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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ccctttcaatttgtcaatgtggcgtgtctgctctggcagcacatagtcttaaccaaagcttctctttttagttgtgaactaatatgttaaaaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT

Basic information

species Physcomitrella patens
transcript PP1S295_30V6.1
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S295_30V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ23006 (Selaginella moellendorffii), 3'ss of exon 1
ccctttcaatttgtcaatgtggcgtgtctgctctggcagcacatagtcttaaccaaagcttctctttttagttgtgaactaatatgttaaaaatgttc--agGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT
                       || |    || | |      |||| ||   |    ||| ||| || | |  ||    |   ||   |      ||  || | ||||| || ||||| ||||| || || || ||||||||||||||||| ||||| ||||| ||| || |||||||| |||| |||||| 
-----------------------gtatggaatccgac------tagtttt---ctggtcttttctattgattcttggggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG

upper sequence: PP1S295_30V6.1 (Physcomitrella patens), 3'ss of exon 1
lower sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
ccctttcaatttgtcaatgtggcgtgtctgctctggcagcacatagtcttaaccaaagcttctctttttagttgtgaactaatatgttaaaaatgttc--agGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT
                       || |    || |||      |||| |         ||| ||| || | |   |    |   ||   |      ||  || | ||||| || ||||| ||||| || || || |||||||||||||| || ||||| ||||| ||| || |||||||| |||| |||||| 
-----------------------gtatggaatccggc------tagtttg---ttggtcttttctattgattctcggggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG
















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|100414507|gb|BY992807.1|BY992807
EST:     TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTG                         GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
genomic: TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
EST: gi|162260165|gb|FC436300.1|FC436300
EST:     TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTG                         GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
genomic: TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
EST: gi|208385598|gb|DC937143.1|DC937143
EST:     TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTG                         GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
genomic: TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
EST: gi|162278111|gb|FC453930.1|FC453930
EST:     TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTG                         GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
genomic: TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
EST: gi|208377957|gb|DC910961.1|DC910961
EST:     TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTG                         GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
genomic: TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
EST: gi|208374777|gb|DC932046.1|DC932046
EST:     TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTG                         GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
genomic: TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
EST: gi|162278110|gb|FC453929.1|FC453929
EST:     TGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTG                         GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
genomic: TGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
EST: gi|208349948|gb|DC913656.1|DC913656
EST:     TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTG                         GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
genomic: TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
EST: gi|208390738|gb|DC937894.1|DC937894
EST:     TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTG                         GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
genomic: TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
EST: gi|100364489|gb|BY984629.1|BY984629
EST:     TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTG                         GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
genomic: TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
EST: gi|162260166|gb|FC436301.1|FC436301
EST:     TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTG                         GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
genomic: TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
EST: gi|18361916|gb|BJ193983.1|BJ193983
EST:     TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTG                         GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
genomic: TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
EST: gi|208386340|gb|DC932836.1|DC932836
EST:     TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTG                         GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
genomic: TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
EST: gi|208387111|gb|DC941283.1|DC941283
EST:     TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTG                         GTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT
genomic: TCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACT

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: 33 (upstream exon), 34 (downstream exon)
Score: 9

CATGGATTGGTGGAATTGGGTGGATTCGTCCGTGCTCTGGCAGGAGCGTATCTGGCTGGGGCTGGCAATTGCGTATTCTTTGATGTCGGTGATTGCACTGgtacgtggtt ... aaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttaaccaaagcttctctttttagttgtgaactaatatgttaaaaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT
                               aactaat  putative branch site (score: 9)
                               aactaatatgttaaaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ccctttcaatttgtcaatgtggcgtgtctgctctggcagcacatagtcttaaccaaagcttctctttttagttgtgaactaatatgttaaaaatgttcagGTGCAACTAATTCGGATAGAGATGCGAGTTCCGGAGTATGGCTGGACCACTCAGAAAGTCTTTCATCTGTTGAATTTCATTGTTAATGGAT

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