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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGGGTCTTCGTCGCCTGGTCTCGGAGCGATCCGCACCGCCATCCGCTCTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttgctgagttttttttttttttcttttttcttttttctttttccttttcctttttagggtttatgtctttgtgatggattagtatggttttgt...

Basic information

species Physcomitrella patens
transcript PP1S79_113V6.1
intron # 1
splice site 5'
intron type U2

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|37853300|gb|BJ611308.1|BJ611308
EST:     CTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|37853057|gb|BJ611065.1|BJ611065
EST:     CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|18367047|gb|BJ199127.1|BJ199127
EST:     CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|37848842|gb|BJ606850.1|BJ606850
EST:     CTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|162273380|gb|FC449829.1|FC449829
EST:     CTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|18359647|gb|BJ191708.1|BJ191708
EST:     CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|37847458|gb|BJ605466.1|BJ605466
EST:     TTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: TTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|162149649|gb|FC325842.1|FC325842
EST:     CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|162225441|gb|FC401206.1|FC401206
EST:     CAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|18372643|gb|BJ204245.1|BJ204245
EST:     CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|19790267|gb|BQ041782.1|BQ041782
EST:     CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|208368458|gb|DC939935.1|DC939935
EST:     CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|162225442|gb|FC401207.1|FC401207
EST:     CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|162206796|gb|FC382658.1|FC382658
EST:     CCAATTTTTTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|162273381|gb|FC449830.1|FC449830
EST:     CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|37852160|gb|BJ610168.1|BJ610168
EST:     TCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: TCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|162244699|gb|FC424627.1|FC424627
EST:     CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|162206797|gb|FC382659.1|FC382659
EST:     CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|18374717|gb|BJ206295.1|BJ206295
EST:     CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
EST: gi|18366439|gb|BJ198518.1|BJ198518
EST:     CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAG                         ATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC
genomic: CTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCAC

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), 30 (downstream exon)
Score: 9

TGCTGGGTCTTCGTCGCCTGGTCTCGGAGCGATCCGCACCGCCATCCGCTCTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttg ... tgttttgtagATTGCAGCTTCCGGAGCATCGAAACCCGAAGACTGGCCTTATGCTGTGCACGTTCTTTCCCATGTTGTGAATCATGACTT




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGGGTCTTCGTCGCCTGGTCTCGGAGCGATCCGCACCGCCATCCGCTCTCTCCAATTTTCTCAGCTTGCGGATCTTCTGGACAATTTGGAGCTTGAGgcaattcttgctgagttttttttttttttcttttttcttttttctttttccttttcctttttagggtttatgtctttgtgatggattagtatggttttgt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT