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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tcttcaccgtattggctttgacaactgcgtcctatcagatatgtgatgaccatcagccgcatacagggaatctgggactcatgttaatattgtgctgcagGAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCTTTGCCTCGATGAAATTGTGGATGGCGG

Basic information

species Physcomitrella patens
transcript PP1S13_191V6.1
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|208395323|gb|DC919927.1|DC919927
EST:     TTGGCAACTGTTTTGCAAGGATTTTTCGATGCAGTCGCACTACTTCTCAG                         GAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCT
genomic: TTGGCAACTGTTTTGCAAGGATTTTTCGATGCAGTCGCACTACTTCTCAGgtgacctcct ... tgtgctgcagGAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCT
EST: gi|208378708|gb|DC914682.1|DC914682
EST:     TTGGCAACTGTTTTGCAAGGATTTTTCGATGCAGTCGCACTACTTCTCAG                         GAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCT
genomic: TTGGCAACTGTTTTGCAAGGATTTTTCGATGCAGTCGCACTACTTCTCAGgtgacctcct ... tgtgctgcagGAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCT
EST: gi|208381770|gb|DC928433.1|DC928433
EST:     TTGGCAACTGTTTTGCAAGGATTTTTCGATGCAGTCGCACTACTTCTCAG                         GAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCT
genomic: TTGGCAACTGTTTTGCAAGGATTTTTCGATGCAGTCGCACTACTTCTCAGgtgacctcct ... tgtgctgcagGAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCT
EST: gi|67573523|gb|BJ946347.1|BJ946347
EST:     TTGGCAACTGTTTTGCAAGGATTTTTCGATGCAGTCGCACTACTTCTCAG                         GAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCT
genomic: TTGGCAACTGTTTTGCAAGGATTTTTCGATGCAGTCGCACTACTTCTCAGgtgacctcct ... tgtgctgcagGAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCT
EST: gi|67696907|gb|BJ957140.1|BJ957140
EST:     TTGGCAACTGTTTTGCAAGGATTTTTCGATGCAGTCGCACTACTTCTCAG                         GAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCT
genomic: TTGGCAACTGTTTTGCAAGGATTTTTCGATGCAGTCGCACTACTTCTCAGgtgacctcct ... tgtgctgcagGAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCT
EST: gi|208350336|gb|DC906038.1|DC906038
EST:     TTGGCAACTGTTTTGCAAGGATTTTTCGATGCAGTCGCACTACTTCTCAG                         GAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCT
genomic: TTGGCAACTGTTTTGCAAGGATTTTTCGATGCAGTCGCACTACTTCTCAGgtgacctcct ... tgtgctgcagGAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCT

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), 22 (downstream exon)
Score: 4

CTGATCTCCATTTCTATGTGACCGGAGGTGAAGATGAGAATGAACTTATTTTGGCAACTGTTTTGCAAGGATTTTTCGATGCAGTCGCACTACTTCTCAGgtgacctcct ... tgtgctgcagGAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCTTTGCCTCGATGAAATTGTGGATGGCGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaccatcagccgcatacagggaatctgggactcatgttaatattgtgctgcagGAACAACGTCGAAAAGAAAAATATTCTGGAGAATTTGGATCTTGTTCTTCTTTGCCTCGATGAAATTGTGGATGGCGG
                                    tgttaat  putative branch site (score: 4)
                                   atgttaatatt  TA-rich tract