DQ714442
 

Information on mRNA DQ714442

Description: Mus musculus piRNA piR-129764, complete sequence.
Gene: n/a
Product: n/a
Author: Lau,N.C., Seto,A.G., Kim,J., Kuramochi-Miyagawa,S., Nakano,T., Bartel,D.P. and Kingston,R.E.
Organism: Mus musculus
Tissue: n/a
Development stage: n/a
Cell line: n/a
Sex: n/a
Library: n/a
Clone: n/a
CDS: n/a
Date: 2006-06-08
Version: 1
mRNA sequence: DQ714442
Position: chr12:57234582-57234606

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 |    25  100.0%         12     -  57234582  57234606              DQ714442     1    25    27
browser |    25  100.0%          1     +   7426640   7426664              DQ714442     1    25    27
browser |    25  100.0%          1     +  60699783  60699807              DQ714442     1    25    27
browser |    25  100.0%          1     +  67500444  67500468              DQ714442     1    25    27
browser |    27  100.0%          1     +  72288806  72288833              DQ714442     1    27    27
browser |    25  100.0%          1     -  79658877  79658901              DQ714442     1    25    27
browser |    27  100.0%          1     -  96177034  96177060              DQ714442     1    27    27
browser |    25  100.0%          1     + 111929393 111929417              DQ714442     1    25    27
browser |    27  100.0%          1     - 123556618 123556644              DQ714442     1    27    27
browser |    25  100.0%          1     + 126835613 126835637              DQ714442     1    25    27
browser |    25  100.0%          1     + 127375987 127376011              DQ714442     1    25    27
browser |    25  100.0%          1     + 134863882 134863906              DQ714442     1    25    27
browser |    25  100.0%          1     - 160077039 160077063              DQ714442     1    25    27
browser |    25  100.0%          1     + 165399702 165399726              DQ714442     1    25    27
browser |    25  100.0%          1     + 167105363 167105387              DQ714442     1    25    27
browser |    27  100.0%          1     - 169366937 169366963              DQ714442     1    27    27
browser |    25  100.0%          1     + 170606988 170607012              DQ714442     1    25    27
browser |    25  100.0%          1     - 174388977 174389001              DQ714442     1    25    27
browser |    27  100.0%          1     + 175071019 175071045              DQ714442     1    27    27
browser |    25  100.0%          1     + 175271276 175271300              DQ714442     1    25    27
browser |    25  100.0%          1     - 180647185 180647209              DQ714442     1    25    27
browser |    25  100.0%          1     - 191825004 191825028              DQ714442     1    25    27
browser |    25  100.0%         10     +  15147229  15147253              DQ714442     1    25    27
browser |    25  100.0%         10     +  20214026  20214050              DQ714442     1    25    27
browser |    25  100.0%         10     -  42304792  42304816              DQ714442     1    25    27
browser |    25  100.0%         10     +  42341873  42341897              DQ714442     1    25    27
browser |    27  100.0%         10     -  64300661  64300687              DQ714442     1    27    27
browser |    25  100.0%         10     -  80810516  80810540              DQ714442     1    25    27
browser |    27  100.0%         10     -  81219186  81219212              DQ714442     1    27    27
browser |    27  100.0%         10     +  88312670  88312696              DQ714442     1    27    27
browser |    26  100.0%         10     +  93608814  93608839              DQ714442     1    26    27
browser |    25  100.0%         10     -  93988050  93988074              DQ714442     1    25    27
browser |    27  100.0%         10     -  96172598  96172624              DQ714442     1    27    27
browser |    25  100.0%         10     - 102199053 102199077              DQ714442     1    25    27
browser |    25  100.0%         10     + 105495153 105495177              DQ714442     1    25    27
browser |    27  100.0%         10     + 110948543 110948569              DQ714442     1    27    27
browser |    27  100.0%         10     - 114567745 114567771              DQ714442     1    27    27
browser |    25  100.0%         10     + 119179664 119179688              DQ714442     1    25    27
browser |    25  100.0%         10     - 121339814 121339838              DQ714442     1    25    27
browser |    25  100.0%         10     + 129311133 129311157              DQ714442     1    25    27
browser |    25  100.0%         11     -   3205358   3205382              DQ714442     1    25    27
browser |    27  100.0%         11     +   4189266   4189292              DQ714442     1    27    27
browser |    25  100.0%         11     -   5620752   5620776              DQ714442     1    25    27
browser |    25  100.0%         11     -  12742721  12742745              DQ714442     1    25    27
browser |    25  100.0%         11     -  23895149  23895173              DQ714442     1    25    27
browser |    25  100.0%         11     +  25132746  25132770              DQ714442     1    25    27
browser |    25  100.0%         11     +  52125722  52125746              DQ714442     1    25    27
browser |    27  100.0%         11     +  53189966  53189993              DQ714442     1    27    27
browser |    25  100.0%         11     -  59232843  59232867              DQ714442     1    25    27
browser |    25  100.0%         11     -  69465260  69465284              DQ714442     1    25    27
browser |    25  100.0%         11     +  70564507  70564531              DQ714442     1    25    27
browser |    25  100.0%         11     +  76644111  76644135              DQ714442     1    25    27
browser |    25  100.0%         11     +  76824904  76824928              DQ714442     1    25    27
browser |    25  100.0%         11     +  79186389  79186413              DQ714442     1    25    27
browser |    25  100.0%         11     +  90941763  90941787              DQ714442     1    25    27
browser |    25  100.0%         11     +  95025626  95025650              DQ714442     1    25    27
browser |    25  100.0%         11     +  96003838  96003862              DQ714442     1    25    27
browser |    27  100.0%         11     +  97325338  97325364              DQ714442     1    27    27
browser |    25  100.0%         11     -  97596317  97596341              DQ714442     1    25    27
browser |    25  100.0%         11     - 100573889 100573913              DQ714442     1    25    27
browser |    25  100.0%         11     + 102751839 102751863              DQ714442     1    25    27
browser |    27  100.0%         11     + 106057130 106057156              DQ714442     1    27    27
browser |    25  100.0%         11     - 109355717 109355741              DQ714442     1    25    27
browser |    27  100.0%         11     - 112279369 112279395              DQ714442     1    27    27
browser |    27  100.0%         12     +   4627069   4627095              DQ714442     1    27    27
browser |    25  100.0%         12     +   8241348   8241372              DQ714442     1    25    27
browser |    25  100.0%         12     +  13238897  13238921              DQ714442     1    25    27
browser |    25  100.0%         12     +  19200762  19200786              DQ714442     1    25    27
browser |    25  100.0%         12     +  20634623  20634647              DQ714442     1    25    27
browser |    25  100.0%         12     -  24175403  24175427              DQ714442     1    25    27
browser |    26  100.0%         12     +  36307117  36307142              DQ714442     1    26    27
browser |    25  100.0%         12     +  47645649  47645673              DQ714442     1    25    27
browser |    25  100.0%         12     -  54588698  54588722              DQ714442     1    25    27
browser |    27  100.0%         12     -  62028924  62028950              DQ714442     1    27    27
browser |    27  100.0%         12     -  80543290  80543316              DQ714442     1    27    27
browser |    25  100.0%         12     -  80682781  80682805              DQ714442     1    25    27
browser |    25  100.0%         12     -  82199984  82200008              DQ714442     1    25    27
browser |    27  100.0%         12     +  85129855  85129881              DQ714442     1    27    27
browser |    25  100.0%         12     +  85299808  85299832              DQ714442     1    25    27
browser |    25  100.0%         12     -  85375264  85375288              DQ714442     1    25    27
browser |    25  100.0%         12     - 101424970 101424994              DQ714442     1    25    27
browser |    25  100.0%         12     - 110966139 110966163              DQ714442     1    25    27
browser |    25  100.0%         12     + 118514068 118514092              DQ714442     1    25    27
browser |    25  100.0%         13     +   3686143   3686167              DQ714442     1    25    27
browser |    25  100.0%         13     +   3757319   3757343              DQ714442     1    25    27
browser |    25  100.0%         13     -   5605727   5605751              DQ714442     1    25    27
browser |    25  100.0%         13     -  39014222  39014246              DQ714442     1    25    27
browser |    25  100.0%         13     -  54639751  54639775              DQ714442     1    25    27
browser |    25  100.0%         13     +  67581498  67581522              DQ714442     1    25    27
browser |    25  100.0%         13     -  68095789  68095813              DQ714442     1    25    27
browser |    25  100.0%         13     -  68111544  68111568              DQ714442     1    25    27
browser |    25  100.0%         13     -  68127269  68127293              DQ714442     1    25    27
browser |    25  100.0%         13     -  68283583  68283607              DQ714442     1    25    27
