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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tagatctgcagttgcagctccggataacattaacaggatgacagatctaacgtctgtttatcaattcttgataatagttgattctatttttatgtggcagACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGTATTGGCAAAAATTCAGTTGTGAAAAGAGCAATTATCGACAAGAATGCAC

Basic information

species Physcomitrella patens
transcript PP1S76_105V6.1
intron # 7
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S76_105V6.1 (Physcomitrella patens), 3'ss of exon 7
lower sequence: GRMZM2G106213_T02 (Zea mays), 3'ss of exon 7
tagatctgcagttgcagctccggataacattaacaggatgacagatctaacgtctgtttatcaattcttgataatagttgatt-ctatttttatgtgg--cagACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGTATTGGCAAAAATTCAGTTGTGAAAAGAGCAATTATCGACAAGAATGCAC
                        |||  |  |    |  | |  |||||  ||     ||  |    | || | |  | ||   | ||| | | | |  ||||| || ||  | |  ||||   | |  |  || |||||||||||||| |||||||| |||||||||  | | | || |||||| || ||||| ||||| |
-----------------------gtaaagtagagtcaaacagaactctaatatcgtgcaatggaaatatcatgagaacttatcattctttctgttttgttcagACTGAGAATGATAAGAATGTCCTTTCTGAGACTGGTGGCATTCCCATTGGTATTGGGAAAAATTCACATATCAGAAAAGCAATCATTGACAAAAATGCTC
















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|162247363|gb|FC421432.1|FC421432
EST:     GCTCTACTCATGGGAGCTGATTACTACGAG                         ACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
genomic: GCTCTACTCATGGGAGCTGATTACTACGAGgtaactatac ... tatgtggcagACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
EST: gi|162192361|gb|FC368575.1|FC368575
EST:     AAGGTGCTGTCATTGAGGATGCTCTACTCATGGGAGCTGATTACTACGAG                         ACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
genomic: AAGGTGCTGTCATTGAGGACGCTCTACTCATGGGAGCTGATTACTACGAGgtaactatac ... tatgtggcagACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
EST: gi|162192360|gb|FC368574.1|FC368574
EST:     AAGGTGCTGTCATTGAGGATGCTCTACTCATGGGAGCTGATTACTACGAG                         ACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
genomic: AAGGTGCTGTCATTGAGGACGCTCTACTCATGGGAGCTGATTACTACGAGgtaactatac ... tatgtggcagACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
EST: gi|18341189|gb|BJ173222.1|BJ173222
EST:     AAGGTGCTGTCATTGAGGACGCTCTACTCATGGGAGCTGATTACTACGAG                         ACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
genomic: AAGGTGCTGTCATTGAGGACGCTCTACTCATGGGAGCTGATTACTACGAGgtaactatac ... tatgtggcagACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
EST: gi|162247364|gb|FC421433.1|FC421433
EST:     AAGGTGCTGTCATTGAGGATGCTCTACTCATGGGAGCTGATTACTACGAG                         ACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGGCATTCCCATGGG
genomic: AAGGTGCTGTCATTGAGGACGCTCTACTCATGGGAGCTGATTACTACGAGgtaactatac ... tatgtggcagACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGG-CATTCCCATGGG
EST: gi|162150332|gb|FC326604.1|FC326604
EST:     AAGGTGCTGTCATTGAGGATGCTCTACTCATGGGAGCTGATTACTACGAG                         ACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
genomic: AAGGTGCTGTCATTGAGGACGCTCTACTCATGGGAGCTGATTACTACGAGgtaactatac ... tatgtggcagACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
EST: gi|162166090|gb|FC343372.1|FC343372
EST:     AAGGTGCTGTCATTGAGGATGCTCTACTCATGGGAGCTGATTACTACGAG                         ACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
genomic: AAGGTGCTGTCATTGAGGACGCTCTACTCATGGGAGCTGATTACTACGAGgtaactatac ... tatgtggcagACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
EST: gi|18334116|gb|BJ166132.1|BJ166132
EST:     AAGGTGCTGTCATTGAGGACGCTCTACTCATGGGAGCTGATTACTACGAG                         ACCGACAAGCAAANAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
genomic: AAGGTGCTGTCATTGAGGACGCTCTACTCATGGGAGCTGATTACTACGAGgtaactatac ... tatgtggcagACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
EST: gi|37829832|gb|BJ587844.1|BJ587844
EST:     AAGGTGCTGTCATTGAGGACGCTCTACTCATGGGAGCTGATTACTACGAG                         ACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT
genomic: AAGGTGCTGTCATTGAGGACGCTCTACTCATGGGAGCTGATTACTACGAGgtaactatac ... tatgtggcagACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGT

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), 35 (downstream exon)
Score: 327

AACGCAAGAATTTTCCACTCAGTGGTTGGTCTACGATCTTGGGTCTCGGAAGGTGCTGTCATTGAGGACGCTCTACTCATGGGAGCTGATTACTACGAGgtaactatac ... tatgtggcagACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGTATTGGCAAAAATTCAGTTGTGAAAAGAGCAATTATCGACAAGAATGCAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctaacgtctgtttatcaattcttgataatagttgattctatttttatgtggcagACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGTATTGGCAAAAATTCAGTTGTGAAAAGAGCAATTATCGACAAGAATGCAC
                                    ttctattttt  CT-rich tract
                         ataatagttgattcta  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tagatctgcagttgcagctccggataacattaacaggatgacagatctaacgtctgtttatcaattcttgataatagttgattctatttttatgtggcagACCGACAAGCAAAGAAATGAGTTGTTAGCCACAGGTGGCATTCCCATGGGTATTGGCAAAAATTCAGTTGTGAAAAGAGCAATTATCGACAAGAATGCAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA