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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggtgatggtgtatagttacacccatgaatctactaactactgagaaatcaccgatgctttttacaattgtgcaatttgcactttaagggaacgaatttcagggtctgacttgttcgttggctttcgtcagcagGGATATGAGACCGAAAATGACTCTAGCGACGTTTGGAAACCTCAATATTCTCGCCTTTTTTGC

Basic information

species Physcomitrella patens
transcript PP1S46_43V6.2
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|100399060|gb|BY954179.1|BY954179
EST:     AATTTTATCGCGTTTGCCGTCTTGGCTCCTTTCGCCTACTATGTCGAGAGCAG                       
genomic: AATTTTATCGCGTTTGCCGTCTTGGCTCCTTTCGCCTACTATGTC--GAG-AGgtaggtgatg ... tcgtcagc
EST: gi|100425493|gb|BY958623.1|BY958623
EST:     AATTTTATCGCGTTTGCCGTCTTGGCTCCTTTCGCCTACTATGTCGAGAG                         GGATATGAGACCGAAAATGACTCTAGCGACGTTTGGAAACCTCAATATTCT
genomic: AATTTTATCGCGTTTGCCGTCTTGGCTCCTTTCGCCTACTATGTCGAGAGgtaggtgatg ... tcgtcagcagGGATATGAGACCGAAAATGACTCTAGCGACGTTTGGAAACCTCAATATTCT

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: 35 (upstream exon), 35 (downstream exon)
Score: 21

GAGTGGCCCTGGTCACTGGCATAGATCCACTCCTGTTTACCTTCTACAGGAATTTTATCGCGTTTGCCGTCTTGGCTCCTTTCGCCTACTATGTCGAGAGgtaggtgatg ... tcgtcagcagGGATATGAGACCGAAAATGACTCTAGCGACGTTTGGAAACCTCAATATTCTCGCCTTTTTTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cactttaagggaacgaatttcagggtctgacttgttcgttggctttcgtcagcagGGATATGAGACCGAAAATGACTCTAGCGACGTTTGGAAACCTCAATATTCTCGCCTTTTTTGC
                        gtctgac  putative branch site (score: 21)
                                          ctttcgtc  putative PPT
               aatttca  TA-rich tract