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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagtctgcttgatttgctatgtttgtttttccattacaaacaatacgttttaattcacgtggggcaatctgttgtaatcacagacaatttttttgacactgaaactaacgtattagaatcacttgcagCTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGTTCAACGGATTCTGGTGCCAG

Basic information

species Physcomitrella patens
transcript PP1S99_240V6.2
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|37852527|gb|BJ610535.1|BJ610535
EST:     TCTGCGGGATGAAAAACCCTGGCTTCGCTCGCACTCGTGCAGCCAATAAA                         CTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGT
genomic: TCTGCGGGATGAAAAACCCTGGC-TCGCTCGCACTCGTGCAGCCAATAAAgtgagtctgc ... tcacttgcagCTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGT
EST: gi|37846308|gb|BJ604316.1|BJ604316
EST:     TGCGGGATGAAAAACCCTGGCTCGCTCGCACTCGTGCAGCCAATAAA                         CTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGT
genomic: TGCGGGATGAAAAACCCTGGCTCGCTCGCACTCGTGCAGCCAATAAAgtgagtctgc ... tcacttgcagCTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGT
EST: gi|162274959|gb|FC450610.1|FC450610
EST:     ATCTGCGGGATGAAAAACCCTGGCTCGCTCGCACTCGTGCAGCCAATAAA                         CTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGT
genomic: ATCTGCGGGATGAAAAACCCTGGCTCGCTCGCACTCGTGCAGCCAATAAAgtgagtctgc ... tcacttgcagCTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGT
EST: gi|37841748|gb|BJ599756.1|BJ599756
EST:     TCGCACTCGTGCAGCCAATAAA                         CTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGT
genomic: TCGCACTCGTGCAGCCAATAAAgtgagtctgc ... tcacttgcagCTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGT
EST: gi|162265494|gb|FC441535.1|FC441535
EST:     ATCTGCGGGATGAAAAACCCTGGCTCGCTCGCACTCGTGCAGCCAATAAA                         CTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGT
genomic: ATCTGCGGGATGAAAAACCCTGGCTCGCTCGCACTCGTGCAGCCAATAAAgtgagtctgc ... tcacttgcagCTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGT
EST: gi|37841193|gb|BJ599201.1|BJ599201
EST:     GCGGGATGAAAAACCCTGGCTCGCTCGCACTCGTGCAGCCAATAAA                         CTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGT
genomic: GCGGGATGAAAAACCCTGGCTCGCTCGCACTCGTGCAGCCAATAAAgtgagtctgc ... tcacttgcagCTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGT

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: 25 (upstream exon), 31 (downstream exon)
Score: 4

GAATGGATGCGCAAGTGGCATATGACTTTCACCATCTGCGGGATGAAAAACCCTGGCTCGCTCGCACTCGTGCAGCCAATAAAgtgagtctgc ... tcacttgcagCTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGTTCAACGGATTCTGGTGCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaatcacagacaatttttttgacactgaaactaacgtattagaatcacttgcagCTTATCTACTCCGGTTTCGGTTGCACGCAAGGTTGGTTCTGCACTGCTTGTTCAACGGATTCTGGTGCCAG
                             aactaac  putative branch site (score: 4)
          acaattttttt  TA-rich tract