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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctcgttttattatcaaggagagagagagagagagagagagagagagagagagagatagagggactgtagttgatttattgttatggtgctcgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG

Basic information

species Physcomitrella patens
transcript PP1S425_12V6.1
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S425_12V6.1 (Physcomitrella patens), 3'ss of exon 10
lower sequence: Vv18s0001g01020.t01 (Vitis vinifera), 3'ss of exon 11
ctcgttttattatcaaggagagagagagagagagagagagagagagagagagagatagagggactgta-gttgatttattgttatggt-gctcgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
 | | ||||  |||   |||     | ||        |||    | |    |  | |  ||    ||| ||| | | |||||  |  | | | |||  |||||| ||||| |||||||||||||| ||||| || |||||||| ||||||
atagatttaa-atccttgagtttttgtgaatctctatgaggttta-actttgttacaagggaggggtatgtttagtgattgtcctttttgtttgtggaacagATATACCCACCTATTAATGTTCTTCCATCACTCTCTCGACTAATGAAG
















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|208363000|gb|DC946897.1|DC946897
EST:     ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG                         ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
genomic: ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctc ... cgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
EST: gi|162186055|gb|FC361883.1|FC361883
EST:     ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG                         ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
genomic: ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctc ... cgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
EST: gi|37828436|gb|BJ586448.1|BJ586448
EST:     ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG                         ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
genomic: ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctc ... cgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
EST: gi|18334455|gb|BJ166472.1|BJ166472
EST:     ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG                         ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
genomic: ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctc ... cgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
EST: gi|37844824|gb|BJ602832.1|BJ602832
EST:     ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG                         ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
genomic: ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctc ... cgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
EST: gi|37848287|gb|BJ606295.1|BJ606295
EST:     ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG                         ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
genomic: ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctc ... cgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
EST: gi|18339737|gb|BJ171764.1|BJ171764
EST:     ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG                         ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
genomic: ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctc ... cgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
EST: gi|162191293|gb|FC366867.1|FC366867
EST:     TCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG                         ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
genomic: TCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctc ... cgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
EST: gi|162158554|gb|FC334557.1|FC334557
EST:     ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG                         ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
genomic: ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctc ... cgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
EST: gi|67700014|gb|BJ960247.1|BJ960247
EST:     ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG                         ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
genomic: ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctc ... cgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
EST: gi|162218504|gb|FC395081.1|FC395081
EST:     ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG                         ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
genomic: ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctc ... cgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
EST: gi|162191294|gb|FC366868.1|FC366868
EST:     ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG                         ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
genomic: ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctc ... cgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
EST: gi|162185240|gb|FC361750.1|FC361750
EST:     ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAG                         ATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
genomic: ATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctc ... cgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG

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: 34 (upstream exon), 34 (downstream exon)
Score: 10

ATATTACCCACCCAATTCCTGATCTTACAGGATATATTACGGAAGGTCAAATTTATGTTGATCGGCAGTTACAAAACAGACAGgtatgtgctc ... cgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagagagagatagagggactgtagttgatttattgttatggtgctcgtgatacagATCTACCCGCCTATTAATGTTCTGCCATCTCTGTCTCGACTGATGAAG
                      agttgat  putative branch site (score: 10)
                        ttgatttattgttat  TA-rich tract