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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaagtgtggatccacaactccaaaatctaagtctagcttcgatgacagttctgtgtctacagtacacttcagcatatcactgtgtctcgtgcttagattatttctagagcggtgctacatgcatataggaggacaatatgagttggatgtactaaggttatcttgatatgcagGAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG

Basic information

species Physcomitrella patens
transcript PP1S100_30V6.1
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|162161220|gb|FC337283.1|FC337283
EST:     AGAAAGAAGAATATCATCTTTATAGCTGGACTGGCCGGTACACCTCTCCT                         GAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTT
genomic: AGAAAGAAGAATATCATCTTTATAGCTGGACTGGCCGGTACACCTCTCCTgtaagtgtgg ... tgatatgcagGAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTT
EST: gi|162256364|gb|FC432374.1|FC432374
EST:     AGAAAGAAGAATATCATCTTTATAGCTGGACTGGCCGGTACACCTCTCCT                         GAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTT
genomic: AGAAAGAAGAATATCATCTTTATAGCTGGACTGGCCGGTACACCTCTCCTgtaagtgtgg ... tgatatgcagGAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTT
EST: gi|162185667|gb|FC362054.1|FC362054
EST:     AGAAAGAAGAATATCATCTTTATAGCTGGACTGGCCGGTACACCTCTCCT                         GAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTT
genomic: AGAAAGAAGAATATCATCTTTATAGCTGGACTGGCCGGTACACCTCTCCTgtaagtgtgg ... tgatatgcagGAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTT
EST: gi|162180210|gb|FC355527.1|FC355527
EST:     AGAAAGAAGAATATCATCTTTATAGCTGGACTGGCCGGTACACCTCTCCT                         GAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTT
genomic: AGAAAGAAGAATATCATCTTTATAGCTGGACTGGCCGGTACACCTCTCCTgtaagtgtgg ... tgatatgcagGAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTT
EST: gi|162255247|gb|FC431557.1|FC431557
EST:     AGAAAGAAGAATATCATCTTTATAGCTGGACTGGCCGGTACACCTCTCCT                         GAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTT
genomic: AGAAAGAAGAATATCATCTTTATAGCTGGACTGGCCGGTACACCTCTCCTgtaagtgtgg ... tgatatgcagGAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTT
EST: gi|162199756|gb|FC375829.1|FC375829
EST:     AGAAAGAAGAATATCATCTTTATAGCTGGACTGGCCGGTACACCTCTCCT                         GAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTT
genomic: AGAAAGAAGAATATCATCTTTATAGCTGGACTGGCCGGTACACCTCTCCTgtaagtgtgg ... tgatatgcagGAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTT

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: 23 (upstream exon), 29 (downstream exon)
Score: 8

CTATGACCACAGCTGCTATGTCGTGATTTATACAGTTCAGGGAGAAGAACAGAAAGAAGAATATCATCTTTATAGCTGGACTGGCCGGTACACCTCTCCTgtaagtgtgg ... tgatatgcagGAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgcatataggaggacaatatgagttggatgtactaaggttatcttgatatgcagGAGGACAAGGTTGCAGCAACGAGAGTTATGAATGAGAAGAATGCCGAACTTAAAGGGCGGGGAGTTCAG
                                          tcttgat  putative branch site (score: 8)
                                       ttatctt  CT-rich tract
              acaatat  TA-rich tract