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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tatggaactagtgtagcagttacacgcttgttggtcagataccagtgccttgagctgaggggtttaattaaaaagttcactttaaattcttattttgcagAATAATTACTCGGCTGCAGTGAAAGAGAGCACGAAGGCTCTAGAGCTTAACCCGAACTACTTGAAAGCCCTAATGAGACGTGCGCAGGCCAATGAAAACC

Basic information

species Physcomitrella patens
transcript PP1S62_216V6.1
intron # 4
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|208379389|gb|DC922947.1|DC922947
EST:     AGCTGCGTGCACAATGCTACTCAAATCGAGCTATTTGCGAAATCAATCTG                         AATAATTACTCGGCTGCAGTGAAAGAGAGCACGAAGGCTCTAGAGCTTAAC
genomic: AGCTGCGTGCACAATGCTACTCAAATCGAGCTATTTGCGAAATCAATCTGgtaattcacg ... tattttgcagAATAATTACTCGGCTGCAGTGAAAGAGAGCACGAAGGCTCTAGAGCTTAAC
EST: gi|208383738|gb|DC911462.1|DC911462
EST:     AGCTGCGTGCACAATGCTACTCAA-TCGAGCTATTTGCGAA-TCANTCTG                         AATAATTACTCGGCTGCAGTGAA
genomic: AGCTGCGTGCACAATGCTACTCAAATCGAGCTATTTGCGAAATCAATCTGgtaattcacg ... tattttgcagAATAATTACTCGGCTGCAGTGAA
EST: gi|37847056|gb|BJ605064.1|BJ605064
EST:     AGCTGCGTGCACAATGCTACTCAAATCGAGCTATTTGCGAAATCAATCTG                         AATAATTACTCGGCTGCAGTGAAAGAGAGCACGAAGGCTCTAGAGCTTAAC
genomic: AGCTGCGTGCACAATGCTACTCAAATCGAGCTATTTGCGAAATCAATCTGgtaattcacg ... tattttgcagAATAATTACTCGGCTGCAGTGAAAGAGAGCACGAAGGCTCTAGAGCTTAAC
EST: gi|208344970|gb|DC909081.1|DC909081
EST:     AGCTGCGTGCACAATGCTACTCAAATCGAGCTATTTGCGAAATCAATCTG                         AATAATTACTCGGCTGCAGTGAAAGA
genomic: AGCTGCGTGCACAATGCTACTCAAATCGAGCTATTTGCGAAATCAATCTGgtaattcacg ... tattttgcagAATAATTACTCGGCTGCAGTGAAAGA
EST: gi|208400047|gb|DC925259.1|DC925259
EST:     AGCTGCGTGCACAATGCTACTCAAATCGAGCTATTTGCGAAATCAATCTG                         AATAATTACTCGGCTGCAGTGAAAGAGAGCACGAAGGCTCTAGAGCTTAAC
genomic: AGCTGCGTGCACAATGCTACTCAAATCGAGCTATTTGCGAAATCAATCTGgtaattcacg ... tattttgcagAATAATTACTCGGCTGCAGTGAAAGAGAGCACGAAGGCTCTAGAGCTTAAC
EST: gi|37847806|gb|BJ605814.1|BJ605814
EST:     AGCTGCGTGCACAATGCTACTCAAATCGAGCTATTTGCGAAATCAATCTG                         AATAATTACTCGGCTGCAGTGAAAGAGAGCACGAAGGCTCTAGAGCTTAAC
genomic: AGCTGCGTGCACAATGCTACTCAAATCGAGCTATTTGCGAAATCAATCTGgtaattcacg ... tattttgcagAATAATTACTCGGCTGCAGTGAAAGAGAGCACGAAGGCTCTAGAGCTTAAC

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: 20 (upstream exon), 27 (downstream exon)
Score: 3

ATGCTACGCTAGTGCATTGGAAGACGTTGCCAATGATCCAAGTGCAAATGAGCTGCGTGCACAATGCTACTCAAATCGAGCTATTTGCGAAATCAATCTGgtaattcacg ... tattttgcagAATAATTACTCGGCTGCAGTGAAAGAGAGCACGAAGGCTCTAGAGCTTAACCCGAACTACTTGAAAGCCCTAATGAGACGTGCGCAGGCCAATGAAAACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgccttgagctgaggggtttaattaaaaagttcactttaaattcttattttgcagAATAATTACTCGGCTGCAGTGAAAGAGAGCACGAAGGCTCTAGAGCTTAACCCGAACTACTTGAAAGCCCTAATGAGACGTGCGCAGGCCAATGAAAACC
                gtttaat  putative branch site (score: 3)
                                         ttcttatttt  putative PPT
                 tttaattaaaaagttc  TA-rich tract