Skip to another splice site:
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GATACATTGTGTGATCTATACGAAACTTTGGCCATTACACAGAGTGTCATATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttcttgaaggaactcctactgatcgaaattttgtggagctgtcgtgacattatgtatactgatgttgatgttctggatttcgtgtgatcag

Basic information

species Physcomitrella patens
transcript PP1S136_29V6.4
intron # 5
splice site 5'
intron type U2

Mapped EST sequences

Showing partial alignments of ESTs and genomic sequences. See full alignments


 ATGC     EST sequence
 ATGC     genomic sequence (exon)
 ATGC     genomic sequence (truncated intron)


EST: gi|67724598|gb|BJ974857.1|BJ974857
EST:     ATTCATTAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|162217509|gb|FC393185.1|FC393185
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|67726507|gb|BJ976766.1|BJ976766
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|67723968|gb|BJ974227.1|BJ974227
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGTTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208365231|gb|DC946804.1|DC946804
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208365823|gb|DC951058.1|DC951058
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208396803|gb|DC924359.1|DC924359
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208365171|gb|DC947351.1|DC947351
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208394036|gb|DC957117.1|DC957117
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208375161|gb|DC945311.1|DC945311
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208345762|gb|DC917653.1|DC917653
EST:     ANTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|67727766|gb|BJ978025.1|BJ978025
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|37839857|gb|BJ597865.1|BJ597865
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|67725370|gb|BJ975629.1|BJ975629
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|67723999|gb|BJ974258.1|BJ974258
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208362288|gb|DC954534.1|DC954534
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|18335376|gb|BJ167395.1|BJ167395
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|162164328|gb|FC340999.1|FC340999
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|18334446|gb|BJ166463.1|BJ166463
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208382954|gb|DC927704.1|DC927704
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|67727613|gb|BJ977872.1|BJ977872
EST:     ACTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208345034|gb|DC925416.1|DC925416
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|67728076|gb|BJ978335.1|BJ978335
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|67699930|gb|BJ960163.1|BJ960163
EST:     ATTCATCAACACTCGCNGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGANCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208394939|gb|DC920198.1|DC920198
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATGTGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208357306|gb|DC949922.1|DC949922
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|7047185|gb|AW477079.1|AW477079
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208362320|gb|DC954566.1|DC954566
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|67723930|gb|BJ974189.1|BJ974189
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|37821711|gb|BJ579777.1|BJ579777
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|37839497|gb|BJ597505.1|BJ597505
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|67723781|gb|BJ974040.1|BJ974040
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208380273|gb|DC919109.1|DC919109
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|37831524|gb|BJ589536.1|BJ589536
EST:     AAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACNGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: AAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208375347|gb|DC940457.1|DC940457
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208364106|gb|DC950398.1|DC950398
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|67726142|gb|BJ976401.1|BJ976401
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|37843006|gb|BJ601014.1|BJ601014
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|208360533|gb|DC950079.1|DC950079
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
EST: gi|67728012|gb|BJ978271.1|BJ978271
EST:     ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAG                         CTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC
genomic: ATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCC

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 35 (upstream exon), 22 (downstream exon)
Score: 15

GATACATTGTGTGATCTATACGAAACTTTGGCCATTACACAGAGTGTCATATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttctt ... gtgtgatcagCTCGCGACCACACCGTGTCTGCGACCCATGGAGATATGGACCAGAACACCCGTGATATTATCATGCGTGAGTTCCGCTCAGGCTCATCCCGAGTGCTTAT




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Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GATACATTGTGTGATCTATACGAAACTTTGGCCATTACACAGAGTGTCATATTCATCAACACTCGCCGAAAGGTCGACTGGCTCACCGACAAGATGCGAGgtaatttcttgaaggaactcctactgatcgaaattttgtggagctgtcgtgacattatgtatactgatgttgatgttctggatttcgtgtgatcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG