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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtccaattttattctgaactctgcatgtcgtactatgtagatgtacgacgtggccgtaactacttcatgtatagtagttcttagaatgaatagaacttatacttggcaatatttgctaccccttcaagagtcttactcttaaccgaagtttttcatattcctttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG

Basic information

species Physcomitrella patens
transcript PP1S197_115V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G061745_T03 (Zea mays), 3'ss of exon 3
gtaagtccaattttattctgaactctgcatgtcgtactatgtagatgtacgacgtggccgtaactacttcatgtatagtagttcttagaatgaatagaacttatacttggcaatatttgctaccccttcaagagtcttactcttaaccgaagtttttcatattcctttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG
                                                                 |  | |  |||  ||| |     | ||  |    ||  | ||        | ||   |  ||   ||    ||| ||  ||     | | | || |||        ||||||||  ||| ||||||||| |||||||||||||||| || || | |||||| || || || || || |||||||| || |||||||  || |||| |
---------------------------------------------------------------taaagttaattatgctagcttcgtcactgggtg---ctcctgctgtattgcctgtggcgcttctcacagctgtttattcc-aattctcgctctccaaatt--------gcagTTATGTTCCTAATCCAGTCTTGGTGATTATTGATGTCCAACCCAAGGAGCTGGGTATACCGACCAAAGCGTACTACGCTGTGGAGGAGGTTAAAGAG

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GRMZM2G368908_T02 (Zea mays), 3'ss of exon 3
gtaagtccaattttattctgaactctgcatgtcgtactatgtagatgtacgacgtggccgtaactacttcatgtatagtagttcttagaatgaatagaacttatacttggcaatatttgctaccccttcaagagtcttactcttaaccgaagtttttcatattcctttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG
                                                                 |  | |    |  ||| |   | | ||  |    || |||||  | | ||  ||   | | ||         | || || |    | || ||| | | |  ||  |||||||||  ||| || || ||||| |||||||||||||| || || | ||||||||| || ||||| |||||||| || || ||||| | ||| |||| |
---------------------------------------------------------------taaagttaatcctgatagcttgaacactgggtg---ctcatact--gtattacctggggctcttttcg-----ctgctgtttattccaattattcctttccaatt--tgcagTTATGTTCCTAACCCTGTCCTAGTGATTATTGATGTTCAACCCAAGGAGCTTGGGATACCCACCAAGGCGTATTACGCCGTGGAAGAAGTTAAAGAG

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G05780.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagt--ccaatt---ttattctgaactctgcatgtcgtactatgtagatgtacgacgtggccgtaactacttcatgtatagtagt--tcttagaatgaatagaacttatacttggcaatatttgctacccctt-caagagtcttactcttaaccgaagtttttcatattcctt-tgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG
|| |||  ||| ||   | |||| ||  ||      | |  || | | |||  | ||  |    ||   ||  |  ||   |  | |  | ||||  ||||       | |  ||  || | |  | |     |  |    || | |     ||   | |||     |  |  |  |  ||||| |||  |||||||||||||||||| ||||||||||| |||||||  || ||||| || || || || || |||||||| |||||||           
gttagtttccagtttaatcattcagatatcaattgattggcctttatggattgaggatcttctggttcttaaattgtgataaagatttgttttaggctgaaatctgtgtttctttcccactttacgttttttgtggcttcggtttcatctccaattaaggttcactttgcttttggttttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAG---------

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT5G05780.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagt--ccaatt---ttattctgaactctgcatgtcgtactatgtagatgtacgacgtggccgtaactacttcatgtatagtagt--tcttagaatgaatagaacttatacttggcaatatttgctacccctt-caagagtcttactcttaaccgaagtttttcatattcctt-tgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG
|| |||  ||| ||   | |||| ||  ||      | |  || | | |||  | ||  |    ||   ||  |  ||   |  | |  | ||||  ||||       | |  ||  || | |  | |     |  |    || | |     ||   | |||     |  |  |  |  ||||| |||  |||||||||||||||||| ||||||||||| |||||||  || ||||| || || || || || |||||||| |||||||  || || | |
gttagtttccagtttaatcattcagatatcaattgattggcctttatggattgaggatcttctggttcttaaattgtgataaagatttgttttaggctgaaatctgtgtttctttcccactttacgttttttgtggcttcggtttcatctccaattaaggttcactttgcttttggttttgcagCTATGTTCCAAATCCAGTCCTGGTCATTATTGATGTCCAGCCTAAAGAACTTGGAATCCCTACCAAAGCATACTATGCAGTGGAGGAGGTTAAGGAG

