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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacccaatttcttattcctggttaactattagaactacttcttaagtaatgtcttttccaccagtatagatacctcctctgcatcaattcctctgcttaacaaacatgcgaaaaatattgtgtctgttctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAGGGACCAGTATTTTTGAG

Basic information

species Physcomitrella patens
transcript PP1S37_122V6.1
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|162235794|gb|FC412345.1|FC412345
EST:     TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG                         GAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
genomic: TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAGgtacccaatt ... ctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
EST: gi|37830933|gb|BJ588945.1|BJ588945
EST:     CCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACCAGGCTCAACGAAG                         GAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
genomic: CCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTA-CAGGCTCAACGAAGgtacccaatt ... ctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
EST: gi|162172093|gb|FC347969.1|FC347969
EST:     TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG                         GAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
genomic: TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAGgtacccaatt ... ctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
EST: gi|162248390|gb|FC422566.1|FC422566
EST:     TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG                         GAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
genomic: TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAGgtacccaatt ... ctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
EST: gi|162161611|gb|FC339026.1|FC339026
EST:     TGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG                         GAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
genomic: TGAGAGCAGAGCAACAGACTACAGGCTCAACGAAGgtacccaatt ... ctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
EST: gi|37828610|gb|BJ586622.1|BJ586622
EST:     TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG                         GAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
genomic: TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAGgtacccaatt ... ctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
EST: gi|162172079|gb|FC347968.1|FC347968
EST:     TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG                         GAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
genomic: TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAGgtacccaatt ... ctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
EST: gi|162235377|gb|FC412344.1|FC412344
EST:     TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG                         GAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
genomic: TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAGgtacccaatt ... ctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
EST: gi|37822289|gb|BJ580355.1|BJ580355
EST:     TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG                         GAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
genomic: TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAGgtacccaatt ... ctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
EST: gi|162266004|gb|FC442689.1|FC442689
EST:     TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG                         GAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
genomic: TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAGgtacccaatt ... ctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
EST: gi|37839391|gb|BJ597399.1|BJ597399
EST:     TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG                         GAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
genomic: TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAGgtacccaatt ... ctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
EST: gi|37837549|gb|BJ595557.1|BJ595557
EST:     TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAG                         GAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG
genomic: TCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAGgtacccaatt ... ctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAG

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: 34 (upstream exon), 34 (downstream exon)
Score: 10

AGTTATCAATTAGCTGAGGATTTGGGCCAAGCATTCTCGGAACGCTCAATCCTGGAGAGCGTCTTGAGAGCAGAGCAACAGACTACAGGCTCAACGAAGgtacccaatt ... ctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAGGGACCAGTATTTTTGAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaattcctctgcttaacaaacatgcgaaaaatattgtgtctgttctatttgcagGAGGTGCTTGGTTTGTTAAGGTCGCTTTACGTGCTATCTGCCGCCGACGAGGGACCAGTATTTTTGAG
           gcttaac  putative branch site (score: 10)
                                       tctgttct  putative PPT
                           aaaaatattgt  TA-rich tract