browser |    25  100.0%         13     +  68361269  68361293              DQ714442     1    25    27
browser |    25  100.0%         13     +  68387453  68387477              DQ714442     1    25    27
browser |    25  100.0%         13     +  68506943  68506967              DQ714442     1    25    27
browser |    25  100.0%         13     +  68517289  68517313              DQ714442     1    25    27
browser |    25  100.0%         13     +  68641498  68641522              DQ714442     1    25    27
browser |    26  100.0%         13     -  77344268  77344293              DQ714442     1    26    27
browser |    25  100.0%         13     +  97302036  97302060              DQ714442     1    25    27
browser |    25  100.0%         13     - 100903460 100903484              DQ714442     1    25    27
browser |    27  100.0%         13     + 116270824 116270852              DQ714442     1    27    27
browser |    25  100.0%         14     -   3248053   3248077              DQ714442     1    25    27
browser |    25  100.0%         14     -  19920368  19920392              DQ714442     1    25    27
browser |    25  100.0%         14     +  21936568  21936592              DQ714442     1    25    27
browser |    27  100.0%         14     -  24414756  24414782              DQ714442     1    27    27
browser |    25  100.0%         14     +  26812754  26812778              DQ714442     1    25    27
browser |    25  100.0%         14     +  47050556  47050580              DQ714442     1    25    27
browser |    25  100.0%         14     +  54897935  54897959              DQ714442     1    25    27
browser |    27  100.0%         14     -  59564355  59564381              DQ714442     1    27    27
browser |    25  100.0%         14     -  71229609  71229633              DQ714442     1    25    27
browser |    27  100.0%         14     -  85550217  85550243              DQ714442     1    27    27
browser |    25  100.0%         14     +  95392696  95392720              DQ714442     1    25    27
browser |    25  100.0%         14     - 101945126 101945150              DQ714442     1    25    27
browser |    27  100.0%         14     - 122054845 122054871              DQ714442     1    27    27
browser |    25  100.0%         15     -  12202244  12202268              DQ714442     1    25    27
browser |    25  100.0%         15     +  17642623  17642647              DQ714442     1    25    27
browser |    25  100.0%         15     -  47918875  47918899              DQ714442     1    25    27
browser |    25  100.0%         15     -  73497304  73497329              DQ714442     1    25    27
browser |    25  100.0%         15     -  76262624  76262648              DQ714442     1    25    27
browser |    25  100.0%         15     -  76739747  76739771              DQ714442     1    25    27
browser |    27  100.0%         15     -  81082619  81082645              DQ714442     1    27    27
browser |    25  100.0%         15     +  81344963  81344987              DQ714442     1    25    27
browser |    27  100.0%         15     -  81582524  81582550              DQ714442     1    27    27
browser |    25  100.0%         15     +  83481556  83481580              DQ714442     1    25    27
browser |    25  100.0%         15     -  98663846  98663870              DQ714442     1    25    27
browser |    25  100.0%         15     + 100356397 100356421              DQ714442     1    25    27
browser |    27  100.0%         15     + 101505250 101505276              DQ714442     1    27    27
browser |    27  100.0%         16     +   4547234   4547260              DQ714442     1    27    27
browser |    25  100.0%         16     -   8643862   8643886              DQ714442     1    25    27
browser |    25  100.0%         16     +  15686678  15686702              DQ714442     1    25    27
browser |    25  100.0%         16     -  17042226  17042250              DQ714442     1    25    27
browser |    27  100.0%         16     +  31382002  31382028              DQ714442     1    27    27
browser |    27  100.0%         16     +  33549453  33549479              DQ714442     1    27    27
browser |    25  100.0%         16     +  37029351  37029375              DQ714442     1    25    27
browser |    25  100.0%         16     +  51460972  51460996              DQ714442     1    25    27
browser |    25  100.0%         16     +  56517284  56517308              DQ714442     1    25    27
browser |    25  100.0%         16     -  58534639  58534663              DQ714442     1    25    27
browser |    25  100.0%         16     +  60683649  60683673              DQ714442     1    25    27
browser |    25  100.0%         16     +  91403859  91403883              DQ714442     1    25    27
browser |    25  100.0%         17     +   7681719   7681743              DQ714442     1    25    27
browser |    25  100.0%         17     +  13392279  13392303              DQ714442     1    25    27
browser |    25  100.0%         17     +  13550018  13550042              DQ714442     1    25    27
browser |    25  100.0%         17     +  13676854  13676878              DQ714442     1    25    27
browser |    25  100.0%         17     -  24635690  24635714              DQ714442     1    25    27
browser |    25  100.0%         17     -  25934318  25934342              DQ714442     1    25    27
browser |    25  100.0%         17     -  27757284  27757308              DQ714442     1    25    27
browser |    25  100.0%         17     -  28674525  28674549              DQ714442     1    25    27
browser |    27  100.0%         17     -  29876439  29876465              DQ714442     1    27    27
browser |    25  100.0%         17     +  30256106  30256130              DQ714442     1    25    27
browser |    27  100.0%         17     -  34209568  34209594              DQ714442     1    27    27
browser |    25  100.0%         17     -  35786667  35786691              DQ714442     1    25    27
browser |    25  100.0%         17     +  36140321  36140345              DQ714442     1    25    27
browser |    25  100.0%         17     -  46914486  46914510              DQ714442     1    25    27
browser |    27  100.0%         17     +  53764495  53764522              DQ714442     1    27    27
browser |    25  100.0%         17     -  56265323  56265347              DQ714442     1    25    27
browser |    25  100.0%         17     -  81122822  81122846              DQ714442     1    25    27
browser |    25  100.0%         17     -  82107564  82107588              DQ714442     1    25    27
browser |    25  100.0%         17     -  93824551  93824575              DQ714442     1    25    27
browser |    27  100.0%         18     -  36569291  36569317              DQ714442     1    27    27
browser |    25  100.0%         18     +  52227242  52227266              DQ714442     1    25    27
browser |    25  100.0%         18     -  77791071  77791095              DQ714442     1    25    27
browser |    25  100.0%         19     +   4622984   4623008              DQ714442     1    25    27
browser |    25  100.0%         19     -   8895320   8895344              DQ714442     1    25    27
browser |    25  100.0%         19     -   9281325   9281349              DQ714442     1    25    27
browser |    25  100.0%         19     +   9611392   9611416              DQ714442     1    25    27
browser |    25  100.0%         19     +  17280861  17280885              DQ714442     1    25    27
browser |    25  100.0%         19     +  24256171  24256195              DQ714442     1    25    27
browser |    27  100.0%         19     -  30180232  30180258              DQ714442     1    27    27
browser |    25  100.0%         19     +  44505133  44505157              DQ714442     1    25    27
browser |    25  100.0%         19     +  46483441  46483465              DQ714442     3    27    27
browser |    25  100.0%          2     -   5676216   5676240              DQ714442     1    25    27
browser |    27  100.0%          2     +   9821735   9821761              DQ714442     1    27    27
browser |    25  100.0%          2     -  14142501  14142525              DQ714442     1    25    27
browser |    25  100.0%          2     +  15706044  15706068              DQ714442     1    25    27
browser |    26  100.0%          2     +  30022264  30022289              DQ714442     1    26    27
browser |    25  100.0%          2     -  40728642  40728666              DQ714442     1    25    27
browser |    25  100.0%          2     -  42453377  42453401              DQ714442     1    25    27
browser |    25  100.0%          2     +  64854077  64854101              DQ714442     1    25    27
browser |    25  100.0%          2     +  83074017  83074041              DQ714442     1    25    27
browser |    27  100.0%          2     -  87350513  87350539              DQ714442     1    27    27
browser |    25  100.0%          2     -  87432819  87432843              DQ714442     1    25    27
browser |    25  100.0%          2     -  91255899  91255923              DQ714442     1    25    27
browser |    25  100.0%          2     - 104490284 104490308              DQ714442     1    25    27
browser |    25  100.0%          2     + 110565394 110565418              DQ714442     1    25    27
browser |    27  100.0%          2     + 113427757 113427783              DQ714442     1    27    27
browser |    25  100.0%          2     + 113708172 113708196              DQ714442     1    25    27
browser |    27  100.0%          2     + 114401458 114401484              DQ714442     1    27    27
browser |    25  100.0%          2     - 116478463 116478487              DQ714442     1    25    27
browser |    25  100.0%          2     + 141241274 141241298              DQ714442     1    25    27
browser |    25  100.0%          2     - 151970506 151970530              DQ714442     1    25    27
browser |    26  100.0%          2     + 155975816 155975841              DQ714442     2    27    27
browser |    25  100.0%          2     + 164710857 164710881              DQ714442     1    25    27
browser |    25  100.0%          2     - 165032694 165032718              DQ714442     1    25    27
browser |    25  100.0%          2     + 165664442 165664466              DQ714442     1    25    27
browser |    25  100.0%          2     + 165785848 165785872              DQ714442     1    25    27
browser |    25  100.0%          2     + 172916463 172916487              DQ714442     1    25    27
browser |    25  100.0%          3     +  13795909  13795933              DQ714442     1    25    27
browser |    25  100.0%          3     +  19379406  19379430              DQ714442     1    25    27
browser |    25  100.0%          3     +  32777619  32777643              DQ714442     1    25    27
browser |    25  100.0%          3     -  51072264  51072288              DQ714442     1    25    27
browser |    27  100.0%          3     -  54534003  54534029              DQ714442     1    27    27
browser |    26  100.0%          3     -  58308347  58308372              DQ714442     1    26    27
browser |    27  100.0%          3     +  69723219  69723245              DQ714442     1    27    27
browser |    25  100.0%          3     +  89102570  89102594              DQ714442     1    25    27
browser |    25  100.0%          3     -  95255039  95255063              DQ714442     1    25    27
browser |    25  100.0%          3     -  95280903  95280927              DQ714442     1    25    27
browser |    25  100.0%          3     - 121051680 121051704              DQ714442     1    25    27
browser |    25  100.0%          3     - 121242805 121242830              DQ714442     1    25    27
browser |    25  100.0%          3     - 133276629 133276653              DQ714442     1    25    27
browser |    27  100.0%          3     + 135573861 135573887              DQ714442     1    27    27
browser |    27  100.0%          3     + 156333144 156333170              DQ714442     1    27    27
browser |    25  100.0%          4     -  25415181  25415205              DQ714442     1    25    27
browser |    25  100.0%          4     +  30002039  30002063              DQ714442     1    25    27
browser |    25  100.0%          4     +  45020067  45020091              DQ714442     1    25    27
browser |    25  100.0%          4     -  62147461  62147485              DQ714442     1    25    27
browser |    26  100.0%          4     -  92707830  92707855              DQ714442     1    26    27
browser |    25  100.0%          4     - 106973952 106973976              DQ714442     1    25    27
browser |    25  100.0%          4     - 123535886 123535910              DQ714442     1    25    27
browser |    25  100.0%          4     - 123549605 123549629              DQ714442     1    25    27
browser |    25  100.0%          4     + 124493138 124493162              DQ714442     1    25    27
browser |    25  100.0%          4     + 129162537 129162561              DQ714442     1    25    27
browser |    25  100.0%          4     - 129453358 129453382              DQ714442     1    25    27
browser |    27  100.0%          4     - 129646836 129646862              DQ714442     1    27    27
browser |    27  100.0%          4     - 129650004 129650030              DQ714442     1    27    27
browser |    25  100.0%          4     - 129662175 129662199              DQ714442     1    25    27
browser |    27  100.0%          4     - 133193543 133193569              DQ714442     1    27    27
browser |    27  100.0%          4     - 135062507 135062533              DQ714442     1    27    27
browser |    25  100.0%          4     - 136339014 136339038              DQ714442     1    25    27
browser |    25  100.0%          4     - 144038249 144038273              DQ714442     1    25    27
browser |    27  100.0%          4     + 148077592 148077618              DQ714442     1    27    27
browser |    27  100.0%          4     - 148120658 148120684              DQ714442     1    27    27
browser |    25  100.0%          4     + 151058384 151058408              DQ714442     1    25    27
browser |    27  100.0%          4     + 152138592 152138618              DQ714442     1    27    27
browser |    25  100.0%          5     -   4249218   4249242              DQ714442     1    25    27
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browser |    25  100.0%          5     +   6430615   6430639              DQ714442     1    25    27
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View details of parts of alignment within browser window
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View table schema

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