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT3G11270.1 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtccaattttattctgaactctg---catgtcgtactatgtagatgtacgacgtggccgt--aactacttcatgtata-gtagttcttagaatgaatagaacttatacttggcaatatttgctacccctt-caagagtcttactcttaaccgaagtttttcatattcctttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG
||||| ||||  | | ||| || | ||    |||  |  |||     || || |   |||  ||     ||  | || |||    |    ||  || | ||  |   | ||  |  |     ||||||  ||||      || |||||        ||   | | |  |||   || ||||| ||   ||||||||||||  |||| ||||||||||| || ||||  || ||||| || |||||||| || ||||||||||| ||||  || |||| |
gtaagaccaaaatcagtctaaaatatgagatatgatggtctaatctaatatatggtttggtggtctgtttaagttatatatgtacaaacgttttaaagcattcacaatctatctctcctctcttgctagaccttatttctgtattacttcggttttaa---tcttagtttctggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAGGTGAAAGAG

upper sequence: PP1S197_115V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT3G11270.2 (Arabidopsis thaliana), 3'ss of exon 3
gtaagtccaattttattctgaactctg---catgtcgtactatgtagatgtacgacgtggccgt--aactacttcatgtata-gtagttcttagaatgaatagaacttatacttggcaatatttgctacccctt-caagagtcttactcttaaccgaagtttttcatattcctttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG
||||| ||||  | | ||| || | ||    |||  |  |||     || || |   |||  ||     ||  | || |||    |    ||  || | ||  |   | ||  |  |     ||||||  ||||      || |||||        ||   | | |  |||   || ||||| ||   ||||||||||||  |||| ||||||||||| || ||||  || ||||| || |||||||| || ||||||||||| ||||           
gtaagaccaaaatcagtctaaaatatgagatatgatggtctaatctaatatatggtttggtggtctgtttaagttatatatgtacaaacgttttaaagcattcacaatctatctctcctctcttgctagaccttatttctgtattacttcggttttaa---tcttagtttctggtgttgcagCTACGTTCCAAATCCAGTGTTGGTCATTATTGATGTCCAACCTAAAGAACTTGGAATCCCCACAAAAGCATACTATGCGGTTGAGGAG---------

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|208351962|gb|DC925771.1|DC925771
EST:     GGGCNTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGA                         TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
genomic: GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGAgtaagtccaa ... tttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
EST: gi|162212343|gb|FC388071.1|FC388071
EST:     GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGA                         TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
genomic: GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGAgtaagtccaa ... tttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
EST: gi|100442139|gb|BY963032.1|BY963032
EST:     GGCCTAAGTTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGGA                         TTATTGTCCAAAATC-AGTCCTGGTGATTATTGATGTACAGCCTAGGGAG
genomic: GGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGG-Agtaagtccaa ... tttgatgcagTTATTGTCCAAA-TCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAG
EST: gi|208368978|gb|DC955063.1|DC955063
EST:     GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGA                         TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
genomic: GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGAgtaagtccaa ... tttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
EST: gi|208391154|gb|DC942066.1|DC942066
EST:     GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGA                         TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
genomic: GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGAgtaagtccaa ... tttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
EST: gi|100398742|gb|BY990493.1|BY990493
EST:     GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGA                         TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
genomic: GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGAgtaagtccaa ... tttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
EST: gi|100426796|gb|BY977367.1|BY977367
EST:     GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGA                         TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
genomic: GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGAgtaagtccaa ... tttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
EST: gi|100362914|gb|BY947592.1|BY947592
EST:     GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATCTCGGGA                         TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
genomic: GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGAgtaagtccaa ... tttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
EST: gi|100387742|gb|BY951742.1|BY951742
EST:     GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGA                         TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
genomic: GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGAgtaagtccaa ... tttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
EST: gi|208371459|gb|DC955795.1|DC955795
EST:     GGGCCTAAG-NTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGA                         TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
genomic: GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGAgtaagtccaa ... tttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
EST: gi|100381366|gb|BY950092.1|BY950092
EST:     GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGA                         TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
genomic: GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGAgtaagtccaa ... tttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT
EST: gi|208361519|gb|DC942804.1|DC942804
EST:     GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGA                         TTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTANGGAGCT
genomic: GGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGAgtaagtccaa ... tttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCT

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), 24 (downstream exon)
Score: 7

CAAAAGAGCATGTGGTGGGGTGGTACAGCACTGGGCCTAAGCTTCGAGAAAATGATCTTGACATTAATGAGCTATTTCGGGAgtaagtccaa ... tttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taccccttcaagagtcttactcttaaccgaagtttttcatattcctttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG
                                tttttcatattccttt  CT-rich tract
                             aagtttttcatatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtccaattttattctgaactctgcatgtcgtactatgtagatgtacgacgtggccgtaactacttcatgtatagtagttcttagaatgaatagaacttatacttggcaatatttgctaccccttcaagagtcttactcttaaccgaagtttttcatattcctttgatgcagTTATTGTCCAAATCCAGTCCTGGTGATTATTGATGTACAGCCTAGGGAGCTTGGCATTCCCACAAAGGCGTACTATGCGGTGGAGGGAGTCAAAGTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG