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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgccctacttttgcctgaaggacaagttaaagcaatcttttttttggattctgacatttttcttcttcactacctttgaaccttgttctgctgttgaatggagatttgttttgagaagtatgaaatgatcttcttttgtgcagGTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTCTCGACG

Basic information

species Physcomitrella patens
transcript PP1S83_162V6.1
intron # 5
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|18329713|gb|BJ161719.1|BJ161719
EST:     GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG                         GTGCCGGAGCTTGAGTTTGAGGTT
genomic: GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAGgtgccctact ... ttttgtgcagGTGCCGGAGCTTGAGTTTGAGGTT
EST: gi|208347445|gb|DC909752.1|DC909752
EST:     GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG                         GTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTC
genomic: GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAGgtgccctact ... ttttgtgcagGTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTC
EST: gi|162240627|gb|FC419365.1|FC419365
EST:     GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG                         GTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTC
genomic: GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAGgtgccctact ... ttttgtgcagGTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTC
EST: gi|18372591|gb|BJ204193.1|BJ204193
EST:     GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG                         GTGCCGGAGCTTGAGTTT
genomic: GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAGgtgccctact ... ttttgtgcagGTGCCGGAGCTTGAGTTT
EST: gi|18356123|gb|BJ188182.1|BJ188182
EST:     GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG                         GTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTC
genomic: GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAGgtgccctact ... ttttgtgcagGTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTC
EST: gi|18349502|gb|BJ181551.1|BJ181551
EST:     GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG                         GTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTC
genomic: GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAGgtgccctact ... ttttgtgcagGTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTC
EST: gi|162150536|gb|FC326392.1|FC326392
EST:     GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG                         GTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTC
genomic: GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAGgtgccctact ... ttttgtgcagGTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTC
EST: gi|18345693|gb|BJ177736.1|BJ177736
EST:     GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAG                         GTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTC
genomic: GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAGgtgccctact ... ttttgtgcagGTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTC

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: 11 (upstream exon), 25 (downstream exon)
Score: 1

GTCTTGAATAGGCAGGTTGTGAAGTCCGACGTTGCTACCATAAAGgtgccctact ... ttttgtgcagGTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTCTCGACG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgctgttgaatggagatttgttttgagaagtatgaaatgatcttcttttgtgcagGTGCCGGAGCTTGAGTTTGAGGTTCCGCCACAATCACAACGCGGGACACTCTCGACG
                                        tcttcttttgt  CT-rich tract
               atttgtttt  TA-rich tract