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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtccctactccacttttatcgtttgcagggatttcgcttctccaaccaggtctaaactttgctcatctggtttttttcttgattgtagaaataatctgacggtaatacgcctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGATCGAGTAGGGAACTACGACACACAG

Basic information

species Physcomitrella patens
transcript PP1S37_83V6.1
intron # 4
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|162196840|gb|FC373895.1|FC373895
EST:     TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTG                         GATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
genomic: TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
EST: gi|162222109|gb|FC397337.1|FC397337
EST:     TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTG                         GATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
genomic: TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
EST: gi|15590622|gb|BI675238.1|BI675238
EST:     GATGAGGCTCTCGCTCACGTAGTGTTG                         GATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
genomic: GATGAGGCTCTCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
EST: gi|162153154|gb|FC329560.1|FC329560
EST:     TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTG                         GATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
genomic: TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
EST: gi|162196839|gb|FC373894.1|FC373894
EST:     TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTG                         GATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
genomic: TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
EST: gi|18337884|gb|BJ169908.1|BJ169908
EST:     TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTG                         GATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
genomic: TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
EST: gi|162222108|gb|FC397336.1|FC397336
EST:     TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTG                         GATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
genomic: TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
EST: gi|15261812|gb|BI437122.1|BI437122
EST:     GATGAGGCTCTCGTTCACGTAGTGTTG                         GATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
genomic: GATGAGGCTCTCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
EST: gi|208361844|gb|DC950116.1|DC950116
EST:     TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTG                         GATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
genomic: TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
EST: gi|162208762|gb|FC384898.1|FC384898
EST:     TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTG                         GATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
genomic: TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
EST: gi|162271019|gb|FC447424.1|FC447424
EST:     TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTG                         GATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
genomic: TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
EST: gi|19785589|gb|BQ040342.1|BQ040342
EST:     TCGTTCACGTAGTGTTG                         GATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
genomic: TCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
EST: gi|37838754|gb|BJ596762.1|BJ596762
EST:     TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTG                         GATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAAATACCCACAGAT
genomic: TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
EST: gi|162150420|gb|FC326692.1|FC326692
EST:     TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTG                         GATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT
genomic: TCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGAT

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: 30 (upstream exon), 35 (downstream exon)
Score: 11

GCGCTTCTAAAAGCTCTAGGTGACCGCAAGGGCATAAGGCGCTTCGGAGATTTTTCAGCTCCACTGGATGAGGCTCTCGTTCACGTAGTGTTGgttagtccct ... ctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGATCGAGTAGGGAACTACGACACACAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctggtttttttcttgattgtagaaataatctgacggtaatacgcctgatgccagGATTTGTCGGGACGGCCATATTTGGGTTATGATCTTGAGATACCCACAGATCGAGTAGGGAACTACGACACACAG
     tttttttcttgatt  TA-rich tract