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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtacgtgcatcgtttttttccatttactttccagtctgttcttcttcacagtatcctgtatgtctggtgggaatatatcatccacgaatttttcaaagcgattgattagcatgtcaatgtgcgcgcagGTTCTGAATCCAGACTCTAAGGAGAAACCTTTAGAATTTAATGAAGGAGATTCTCTCGTTGTAATTTCAGAAAATGAGTAATTATTGGGTAACTCGTTGC

Basic information

species Physcomitrella patens
transcript PP1S98_138V6.1
intron # 24
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|37821426|gb|BJ579492.1|BJ579492
EST:     CTGCATCGCGGTCTGAAGTTGCTATAGGTTACCGACATAATAACAAAGTG                         GTTCTGAATCCAGACTCTAAGGAGAAACCTTTAGAATTTAATGAAGGAGAT
genomic: CTGCATCGCGGTCTGAAGTTGCTATAGGTTACCGACATAATAACAAAGTGgtacgtgcat ... gtgcgcgcagGTTCTGAATCCAGACTCTAAGGAGAAACCTTTAGAATTTAATGAAGGAGAT
EST: gi|37832217|gb|BJ590229.1|BJ590229
EST:     CTGCATCGCGGTCTGAAGTTGCTATAGGTTACCGACATAATAACAAAGTG                         GTTCTGAATCCAGACTCTAAGGAGAAACCTTTAGAATTTAATGAAGGAGAT
genomic: CTGCATCGCGGTCTGAAGTTGCTATAGGTTACCGACATAATAACAAAGTGgtacgtgcat ... gtgcgcgcagGTTCTGAATCCAGACTCTAAGGAGAAACCTTTAGAATTTAATGAAGGAGAT
EST: gi|162162120|gb|FC337694.1|FC337694
EST:     CTGCATCGCGGTCTGAAGTTGCTATAGGTTACCGACATAATAACAAAGTG                         GTTCTGAATCCAGACTCTAAGGAGAAACCTTTAGAATTTAATGAAGGAGAT
genomic: CTGCATCGCGGTCTGAAGTTGCTATAGGTTACCGACATAATAACAAAGTGgtacgtgcat ... gtgcgcgcagGTTCTGAATCCAGACTCTAAGGAGAAACCTTTAGAATTTAATGAAGGAGAT

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: 9 (upstream exon), 35 (downstream exon)
Score: 2

ATACATAAAAGAGGGCGAATCACCATCTTTTTCTGAGCTTCAAGAACGGGCTGCATCGCGGTCTGAAGTTGCTATAGGTTACCGACATAATAACAAAGTGgtacgtgcat ... gtgcgcgcagGTTCTGAATCCAGACTCTAAGGAGAAACCTTTAGAATTTAATGAAGGAGATTCTCTCGTTGTAATTTCAGAAAATGAGTAATTATTGGGTAACTCGTTGC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatatcatccacgaatttttcaaagcgattgattagcatgtcaatgtgcgcgcagGTTCTGAATCCAGACTCTAAGGAGAAACCTTTAGAATTTAATGAAGGAGATTCTCTCGTTGTAATTTCAGAAAATGAGTAATTATTGGGTAACTCGTTGC
                          gattgat  putative branch site (score: 2)
             aatttttcaaa  TA-rich tract