120   120
browser |   118   99.2%         17     +  52173165  52173282              AK209157     3   120   120
browser |   118   99.2%         17     +  64070406  64070523              AK209157     3   120   120
browser |   118   99.2%         17     +  69639039  69639156              AK209157     3   120   120
browser |   118   99.2%         17     +  83565202  83565319              AK209157     3   120   120
browser |   118   99.2%         17     +  88058289  88058406              AK209157     3   120   120
browser |   118   99.2%         18     -   6866546   6866663              AK209157     3   120   120
browser |   118   99.2%         18     +  15360288  15360405              AK209157     3   120   120
browser |   118   99.2%         18     +  21396537  21396654              AK209157     3   120   120
browser |   116   99.2%         18     -  29153087  29153202              AK209157     3   118   120
browser |   118   99.2%         18     -  37119842  37119959              AK209157     3   120   120
browser |   118   99.2%         18     +  47904829  47904946              AK209157     3   120   120
browser |   118   99.2%         18     -  48844232  48844349              AK209157     3   120   120
browser |   118   99.2%         18     +  50766972  50767089              AK209157     3   120   120
browser |   118   99.2%         18     +  51206867  51206984              AK209157     3   120   120
browser |   118   99.2%         18     -  58420160  58420277              AK209157     3   120   120
browser |   118   99.2%         18     -  62408661  62408778              AK209157     3   120   120
browser |   118   99.2%         18     -  73395274  73395391              AK209157     3   120   120
browser |   118   99.2%         18     +  83191041  83191158              AK209157     3   120   120
browser |   118   99.2%         18     -  90134749  90134866              AK209157     3   120   120
browser |   118   99.2%         19     -   3086808   3086925              AK209157     3   120   120
browser |   118   99.2%         19     -  12430088  12430205              AK209157     3   120   120
browser |   118   99.2%         19     +  15818508  15818625              AK209157     3   120   120
browser |   118   99.2%         19     +  32420985  32421102              AK209157     3   120   120
browser |   118   99.2%         19     -  37611112  37611229              AK209157     3   120   120
browser |   118   99.2%         19     -  38481824  38481941              AK209157     3   120   120
browser |   118   99.2%         19     +  41132962  41133079              AK209157     3   120   120
browser |   118   99.2%         19     +  42336124  42336241              AK209157     3   120   120
browser |   118   99.2%         19     +  45689289  45689406              AK209157     3   120   120
browser |   118   99.2%         19     -  50100994  50101111              AK209157     3   120   120
browser |   118   99.2%         19     +  55966910  55967027              AK209157     3   120   120
browser |   118   99.2%          2     -  15438025  15438142              AK209157     3   120   120
browser |   118   99.2%          2     +  21081442  21081559              AK209157     3   120   120
browser |   118   99.2%          2     +  35411221  35411338              AK209157     3   120   120
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browser |   118   99.2%  5_JH584298v1_random     -     19808     19925              AK209157     3   120   120
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browser |   118   99.2%          X     - 161766918 161767035              AK209157     3   120   120
browser |   118   99.2%          Y     +   3337200   3337317              AK209157     3   120   120
browser |   118   99.2%          Y     +  21227782  21227899              AK209157     3   120   120
browser |   118   99.2%          Y     -  31294296  31294413              AK209157     3   120   120
browser |   118   99.2%          Y     -  33167491  33167608              AK209157     3   120   120

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