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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgggtgacctcctttgtaaacaatagtattgaacgatgcacgcaagttgataatctgctgtcatgctctactaaaggatttttcgtcttaaaatatgcagGGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCGCCTAGTTATTATCAGAACACTACCTTATACCCCAGCAGAAATGATTCAG

Basic information

species Physcomitrella patens
transcript PP1S4_73V6.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S4_73V6.1 (Physcomitrella patens), 3'ss of exon 9
lower sequence: Vv06s0004g02910.t01 (Vitis vinifera), 3'ss of exon 8
tgggtgacctcctttgtaaacaatagtat-tgaacgatgcacgcaa--gttgataatctgctgtcatgctctactaaaggatttttcgtcttaaaatatgcagGGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCGCCTAGTTATTATCAGAACACTACCTTATACCCCAGCAGAAATGATTCAG
 |     |    ||| || |   ||  || |   || |||  | |    ||||| | ||   |   |  | | || ||        | ||| |   | ||||| ||||||||||| || ||||| ||||| || ||||||||||||||||| ||  | || ||| |  | ||   | |||||   || || || |||||||||
agtactccgatttttatagaagttaacatctaggcgttgcctggattccttgatcaccttaagctcttgttt-ctgaacatggccccttctcat--tttgcagAGGAACTGATATGAGTAGTCCTCATGGCATACCTGTTGACTTGTTAGACCGGTTGGTGATTGTACGGACGGAAACTTATGGTCCTGCTGATATGATTCAG
















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|37832087|gb|BJ590099.1|BJ590099
EST:     TTGGCACCCATTGTCGTATTTGCCACTAATCGAGGCATTTGCCACATAAA                         GGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCG
genomic: TTGGCACCCATTGTCGTATTTGCCACTAATCGAGGCATTTGCCACATAAAgtatgtccta ... aaatatgcagGGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCG
EST: gi|162250403|gb|FC426265.1|FC426265
EST:     TTGGCACCCATTGTCGTATTTGCCACTAATCGAGGCATTTGCCACATAAA                         GGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCG
genomic: TTGGCACCCATTGTCGTATTTGCCACTAATCGAGGCATTTGCCACATAAAgtatgtccta ... aaatatgcagGGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCG
EST: gi|67728088|gb|BJ978347.1|BJ978347
EST:     TTGGCACCCATTGTCGTATTTGCCACTAATCGAGGCATTTGCCACATAAA                         GGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCG
genomic: TTGGCACCCATTGTCGTATTTGCCACTAATCGAGGCATTTGCCACATAAAgtatgtccta ... aaatatgcagGGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCG
EST: gi|67726395|gb|BJ976654.1|BJ976654
EST:     TTGGCACCCATTGTCGTATTTGCCACTAATCGAGGCATTTGCCACATAAA                         GGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCG
genomic: TTGGCACCCATTGTCGTATTTGCCACTAATCGAGGCATTTGCCACATAAAgtatgtccta ... aaatatgcagGGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCG
EST: gi|162252177|gb|FC425855.1|FC425855
EST:     TTGGCACCCATTGTCGTATTTGCCACTAATCGAGGCATTTGCCACATAAA                         GGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCG
genomic: TTGGCACCCATTGTCGTATTTGCCACTAATCGAGGCATTTGCCACATAAAgtatgtccta ... aaatatgcagGGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCG
EST: gi|162237932|gb|FC412533.1|FC412533
EST:     TTGGCACCCATTGTCGTATTTGCCACTAATCGAGGCATTTGCCACATAAA                         GGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCG
genomic: TTGGCACCCATTGTCGTATTTGCCACTAATCGAGGCATTTGCCACATAAAgtatgtccta ... aaatatgcagGGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCG

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: 19 (upstream exon), 20 (downstream exon)
Score: 3

TGCTAGACATGGAATGTTTCACGTATTTGAATCGTGCTCTCGAAAGTTCATTGGCACCCATTGTCGTATTTGCCACTAATCGAGGCATTTGCCACATAAAgtatgtccta ... aaatatgcagGGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCGCCTAGTTATTATCAGAACACTACCTTATACCCCAGCAGAAATGATTCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgataatctgctgtcatgctctactaaaggatttttcgtcttaaaatatgcagGGGAACTGATATTAGCAGTCCACATGGTATTCCTGTTGACTTGTTAGATCGCCTAGTTATTATCAGAACACTACCTTATACCCCAGCAGAAATGATTCAG
                       tactaaa  putative branch site (score: 3)
                                        tcttaaaatat  TA-rich tract