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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacttgaaaataaatcatcagcagtatgaggcttatgtcatgtgtgaattcgtaaatactccaaaaagttctattcaatttgacgcattacgactatctgccttgttgatcacgtgaaggactttttgtgccaatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCATGTACGACTATGTCACAAAGGAGCTCCCCTCTCTTCTGAGCTCTCACTT

Basic information

species Physcomitrella patens
transcript PP1S61_17V6.2
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S61_17V6.5 (Physcomitrella patens), 3'ss of exon 4
lower sequence: GRMZM2G046558_T01 (Zea mays), 3'ss of exon 3
gtacttgaaaataaatcatcagcagtatgaggcttatgtcatgtgtgaattcgtaaatactccaaaaagttctattcaatttgacgcattacgactatctgccttgttgatcacgtgaaggactttttgtgccaatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCATGTACGACTATGTCACAAAGGAGCTCCCCTCTCTTCTGAGCTCTCACTT
                           |   |   |   |   ||  | || ||| | |||   |  || |    | | |||    |   ||    ||     |   | | ||  |      ||||||||  |        ||| ||| | || ||  | ||||||||  | || ||||||||||||||||||||||| |||||  |    ||||| || ||     || | ||   | ||||
---------------------------ttgcggaaacaccgcttg-aattttgtatacact---agcagcttggatgattttatttctgcacactcattcagatatcttaacatttc-----ctttttgttac-------tagGTGCCGGGTTTTATTTGAATGCCACAAATGAAAAGTGGAAAAACTGGCGCATGTATGACTACATTGTGAAGGAACTTCCAAAAGTTTTAAGTGATAACTT
















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|208364085|gb|DC943397.1|DC943397
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|18343395|gb|BJ175433.1|BJ175433
EST:     GAGGGNTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCNCTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|67719202|gb|BJ969461.1|BJ969461
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|208380226|gb|DC919062.1|DC919062
EST:     GCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|208381483|gb|DC919485.1|DC919485
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|162192829|gb|FC370161.1|FC370161
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCGGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|67727505|gb|BJ977764.1|BJ977764
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|208350927|gb|DC910474.1|DC910474
EST:     GANGGCTGAATGTGGAAGGGGAGTCNGATAGCTGGGATT-CGGCACAG                         GAGCCAGTTTCTACCTAA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAA
EST: gi|208348165|gb|DC920956.1|DC920956
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACNTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|100394127|gb|BY971952.1|BY971952
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|208396633|gb|DC924301.1|DC924301
EST:     GAGGGCTGAATGTGGNAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|100421061|gb|BY993592.1|BY993592
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|100383603|gb|BY950387.1|BY950387
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTTAATGCCACTCAGGAAAAGTGGAAAA-CTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|208345645|gb|DC905603.1|DC905603
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|162267025|gb|FC443074.1|FC443074
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|162267024|gb|FC443073.1|FC443073
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|67694518|gb|BJ954751.1|BJ954751
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|208384596|gb|DC907083.1|DC907083
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|208344728|gb|DC905177.1|DC905177
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA
EST: gi|208371948|gb|DC948351.1|DC948351
EST:     GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAG                         GAGCCAGTTTCTACNTAAATGCCACTCAGGAGAAGTGGAAAANCTGGCGCA
genomic: GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCA

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), 33 (downstream exon)
Score: 23

GAGGGCTGAATGTGGAAGGGGAGTCGGATAGCTGGGATTTCGGCACAGgtacttgaaa ... aatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCATGTACGACTATGTCACAAAGGAGCTCCCCTCTCTTCTGAGCTCTCACTT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttacgactatctgccttgttgatcacgtgaaggactttttgtgccaatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCATGTACGACTATGTCACAAAGGAGCTCCCCTCTCTTCTGAGCTCTCACTT
                tgttgat  putative branch site (score: 23)
                                 acttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtacttgaaaataaatcatcagcagtatgaggcttatgtcatgtgtgaattcgtaaatactccaaaaagttctattcaatttgacgcattacgactatctgccttgttgatcacgtgaaggactttttgtgccaatgggacagGAGCCAGTTTCTACCTAAATGCCACTCAGGAGAAGTGGAAAAACTGGCGCATGTACGACTATGTCACAAAGGAGCTCCCCTCTCTTCTGAGCTCTCACTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT