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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aatcacgatcttcatcttgataattttcacgaactttgtgttctctaaacaccaacatctggatttttggatatggaataattgttatggttgcttgcagGTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGTAGATACATCTCCCGGAACCAG

Basic information

species Physcomitrella patens
transcript PP1S43_166V6.1
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|18372735|gb|BJ204337.1|BJ204337
EST:     CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACC                         GTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
genomic: CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACCgtaagtattt ... ttgcttgcagGTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
EST: gi|18349762|gb|BJ181812.1|BJ181812
EST:     CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACC                         GTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
genomic: CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACCgtaagtattt ... ttgcttgcagGTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
EST: gi|18368128|gb|BJ200213.1|BJ200213
EST:     CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACC                         GTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
genomic: CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACCgtaagtattt ... ttgcttgcagGTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
EST: gi|18357482|gb|BJ189541.1|BJ189541
EST:     CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACC                         GTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
genomic: CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACCgtaagtattt ... ttgcttgcagGTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
EST: gi|18370312|gb|BJ201914.1|BJ201914
EST:     CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACC                         GTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
genomic: CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACCgtaagtattt ... ttgcttgcagGTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
EST: gi|18364594|gb|BJ196667.1|BJ196667
EST:     CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACC                         GTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
genomic: CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACCgtaagtattt ... ttgcttgcagGTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
EST: gi|100371663|gb|BY968088.1|BY968088
EST:     CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACC                         GTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
genomic: CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACCgtaagtattt ... ttgcttgcagGTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
EST: gi|18364941|gb|BJ197015.1|BJ197015
EST:     CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACC                         GTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT
genomic: CAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACCgtaagtattt ... ttgcttgcagGTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGT

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: 35 (upstream exon), 21 (downstream exon)
Score: 9

GCAGGTGTTGAGAATGGCTGCGACAAGTCGGTGGGCAATCTCCTCTACACCgtaagtattt ... ttgcttgcagGTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGTAGATACATCTCCCGGAACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaacaccaacatctggatttttggatatggaataattgttatggttgcttgcagGTTGCCACCAAGTTTCCGGCCAACGCACTGAGCCATCGGGCGGACTTGTGTAGATACATCTCCCGGAACCAG
 ctctaaa  putative branch site (score: 9)
                               aataattgttat  TA-rich tract