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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cttgaaactacactcctgactacctgaattgatatcagtgctcgttacgaggacacctctttagttagccctaatctgttggagttttcttttcttacagGAACTATCGATGTGGTGGTGGTTAACCTATATCCTTTCTATAGTACCGTAACATCCTCAAACGTAGATTTTGAGACGGGGGTTGAGAACATCGACATTGG

Basic information

species Physcomitrella patens
transcript PP1S160_136V6.1
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|162190251|gb|FC366409.1|FC366409
EST:     TCCAGCAGCATGGAATTG                         GAACTATCGATGTGGTGGTGGTTAACCTATATCCTTTCTATAGTACCGTAA
genomic: TCCAGCAGCATGGAATTGgtgagctcat ... tttcttacagGAACTATCGATGTGGTGGTGGTTAACCTATATCCTTTCTATAGTACCGTAA
EST: gi|162257625|gb|FC433759.1|FC433759
EST:     AAGGCGAGACATGCAGTCCCACATGGAAGCACTCCAGCAGCATGGAATTG                         GAACTATCGATGTGGTGGTGGTTAACCTATATCCTTTCTATAGTACCGTAA
genomic: AAGGCGAGACATGCAGTCCCACATGGAAGCACTCCAGCAGCATGGAATTGgtgagctcat ... tttcttacagGAACTATCGATGTGGTGGTGGTTAACCTATATCCTTTCTATAGTACCGTAA

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: 31 (upstream exon), 35 (downstream exon)
Score: 7

GATGGGCGCGTGAAAACATTACATCCAGCAGTTCACGGCGGTATTTTGGCAAGGCGAGACATGCAGTCCCACATGGAAGCACTCCAGCAGCATGGAATTGgtgagctcat ... tttcttacagGAACTATCGATGTGGTGGTGGTTAACCTATATCCTTTCTATAGTACCGTAACATCCTCAAACGTAGATTTTGAGACGGGGGTTGAGAACATCGACATTGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tacgaggacacctctttagttagccctaatctgttggagttttcttttcttacagGAACTATCGATGTGGTGGTGGTTAACCTATATCCTTTCTATAGTACCGTAACATCCTCAAACGTAGATTTTGAGACGGGGGTTGAGAACATCGACATTGG
                       ccctaat  putative branch site (score: 7)
                                       ttttcttttcttac  putative PPT
                                       ttttctttt  TA-rich tract