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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtcatgctgccgtactctctagaaaccactactgtgagaacaatgcaatttaacttgactgtcccacatgccgcttttctttaactttttaatctgaggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAACCCCGAGGTCGGTCAGATGATCGCCGAAGCCATGAGCAAAGTCGGGCGCA

Basic information

species Physcomitrella patens
transcript PP1S14_298V6.1
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S14_298V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: LOC_Os02g01280.1 (Oryza sativa), 3'ss of exon 5
gtaagtcatgctgccgtactctctagaaaccactactgtgagaacaatgcaatttaacttgactgtcccacatgccgcttttctttaactttttaatctgaggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAACCCCGAGGTCGGTCAGATGATCGCCGAAGCCATGAGCAAAGTCGGGCGCA
       || | |  | | |  ||   |      |  ||   |   || |  |  | |   | | |    | ||    ||   | || | | ||      |   |  |||||||||||||| ||||| |||||||| ||||| || ||||| || ||||||  |||  | ||  | ||||| || ||||| |||| ||| || || ||  
-----gaattcaggagcattggctgccagtttgaatcgt---actcatccgctacagcactattttt--gcttgaaatttgaatctatcatattgcatgcaactttgcagGTTGAAGACAGCGAACTTGCTGATGTTGCTGCGGTAAGTGCTGGAAATAACTACGAAATTGGCAACATGATAGCTGAAGCTATGAACAAGGTTGGACGAC

upper sequence: PP1S14_298V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT3G13470.1 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtcatgctgccgtactctctagaaaccactactgtgagaacaa-tgcaatttaacttgactgtcccacatgccgcttttctttaactttttaatc-tgaggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAACCCCGAGGTCGGTCAGATGATCGCCGAAGCCATGAGCAAAGTCGGGCGCA
                        || ||| | ||   | | |     | |   |||| ||  |        ||  |    |  | |||   ||   || |  | |  | ||||||||||||||||||| |||||||| || ||||| ||||| |||||||||| ||| || ||    ||||| || ||||| ||||||||||| ||  | |
---------------------gtaagtaactattatgctaaaacttccttcttcttaatttttcgagagtctatagcaagatggtctaaaggttatgtcattggaaatatagGTTGAAGACAGTGAACTTGCTGATGTGGCAGCTGTTAGTGCGGGTAATAACCACGAAGTTGGAAGTATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA

upper sequence: PP1S14_298V6.1 (Physcomitrella patens), 3'ss of exon 4
lower sequence: AT1G55490.2 (Arabidopsis thaliana), 3'ss of exon 5
gtaagtcatgctgccgtactctctagaaaccactactgtgagaacaatgcaatttaacttgactgtcccacatgccgcttttctttaactttttaatctgag----gatgac--agGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAACCCCGAGGTCGGTCAGATGATCGCCGAAGCCATGAGCAAAGTCGGGCGCA
                                | | | |    |  |  |  |||   || | | |   |   | |  |||||   |  || | ||| | ||    |  ||   ||||||||||||||||||| || ||||| || ||||| ||||| ||||| |||  |||  | ||  | ||||| || ||||| ||||||||||| ||  | |
----------------------------gtttcaaatttataga--actctctttcttttaa-tatgttaagagtc-tttttcaaaaggttctgaatgtaagtcatgtcgatgtagGTTGAAGACAGTGAACTTGCAGATGTTGCAGCTGTTAGTGCGGGTAACAACGACGAAATTGGAAATATGATTGCTGAAGCAATGAGCAAAGTGGGCAGGA

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|162171350|gb|FC346443.1|FC346443
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162246717|gb|FC422710.1|FC422710
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162203804|gb|FC379901.1|FC379901
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|208353715|gb|DC929716.1|DC929716
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162195954|gb|FC372151.1|FC372151
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|208351065|gb|DC913501.1|DC913501
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCANTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162170824|gb|FC347438.1|FC347438
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162157418|gb|FC333195.1|FC333195
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|100446886|gb|CJ971185.1|CJ971185
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAACAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162187436|gb|FC362658.1|FC362658
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162193667|gb|FC371246.1|FC371246
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162173847|gb|FC349439.1|FC349439
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162158432|gb|FC334227.1|FC334227
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162195933|gb|FC372143.1|FC372143
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|208359427|gb|DC939152.1|DC939152
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|208399108|gb|DC904517.1|DC904517
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162167160|gb|FC343636.1|FC343636
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162255992|gb|FC431756.1|FC431756
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162175554|gb|FC350972.1|FC350972
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162227587|gb|FC403529.1|FC403529
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|208362500|gb|DC939480.1|DC939480
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162158158|gb|FC333953.1|FC333953
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
EST: gi|162149659|gb|FC326710.1|FC326710
EST:     AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAA                         GTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC
genomic: AAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAAC

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: 29 (upstream exon), 31 (downstream exon)
Score: 16

GTTGTTGCAGCGGGAGCCAATCCAGTACAGATCACAAGAGGCATTGAAAAAACTGTGGCTGCCCTGGTCAAGGAGTTGAAAAAGCTTTCCAAGGAAgtaagtcatg ... aggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAACCCCGAGGTCGGTCAGATGATCGCCGAAGCCATGAGCAAAGTCGGGCGCA




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aacttgactgtcccacatgccgcttttctttaactttttaatctgaggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAACCCCGAGGTCGGTCAGATGATCGCCGAAGCCATGAGCAAAGTCGGGCGCA
                                   ttttaat  putative branch site (score: 16)
                       ttttctttaacttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaagtcatgctgccgtactctctagaaaccactactgtgagaacaatgcaatttaacttgactgtcccacatgccgcttttctttaactttttaatctgaggatgacagGTTGAAGACAGTGAACTGGCTGATGTCGCTGCTGTCAGTGCCGGTAATAACCCCGAGGTCGGTCAGATGATCGCCGAAGCCATGAGCAAAGTCGGGCGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAAG