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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgtaagcacaagatcttacaaagggatttgtatgcttgtgcataatacgaattggtctgtatcaacctgactgaaattccggtgtgcctggttgtagTGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGATACGAGAGGCTGCCACTCTTTTCCGACTTCTGAAGACATTGGAATGCTG

Basic information

species Physcomitrella patens
transcript PP1S82_30V6.1
intron # 11
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|18334747|gb|BJ166764.1|BJ166764
EST:     ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACG                         TGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
genomic: ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACGgtatgaaagc ... ctggttgtagTGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
EST: gi|37822015|gb|BJ580081.1|BJ580081
EST:     ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACG                         TGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
genomic: ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACGgtatgaaagc ... ctggttgtagTGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
EST: gi|162165273|gb|FC341931.1|FC341931
EST:     ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACG                         TGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATNCA-CTTTTCACAG
genomic: ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACGgtatgaaagc ... ctggttgtagTGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCAT-CAACTTTTCACAG
EST: gi|208360796|gb|DC946492.1|DC946492
EST:     ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACG                         TGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
genomic: ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACGgtatgaaagc ... ctggttgtagTGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
EST: gi|162165272|gb|FC341930.1|FC341930
EST:     ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACG                         TGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
genomic: ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACGgtatgaaagc ... ctggttgtagTGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
EST: gi|162228505|gb|FC404129.1|FC404129
EST:     ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACG                         TGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
genomic: ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACGgtatgaaagc ... ctggttgtagTGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
EST: gi|37822839|gb|BJ580905.1|BJ580905
EST:     ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACG                         TGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
genomic: ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACGgtatgaaagc ... ctggttgtagTGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
EST: gi|18339762|gb|BJ171789.1|BJ171789
EST:     ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACG                         TGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
genomic: ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACGgtatgaaagc ... ctggttgtagTGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
EST: gi|162215781|gb|FC390846.1|FC390846
EST:     ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACG                         TGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA
genomic: ATTGGTTTGTGTCTTTTTGCAAAGCTTGATTCGAAACAAGACAATCAACGgtatgaaagc ... ctggttgtagTGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taatacgaattggtctgtatcaacctgactgaaattccggtgtgcctggttgtagTGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGATACGAGAGGCTGCCACTCTTTTCCGACTTCTGAAGACATTGGAATGCTG
                      acctgac  putative branch site (score: 3)
                             tgaaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgtaagcacaagatcttacaaagggatttgtatgcttgtgcataatacgaattggtctgtatcaacctgactgaaattccggtgtgcctggttgtagTGCAAGACTTGTTCATAGAGGTTCAGGCGTTTTGCATCAACTTTTCACAGATACGAGAGGCTGCCACTCTTTTCCGACTTCTGAAGACATTGGAATGCTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ATGCTG