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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgctcttggcgaatgtgtacatagccgtgttaggtttgtggaaacggcaaaaataggaactgtcgttaacatgtgggattttttttgcgtcttcgattgggctttttggtagtgagcgagatgaggtgagattttaggtgagccctgtgtttaatatcgttgtggtttgtttatgcag

Basic information

species Physcomitrella patens
transcript PP1S61_262V6.1
intron # 2
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|67726792|gb|BJ977051.1|BJ977051
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|18357028|gb|BJ189087.1|BJ189087
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|18342257|gb|BJ174292.1|BJ174292
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|18358512|gb|BJ190571.1|BJ190571
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|37841638|gb|BJ599646.1|BJ599646
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|67694213|gb|BJ954446.1|BJ954446
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|67570911|gb|BJ943735.1|BJ943735
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|162271048|gb|FC446608.1|FC446608
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|67704114|gb|BJ964347.1|BJ964347
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTAC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTAC
EST: gi|37821363|gb|BJ579429.1|BJ579429
EST:     CTGGAGAAGTTCAGCACGCNTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: CTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|15327310|gb|BI487899.1|BI487899
EST:     TTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: TTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|162217190|gb|FC392554.1|FC392554
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|162217189|gb|FC392553.1|FC392553
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|162279151|gb|FC455490.1|FC455490
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|22131587|gb|BQ826691.1|BQ826691
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|162219652|gb|FC395648.1|FC395648
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|22492043|gb|BU051966.1|BU051966
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|162214750|gb|FC391821.1|FC391821
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|37851018|gb|BJ609026.1|BJ609026
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|37837722|gb|BJ595730.1|BJ595730
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|37837957|gb|BJ595965.1|BJ595965
EST:     CTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: CTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|37836397|gb|BJ594405.1|BJ594405
EST:     CTGGAGAAGTTCCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: CTGGAGAAGTT-CAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|162279150|gb|FC455489.1|FC455489
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|22131404|gb|BQ826597.1|BQ826597
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|22491946|gb|BU051869.1|BU051869
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|67720461|gb|BJ970720.1|BJ970720
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|67701971|gb|BJ962204.1|BJ962204
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTG
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTG
EST: gi|100422336|gb|BY976324.1|BY976324
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|162214749|gb|FC391820.1|FC391820
EST:     GAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTA-TGATTT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAG
genomic: GAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGA-TTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAG
EST: gi|18358618|gb|BJ190677.1|BJ190677
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|162219651|gb|FC395647.1|FC395647
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|162251659|gb|FC426065.1|FC426065
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTTAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|37840626|gb|BJ598634.1|BJ598634
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|162258978|gb|FC435921.1|FC435921
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|18370194|gb|BJ201796.1|BJ201796
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|67718302|gb|BJ968561.1|BJ968561
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|162271047|gb|FC446607.1|FC446607
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
EST: gi|18364714|gb|BJ196787.1|BJ196787
EST:     AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATT                         CGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC
genomic: AGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGC

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), 34 (downstream exon)
Score: 125

GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgct ... gtttatgcagCGCTCAGTGACCCCATCGATGTCTACAGTGACTGGATTGACGAGTGCGAGCGTATCAATGGTGGAGCGGAATCTTGAGATCTTTGAACGAGGGTTCAAGT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGATCGCAAAAACCAAATTGGAGAGGCGTCTTGTCGAATATGTCTGGAGAAGTTCAGCACGCCTATTGATTgtaagtcgctcttggcgaatgtgtacatagccgtgttaggtttgtggaaacggcaaaaataggaactgtcgttaacatgtgggattttttttgcgtcttcgattgggctttttggtagtgagcgagatgaggtgagattttaggtgagccctgtgtttaatatcgttgtggtttgtttatgcag

- - - - - - - - - - - - - - - - - - - - - - TGGAGA
- - - - - - - - - - - - - - - - - - - - - -  GGAGAA
- - - - - - - - - - - - - - - - - - - - - - -  AGAAGT