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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatgcatttcaatctagtagatattcgtgcaattttacagttgactgattatcatgcttaactagaacgaaccaatcaaactaaatttttgtagggcttcatatctaccgtactttatttcgtaggttctctgacaatcgtctgacatgacatgcagCATCGTTTTGCTGCTAGTGCACCGCCACTAACTGCACCACCAGAAGAGCATATTGCAACTTTAGTAGCGATGGGATTTGATCGAAGCGATGCCATGCAAG

Basic information

species Physcomitrella patens
transcript PP1S78_54V6.2
intron # 8
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|208346567|gb|DC916833.1|DC916833
EST:     CAACAGCTAGGGGAGGAAGAGCTTCGGGTCAAAATGGTCATGCATTCCAG                         CATCGTTTTGCTGCTAGTGCACCGCCACTAACTGCACCACCAGAAGAGCAT
genomic: CAACAGCTAGGGGAGGAAGAGCTTCGGGTCAAAATGGTCATGCATTCCAGgtatgcattt ... tgacatgcagCATCGTTTTGCTGCTAGTGCACCGCCACTAACTGCACCACCAGAAGAGCAT
EST: gi|37851035|gb|BJ609043.1|BJ609043
EST:     CAACAGCTAGGGGAGGAAGAGCTTCGGGTCAAAATGGTCATGCATTCCAG                         CATCGTTTTGCTGCTAGTGCACCGCCACTAACTGCACCACCAGAAGAGCAT
genomic: CAACAGCTAGGGGAGGAAGAGCTTCGGGTCAAAATGGTCATGCATTCCAGgtatgcattt ... tgacatgcagCATCGTTTTGCTGCTAGTGCACCGCCACTAACTGCACCACCAGAAGAGCAT
EST: gi|18338610|gb|BJ170634.1|BJ170634
EST:     CAACAGCTAGGGGAGGAAGAGCTTCGGGTCAAAATGGTCATGCATTCCAG                         CATCGTTTTGCTGCTAGTGCACCGCCACTAACTGCACCACCAGAAGAGCAT
genomic: CAACAGCTAGGGGAGGAAGAGCTTCGGGTCAAAATGGTCATGCATTCCAGgtatgcattt ... tgacatgcagCATCGTTTTGCTGCTAGTGCACCGCCACTAACTGCACCACCAGAAGAGCAT
EST: gi|37842140|gb|BJ600148.1|BJ600148
EST:     CAACAGCTAGGGGAGGAAGAGCTTCGGGTCAAAATGGTCATGCATTCCAG                         CATCGTTTTGCTGCTAGTGCACCGCCACTAACTGCACCACCAGAAGAGCAT
genomic: CAACAGCTAGGGGAGGAAGAGCTTCGGGTCAAAATGGTCATGCATTCCAGgtatgcattt ... tgacatgcagCATCGTTTTGCTGCTAGTGCACCGCCACTAACTGCACCACCAGAAGAGCAT
EST: gi|208366589|gb|DC955637.1|DC955637
EST:     CAACAGCTAGGGGAGGAAGAGCTTCGGGTCAAAATGGTCATGCATTCCAG                         CATCGTTTTGCTGCTAGTGCACCGCCACTAACTGCACCACCAGAAGAGCAT
genomic: CAACAGCTAGGGGAGGAAGAGCTTCGGGTCAAAATGGTCATGCATTCCAGgtatgcattt ... tgacatgcagCATCGTTTTGCTGCTAGTGCACCGCCACTAACTGCACCACCAGAAGAGCAT

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: 24 (upstream exon), 12 (downstream exon)
Score: 1

AGCAGCTGCAAGGCTGTTCGCGCCACTTCTTTCGTCAAACTCTGCACCACCAACAGCTAGGGGAGGAAGAGCTTCGGGTCAAAATGGTCATGCATTCCAGgtatgcattt ... tgacatgcagCATCGTTTTGCTGCTAGTGCACCGCCACTAACTGCACCACCAGAAGAGCATATTGCAACTTTAGTAGCGATGGGATTTGATCGAAGCGATGCCATGCAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atctaccgtactttatttcgtaggttctctgacaatcgtctgacatgacatgcagCATCGTTTTGCTGCTAGTGCACCGCCACTAACTGCACCACCAGAAGAGCATATTGCAACTTTAGTAGCGATGGGATTTGATCGAAGCGATGCCATGCAAG
                                     gtctgac  putative branch site (score: 1)
        tactttattt  TA-rich tract