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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcgttatcccgcaaaggaaacataaccgaggtgaagttgatgtaccagtttacatcactgatggtcttattctgaactatgtgtatggttggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG

Basic information

species Physcomitrella patens
transcript PP1S97_54V6.4
intron # 2
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|37841964|gb|BJ599972.1|BJ599972
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|18332442|gb|BJ164455.1|BJ164455
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|208388641|gb|DC953431.1|DC953431
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|67696509|gb|BJ956742.1|BJ956742
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|37835663|gb|BJ593675.1|BJ593675
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|18337853|gb|BJ169877.1|BJ169877
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|162249476|gb|FC426746.1|FC426746
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|18338064|gb|BJ170088.1|BJ170088
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|67574156|gb|BJ946980.1|BJ946980
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|162248874|gb|FC422881.1|FC422881
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|18341780|gb|BJ173815.1|BJ173815
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|37850242|gb|BJ608250.1|BJ608250
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|18364771|gb|BJ196844.1|BJ196844
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|37845267|gb|BJ603275.1|BJ603275
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|37853392|gb|BJ611400.1|BJ611400
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|18354273|gb|BJ186329.1|BJ186329
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|67697554|gb|BJ957787.1|BJ957787
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|18347001|gb|BJ179047.1|BJ179047
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|162258316|gb|FC434243.1|FC434243
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|162210551|gb|FC386847.1|FC386847
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|37835745|gb|BJ593757.1|BJ593757
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|162224213|gb|FC399277.1|FC399277
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|208368661|gb|DC947936.1|DC947936
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|162258317|gb|FC434244.1|FC434244
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|18354193|gb|BJ186249.1|BJ186249
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|67692998|gb|BJ953231.1|BJ953231
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|67573124|gb|BJ945948.1|BJ945948
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|162249477|gb|FC426747.1|FC426747
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|67569732|gb|BJ942556.1|BJ942556
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|162210550|gb|FC386846.1|FC386846
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
EST: gi|67508263|gb|BJ941132.1|BJ941132
EST:     ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAG                         CTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG
genomic: ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCG

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: 31 (upstream exon), 35 (downstream exon)
Score: 50

ACTGGAGCAGAAGATGAAAGGGACTTCGTTCACAACAAGgtatgcgtta ... ggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtttacatcactgatggtcttattctgaactatgtgtatggttggtattgcagCTTCAAGCTCTGAGCAACACGCATCTGAGTAGTATGGTTGAGTTGTATTCGACTCTTACAGCCCGAAGTAACCAG
          cactgat  putative branch site (score: 50)
                   tcttatt  TA-rich tract