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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaagctcttttgcgcatggatttcatattcttcatgactaagatttcaaagaggagaactagggtttggagtttaggttctaaaaactacgactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAAGGTATTACCAAGGTGGCCTTTGATAGGGGAGGCTTTGTTTACCACGGAC

Basic information

species Physcomitrella patens
transcript PP1S97_12V6.1
intron # 3
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|67573622|gb|BJ946446.1|BJ946446
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|18361696|gb|BJ193763.1|BJ193763
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAA
EST: gi|208377631|gb|DC932167.1|DC932167
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|37841451|gb|BJ599459.1|BJ599459
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|162237052|gb|FC413211.1|FC413211
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|162272082|gb|FC447876.1|FC447876
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|162271630|gb|FC447515.1|FC447515
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|19783629|gb|BQ040047.1|BQ040047
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|208361024|gb|DC946671.1|DC946671
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|67578839|gb|BJ951006.1|BJ951006
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|162225027|gb|FC401443.1|FC401443
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|37845987|gb|BJ603995.1|BJ603995
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|67507573|gb|BJ940454.1|BJ940454
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|67697007|gb|BJ957240.1|BJ957240
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|67693764|gb|BJ953997.1|BJ953997
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|208395976|gb|DC915736.1|DC915736
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|162234108|gb|FC410543.1|FC410543
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|162234312|gb|FC410058.1|FC410058
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|162206486|gb|FC382855.1|FC382855
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|162247010|gb|FC423952.1|FC423952
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|162225028|gb|FC401444.1|FC401444
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|37839389|gb|BJ597397.1|BJ597397
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|67570482|gb|BJ943306.1|BJ943306
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|162268056|gb|FC443526.1|FC443526
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|67697603|gb|BJ957836.1|BJ957836
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
EST: gi|162234311|gb|FC410057.1|FC410057
EST:     GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATT                         GACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA
genomic: GCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAA

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: 33 (upstream exon), 35 (downstream exon)
Score: 42

CCAAGTCATTGATGACACAAAGCAGCACACTTTGGCTGCCGCATCCACCCGCACGAAGGAGATCCGTGATACCATTGAGGACACAGCAGGTCCAACCATTgtgagtctct ... gactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAAGGTATTACCAAGGTGGCCTTTGATAGGGGAGGCTTTGTTTACCACGGAC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tcaaagaggagaactagggtttggagtttaggttctaaaaactacgactgtgcagGACTCGGCTAAGAAAGTTGGAGAGGCCATTGGCAAGCTCTGCTTAGAAAAAGGTATTACCAAGGTGGCCTTTGATAGGGGAGGCTTTGTTTACCACGGAC
                                ttctaaa  putative branch site (score: 42)
                                ttctaaaaa  TA-rich tract