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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgttatcccgtttgcttgtacttcgacgatcttttgaatgaagaggttcagtggtttgtgacttctctatgaggataattttttatctgatagcttgtgaatcaacaatttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTCCCATTCTTCTACTCCCGCTCCTTCAATCTGTCGTGGCAGTTCTACGGCG

Basic information

species Physcomitrella patens
transcript PP1S90_28V6.4
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S90_28V6.4 (Physcomitrella patens), 3'ss of exon 10
lower sequence: LOC_Os08g44340.1 (Oryza sativa), 3'ss of exon 9
gtatgttatcccgtttgcttgtacttcgacgatcttttgaatgaagaggttcagtggtttgtgacttctctatgaggataattttttatctgatagcttgtgaatcaacaatttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTCCCATTCTTCTACTCCCGCTCCTTCAATCTGTCGTGGCAGTTCTACGGCG
||  |  |||| ||| | |  |  |||  |   ||  |    |     | |||| | ||    | |||| | |||  |  |      ||    | ||||      |||  |  | | ||||||||||| ||    |||   |||||    |||   |||||||| ||||| || | |||||||||||| || ||| | || |||||||||||||||||||
gtgagccatcc-gttcgttcttgattcttcatcctcgttgccgccattgatcag-gattcagaagttctttgtgataaccaa-----attcactggctt------caatgaacttg-cagGCGATCAAGGCGAAGGAGGCCGGCGAGTCGGTGCCGGAGTACGACTACCTGCCCTACTTCTACTCCCGGTCGTTCGACCTCTCGTGGCAGTTCTACGGCG

upper sequence: PP1S90_28V6.4 (Physcomitrella patens), 3'ss of exon 10
lower sequence: AT3G52880.1 (Arabidopsis thaliana), 3'ss of exon 9
-------------------------gtat-gttatcccgtttgcttgtacttcgacgatcttttgaatgaag----aggttcagtggtttgtgacttctctatgaggata-attttt---tatctgata----gcttgtgaat-caaca-atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTCCCATTCTTCTACTCCCGCTCCTTCAATCTGTCGTGGCAGTTCTACGGCG
                          ||| | ||  ||     | | |   || |     |    |||| |     |  |   | ||  |    ||| |  || |  ||| | || |   ||||||||     | || |  ||   | | |||  |||||||||||||||| ||||||   |||| ||  ||||| || ||||| || || |||||||||||||| ||||||||  |||| || |||||||||||||| |
gtaaataatgcttacaatatggctgatatcgctacaccaaaaccctattaatccataccataaaaaatgcaacgcaaactcttgaggcctaaatcttatagattaacatacagttgtatatatctgatgaagcgtttatatatgtgatacattgtggcagGCGATCAAAGCGGCTGAGGGAGGCGCAGCGGTGGAGGAATACGACTATCTTCCATTCTTCTACTCTCGCTCCTTTGATCTCTCATGGCAGTTCTACGGAG
















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|162158959|gb|FC334819.1|FC334819
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|162166733|gb|FC342702.1|FC342702
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|162178357|gb|FC355179.1|FC355179
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|37828254|gb|BJ586266.1|BJ586266
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|37833129|gb|BJ591141.1|BJ591141
EST:     AGTGGAGCATGTGGACCATGCAAGGAAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: AGTGGAGCATGTGGACCATGCAAGG-AAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|67696822|gb|BJ957055.1|BJ957055
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|162225063|gb|FC401687.1|FC401687
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|37838802|gb|BJ596810.1|BJ596810
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|37852518|gb|BJ610526.1|BJ610526
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|18341461|gb|BJ173496.1|BJ173496
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|37836214|gb|BJ594222.1|BJ594222
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|162181159|gb|FC357604.1|FC357604
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|208373118|gb|DC948883.1|DC948883
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|162221160|gb|FC397801.1|FC397801
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|208387453|gb|DC949238.1|DC949238
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|208392192|gb|DC957271.1|DC957271
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|162278697|gb|FC454807.1|FC454807
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|37850756|gb|BJ608764.1|BJ608764
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|162178358|gb|FC355180.1|FC355180
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTG
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTG
EST: gi|37842364|gb|BJ600372.1|BJ600372
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|18340059|gb|BJ172087.1|BJ172087
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|162237032|gb|FC413191.1|FC413191
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|162172811|gb|FC348400.1|FC348400
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATTTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|162181158|gb|FC357603.1|FC357603
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|37830452|gb|BJ588464.1|BJ588464
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|37841480|gb|BJ599488.1|BJ599488
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|208378994|gb|DC922840.1|DC922840
EST:     GAGTGGAGCATGTGGACCANGCAAGGAAATCTNCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGNTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|162221161|gb|FC397802.1|FC397802
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|37824881|gb|BJ582947.1|BJ582947
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
EST: gi|208395391|gb|DC919967.1|DC919967
EST:     GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAG                         GCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC
genomic: GAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTC

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: 27 (upstream exon), 9 (downstream exon)
Score: 1

CGTAGGTGACATTGCAACATTCCCAATGAAGATGTATGGTGATAGCCGGCGAGTGGAGCATGTGGACCATGCAAGGAAATCTGCCATGCAGGCTGTTCAGgtatgttatc ... atttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTCCCATTCTTCTACTCCCGCTCCTTCAATCTGTCGTGGCAGTTCTACGGCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttctctatgaggataattttttatctgatagcttgtgaatcaacaatttgggcagGCGATCAAAGCCGCTGAGAAGGGCGAAGTCGTGGACGAGTACGATTACCTCCCATTCTTCTACTCCCGCTCCTTCAATCTGTCGTGGCAGTTCTACGGCG
                      atctgat  putative branch site (score: 1)
            ataattttttatctga  TA-rich tract