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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttgcttatttaatttctattgacctaaatttgtgtgaaataacagtgtatgtcttgcattttggaaccccatctaaatcagtatttcaatctttcagATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGATTTATTTTTCGAAGTACCATCTTCAAAGCATTTCTCTCTTTTGTACCAG

Basic information

species Physcomitrella patens
transcript PP1S477_4V6.2
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|67569517|gb|BJ942341.1|BJ942341
EST:     AGGAGCTGACGAAACAGCTAAAGAGTTACTCGGAACAGTTTGGACAAGAG                         ATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGA
genomic: AGGAGCTGACGAAACAGCTAAAGAGTTACTCGGAACAGTTTGGACAAGAGgttagtttac ... aatctttcagATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGA
EST: gi|162209672|gb|FC386171.1|FC386171
EST:     AGGAGCTGACGAAACAGCTAAAGAGTTACTCGGAACAGTTTGGACAAGAG                         ATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGA
genomic: AGGAGCTGACGAAACAGCTAAAGAGTTACTCGGAACAGTTTGGACAAGAGgttagtttac ... aatctttcagATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGA
EST: gi|162209671|gb|FC386170.1|FC386170
EST:     AGGAGCTGACGAAACAGCTAAAGAGTTACTCGGAACAGTTTGGACAAGAG                         ATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGA
genomic: AGGAGCTGACGAAACAGCTAAAGAGTTACTCGGAACAGTTTGGACAAGAGgttagtttac ... aatctttcagATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGA
EST: gi|67692786|gb|BJ953019.1|BJ953019
EST:     AGGAGCTGACGAAACAGCTAAAGAGTTACTCGGAACAGTTTGGACAAGAG                         ATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGA
genomic: AGGAGCTGACGAAACAGCTAAAGAGTTACTCGGAACAGTTTGGACAAGAGgttagtttac ... aatctttcagATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGA
EST: gi|208397376|gb|DC916330.1|DC916330
EST:     AGGAGCTGACGAAACAGCTAAAGAGTTACTCGGAACAGTTTGGACAAGAG                         ATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGA
genomic: AGGAGCTGACGAAACAGCTAAAGAGTTACTCGGAACAGTTTGGACAAGAGgttagtttac ... aatctttcagATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGA
EST: gi|208354215|gb|DC902457.1|DC902457
EST:     AGGAGCTGACGAAACAGCTAAAGAGTTACTCGGAACAGTTTGGACAAGAG                         ATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGA
genomic: AGGAGCTGACGAAACAGCTAAAGAGTTACTCGGAACAGTTTGGACAAGAGgttagtttac ... aatctttcagATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGA

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: 22 (upstream exon), 14 (downstream exon)
Score: 1

GAGTTCAAACAAAGGAGGAGCTGACGAAACAGCTAAAGAGTTACTCGGAACAGTTTGGACAAGAGgttagtttac ... aatctttcagATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGATTTATTTTTCGAAGTACCATCTTCAAAGCATTTCTCTCTTTTGTACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtgtatgtcttgcattttggaaccccatctaaatcagtatttcaatctttcagATTGAGAAGCAATTGAAGGATCCAAACAAAAAGTGATAGACCAGTCCAAGATTTATTTTTCGAAGTACCATCTTCAAAGCATTTCTCTCTTTTGTACCAG
                            atctaaa  putative branch site (score: 1)
                                               tctttc  putative PPT
                                       tatttcaat  TA-rich tract