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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtctatctccgatgctgttgaaattcttgcacgtgtaattatttggaacaaggaaaggtttatgattaggattgtcatctcttgtaatgatttttgtgataaaattacatgcgataagcagcaagtttctacgtgtgttttctttatgacatctctgcatttgtagttttcttcaacctatactttttgttgcagATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCCTTTAGGGATGTGAAAG

Basic information

species Physcomitrella patens
transcript PP1S208_168V6.2
intron # 5
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|18366432|gb|BJ198511.1|BJ198511
EST:     ATGGCCCCACATTTGGGAAAGGAGATGTCATTGGGTGCATCCTCAATCAG                         ATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCC
genomic: ATGGCCCCACATTTGGGAAAGGAGATGTCATTGGGTGCATCCTCAATCAGgttagtctat ... tttgttgcagATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCC
EST: gi|208344499|gb|DC905060.1|DC905060
EST:     ATGGCCCCACATTTGGGAAAGGAGATGTCATTGGGTGCATCCTCAATCAG                         ATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCC
genomic: ATGGCCCCACATTTGGGAAAGGAGATGTCATTGGGTGCATCCTCAATCAGgttagtctat ... tttgttgcagATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCC
EST: gi|18361861|gb|BJ193928.1|BJ193928
EST:     ATGGCCCCACATTTGGGAAAGGAGATGTCATTGGGTGCATCCTCAATCAG                         ATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCC
genomic: ATGGCCCCACATTTGGGAAAGGAGATGTCATTGGGTGCATCCTCAATCAGgttagtctat ... tttgttgcagATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCC
EST: gi|100400993|gb|BY973046.1|BY973046
EST:     ATGGCCCCACATTTGGGANAGGAGATGTCATTGGGTGCATCCTCAATCAG                         ATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCC
genomic: ATGGCCCCACATTTGGGAAAGGAGATGTCATTGGGTGCATCCTCAATCAGgttagtctat ... tttgttgcagATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCC
EST: gi|100390547|gb|BY952955.1|BY952955
EST:     ATGGCCCCACATTTGGGAAAGGAGATGTCATTGGGTGCATCCTCAATCAG                         ATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCC
genomic: ATGGCCCCACATTTGGGAAAGGAGATGTCATTGGGTGCATCCTCAATCAGgttagtctat ... tttgttgcagATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCC
EST: gi|208390623|gb|DC937555.1|DC937555
EST:     ATGGCCCCACATTTGGGAAAGGAGATGTCATTGGGTGCATCCTCAATCAG                         ATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCC
genomic: ATGGCCCCACATTTGGGAAAGGAGATGTCATTGGGTGCATCCTCAATCAGgttagtctat ... tttgttgcagATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCC

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: 30 (upstream exon), 27 (downstream exon)
Score: 7

TTGTACATCAACCTTGAGCCACGAAGGCACCGCATATGGCCCCACATTTGGGAAAGGAGATGTCATTGGGTGCATCCTCAATCAGgttagtctat ... tttgttgcagATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCCTTTAGGGATGTGAAAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctttatgacatctctgcatttgtagttttcttcaacctatactttttgttgcagATGGACCACACAATATCGTACACTAAGAATGGTGTCAACCTAGGAGTTGCCTTTAGGGATGTGAAAG
                                          ctttttgtt  CT-rich tract
                                      tatacttttt  TA-rich tract