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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacatgttactttaatctgagacttttaatttaagaaaattcggtggtttttttatattgtttgtttgtttgtgggggttttgattttgtttcgttttcaaaaatatatttttacttttccacttgatgtgggtaaaaatcaatctctaaatgcgcgagtttacgttttcattgacctctgtgcaacagTTCGCAAGAATCAAACAGGATTGAAGAACTATTACAAGAAGATCAAGAGGTTAAAGCTCGGCGTGAGAAAGCTCTTAGGCAAGCGGCAGCATTATCCAAG

Basic information

species Physcomitrella patens
transcript PP1S33_163V6.1
intron # 19
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|162209952|gb|FC385782.1|FC385782
EST:     GTGGAGAGGGCCAAGGATGCTATGCTAAATCACCTTTATAGCTCCATCAG                         TTCGCAAGAATCAAACAGGATTGAAGAACTATTACAAGAAGATCAAGAGGT
genomic: GTGGAGAGGGCCAAGGATGCTATGCTAAATCACCTTTATAGCTCCATCAGgtacatgtta ... tgtgcaacagTTCGCAAGAATCAAACAGGATTGAAGAACTATTACAAGAAGATCAAGAGGT
EST: gi|162268866|gb|FC445701.1|FC445701
EST:     GTGGAGAGGGCCAAGGATGCTATGCTAAATCACCTTTATAGCTCCATCAG                         TTCGCAAGAATCAAACAGGATTGAAGAACTATTACAAGAAGATCAAGAGGT
genomic: GTGGAGAGGGCCAAGGATGCTATGCTAAATCACCTTTATAGCTCCATCAGgtacatgtta ... tgtgcaacagTTCGCAAGAATCAAACAGGATTGAAGAACTATTACAAGAAGATCAAGAGGT
EST: gi|162268865|gb|FC445700.1|FC445700
EST:     GTGGAGAGGGCCAAGGATGCTATGCTAAATCACCTTTATAGCTCCATCAG                         TTCGCAAGAATCAAACAGGATTGAAGAACTATTACAAGAAGATCAAGAGGT
genomic: GTGGAGAGGGCCAAGGATGCTATGCTAAATCACCTTTATAGCTCCATCAGgtacatgtta ... tgtgcaacagTTCGCAAGAATCAAACAGGATTGAAGAACTATTACAAGAAGATCAAGAGGT

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: 28 (upstream exon), 31 (downstream exon)
Score: 7

GCAGTGGTCCTTTGTCAAGTGGAGAGGGCCAAGGATGCTATGCTAAATCACCTTTATAGCTCCATCAGgtacatgtta ... tgtgcaacagTTCGCAAGAATCAAACAGGATTGAAGAACTATTACAAGAAGATCAAGAGGTTAAAGCTCGGCGTGAGAAAGCTCTTAGGCAAGCGGCAGCATTATCCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaaatcaatctctaaatgcgcgagtttacgttttcattgacctctgtgcaacagTTCGCAAGAATCAAACAGGATTGAAGAACTATTACAAGAAGATCAAGAGGTTAAAGCTCGGCGTGAGAAAGCTCTTAGGCAAGCGGCAGCATTATCCAAG
                                   cattgac  putative branch site (score: 7)
                                         cctctgt  CT-rich tract
                               ttttcatt  TA-rich tract