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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgatgcacactcctctcataatattcattgtcgtagtcagaaagagaatgaaatgatcatgtttctcactttctgcttgcgagggtccttacaacagaaatggaatctgtttttcgtttgtttgtttgtttttgtttatactttgctaaatggcactttttgatattgagctgttgttttactatcggagcagAAACTGGAGTTACCAACGATCGACAGACGAAGTGGGCATCTTGGATTATGATGGGCACGTTTCTCTCCTTGTTCGTGGCGCAGTTTCCTCGTCTATTCCG

Basic information

species Physcomitrella patens
transcript PP1S6_337V6.1
intron # 2
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|208380580|gb|DC903184.1|DC903184
EST:     CCAGCTCATAGCCAAAGACAGGACTCTGACACAGGGATTCAATCTCACCA                         AAACTGGAGTTACCAACGATCGACAGACNAN-TGGGCATCTT
genomic: CCAGCTCATAGCCAAAGACAGGACTCTGACACAGGGATTCAATCTCACCAgtacgatgca ... atcggagcagAAACTGGAGTTACCAACGATCGACAGACGAAGTGGGCATCTT
EST: gi|208389783|gb|DC938331.1|DC938331
EST:     CCAGCTCATAGCCAAAGACAGGACTCTGACACAGGGATTCAATCTCACCA                         AAACTGGAGTTACCAACGATCGACAGACGAAGTGGGCATCTTGGATTATGA
genomic: CCAGCTCATAGCCAAAGACAGGACTCTGACACAGGGATTCAATCTCACCAgtacgatgca ... atcggagcagAAACTGGAGTTACCAACGATCGACAGACGAAGTGGGCATCTTGGATTATGA
EST: gi|100405147|gb|BY955386.1|BY955386
EST:     CCAGCTCATAGCCAAAGACAGGACTCTGACACAGGGATTCAATCTCACCA                         AAACTGGAGTTACCAACGATCGACAGACGAAGTGGGCATCTTGGATTATGA
genomic: CCAGCTCATAGCCAAAGACAGGACTCTGACACAGGGATTCAATCTCACCAgtacgatgca ... atcggagcagAAACTGGAGTTACCAACGATCGACAGACGAAGTGGGCATCTTGGATTATGA
EST: gi|100399021|gb|BY990633.1|BY990633
EST:     CCAGCTCATAGCCCAAGACAGGACTCTGACACAGGGATTCAATCTCACCA                         AAACTGGAGTTACCAACGATCGACAGACGAAGTGGGCATCTTGGATTATGA
genomic: CCAGCTCATAGCCAAAGACAGGACTCTGACACAGGGATTCAATCTCACCAgtacgatgca ... atcggagcagAAACTGGAGTTACCAACGATCGACAGACGAAGTGGGCATCTTGGATTATGA
EST: gi|100442981|gb|BY963476.1|BY963476
EST:     CCAGCTCATAGCCAAAGACAGGACTCTGACACAGGGATTCAATCTCACCA                         AAACTGGAGTTACCAACGATCGACAGACGAAG-GGTGCATCTTGGATTATG
genomic: CCAGCTCATAGCCAAAGACAGGACTCTGACACAGGGATTCAATCTCACCAgtacgatgca ... atcggagcagAAACTGGAGTTACCAACGATCGACAGACGAAGTGG-GCATCTTGGATTATG

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: 31 (upstream exon), 31 (downstream exon)
Score: 15

TCATGCCTTATTCTCGGCCGATGCGATCTTGTTCCACATCCGACGACCGGCCAGCTCATAGCCAAAGACAGGACTCTGACACAGGGATTCAATCTCACCAgtacgatgca ... atcggagcagAAACTGGAGTTACCAACGATCGACAGACGAAGTGGGCATCTTGGATTATGATGGGCACGTTTCTCTCCTTGTTCGTGGCGCAGTTTCCTCGTCTATTCCG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tactttgctaaatggcactttttgatattgagctgttgttttactatcggagcagAAACTGGAGTTACCAACGATCGACAGACGAAGTGGGCATCTTGGATTATGATGGGCACGTTTCTCTCCTTGTTCGTGGCGCAGTTTCCTCGTCTATTCCG
                  tttttgatatt  TA-rich tract