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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtagcttcatcacccgcctgaatgtcttcttaatgtagtatttgcgatctttcaaagttactcctcagttgttatcgcactcgaatcgaatattcggctcaatctatgaagttgagctaatctggtcaactttcttcacacgtagGTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAAACTGTCGTCGCTTTGGTTAAAGAGTTGAAGAAGATGTCTAAGGAG

Basic information

species Physcomitrella patens
transcript PP1S276_75V6.1
intron # 3
splice site 3'
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|162163834|gb|FC340056.1|FC340056
EST:     CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAG                         GTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
genomic: CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAGgtagcttcat ... tcacacgtagGTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
EST: gi|208357238|gb|DC910649.1|DC910649
EST:     CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGANGGTGTCAAG                         GTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGANGCATTGACAAA
genomic: CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAGgtagcttcat ... tcacacgtagGTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
EST: gi|162187015|gb|FC363421.1|FC363421
EST:     CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAG                         GTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
genomic: CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAGgtagcttcat ... tcacacgtagGTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
EST: gi|67569513|gb|BJ942337.1|BJ942337
EST:     CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAG                         GTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
genomic: CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAGgtagcttcat ... tcacacgtagGTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
EST: gi|18369385|gb|BJ201471.1|BJ201471
EST:     CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGANGGTGTCAAG                         GNTGTCGCTGCA
genomic: CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAGgtagcttcat ... tcacacgtagGTTGTCGCTGCA
EST: gi|162185158|gb|FC362292.1|FC362292
EST:     CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAG                         GTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
genomic: CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAGgtagcttcat ... tcacacgtagGTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
EST: gi|162186625|gb|FC363597.1|FC363597
EST:     CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAG                         GTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
genomic: CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAGgtagcttcat ... tcacacgtagGTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
EST: gi|18372339|gb|BJ203941.1|BJ203941
EST:     CACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAAG                         GTTGTCGCTGCAG
genomic: CACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAA-Ggtagcttcat ... tcacacgtagGTTGTCGCTGCAG
EST: gi|162176794|gb|FC352808.1|FC352808
EST:     CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAG                         GTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
genomic: CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAGgtagcttcat ... tcacacgtagGTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
EST: gi|162191287|gb|FC366861.1|FC366861
EST:     CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAG                         GTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
genomic: CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAGgtagcttcat ... tcacacgtagGTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
EST: gi|100363541|gb|BY966441.1|BY966441
EST:     CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAG                         GTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAAGCATTGACAAA
genomic: CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAGgtagcttcat ... tcacacgtagGTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
EST: gi|22492170|gb|BU052093.1|BU052093
EST:     CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAG                         GTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA
genomic: CCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAGgtagcttcat ... tcacacgtagGTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAA

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), 16 (downstream exon)
Score: 6

GTTGGTTAGGCAAGCTTCTGCCAAGACCAACGATTTGGCTGGTGATGGTACCACCACCTCTGTGGTTCTTGCTCAAGGGCTCATTGCCGAGGGTGTCAAGgtagcttcat ... tcacacgtagGTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAAACTGTCGTCGCTTTGGTTAAAGAGTTGAAGAAGATGTCTAAGGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tattcggctcaatctatgaagttgagctaatctggtcaactttcttcacacgtagGTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAAACTGTCGTCGCTTTGGTTAAAGAGTTGAAGAAGATGTCTAAGGAG
                        agctaat  putative branch site (score: 6)
                                       ctttcttcac  putative PPT
          aatctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtagcttcatcacccgcctgaatgtcttcttaatgtagtatttgcgatctttcaaagttactcctcagttgttatcgcactcgaatcgaatattcggctcaatctatgaagttgagctaatctggtcaactttcttcacacgtagGTTGTCGCTGCAGGAGCCAACCCAGTGCAAATCACCAGAGGCATTGACAAAACTGTCGTCGCTTTGGTTAAAGAGTTGAAGAAGATGTCTAAGGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGGAG