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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagttagattcgctcttgactaccttacatgatgttctaaatgttaagtttgtcttgtattaatcgcaggacatgttcgaatgtgctgggacaatttataatgtgtcataatctcttcttttgcagGGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCAACATTTAAGTATGTATTTAGGTTGCACCCTAGGGATAGAGTAACATAGT

Basic information

species Physcomitrella patens
transcript PP1S18_8V6.2
intron # 7
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|162188273|gb|FC364767.1|FC364767
EST:     TGGTGTCTTGCAGCGCCGGCTCTTGATGGTTTCTGACAAGCACAGAAGCA                         GGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCA
genomic: TGGTGTCTTGCAGCGCCGGCTCTTGATGGTTTCTGACAAGCACAGAAGCAgtgagttaga ... tcttttgcagGGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCA
EST: gi|162157593|gb|FC332915.1|FC332915
EST:     TTCTGACAAGCACAGAAGCA                         GGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCA
genomic: TTCTGACAAGCACAGAAGCAgtgagttaga ... tcttttgcagGGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCA
EST: gi|67699475|gb|BJ959708.1|BJ959708
EST:     TGGTGTCTTGCAGCGCCGGCTCTTGATGGTTTCTGACAAGCACAGAAGCA                         GGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCA
genomic: TGGTGTCTTGCAGCGCCGGCTCTTGATGGTTTCTGACAAGCACAGAAGCAgtgagttaga ... tcttttgcagGGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCA
EST: gi|208372439|gb|DC952283.1|DC952283
EST:     TGGTGTCTTGCAGCGCCGGCTCTTGATGGTTTCTGACAAGCACAGAAGCA                         GGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCA
genomic: TGGTGTCTTGCAGCGCCGGCTCTTGATGGTTTCTGACAAGCACAGAAGCAgtgagttaga ... tcttttgcagGGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCA
EST: gi|67694445|gb|BJ954678.1|BJ954678
EST:     TGGTGTCTTGCAGCGCCGGCTCTTGATGGTTTCTGACAAGCACAGAAGCA                         GGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCA
genomic: TGGTGTCTTGCAGCGCCGGCTCTTGATGGTTTCTGACAAGCACAGAAGCAgtgagttaga ... tcttttgcagGGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCA
EST: gi|162268231|gb|FC444520.1|FC444520
EST:     TGGTGTCTTGCAGCGCCGGCTCTTGATGGTTTCTGACAAGCACAGAAGCA                         GGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCA
genomic: TGGTGTCTTGCAGCGCCGGCTCTTGATGGTTTCTGACAAGCACAGAAGCAgtgagttaga ... tcttttgcagGGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCA

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: 34 (upstream exon), 33 (downstream exon)
Score: 15

TTCCCTATCAGTGTGATGTTTGGAATGTGCGCAATATTTCTGGCACTGGCTGGTGTCTTGCAGCGCCGGCTCTTGATGGTTTCTGACAAGCACAGAAGCAgtgagttaga ... tcttttgcagGGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCAACATTTAAGTATGTATTTAGGTTGCACCCTAGGGATAGAGTAACATAGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgttcgaatgtgctgggacaatttataatgtgtcataatctcttcttttgcagGGTCAATTGAGACGTGGACGACTGAGAAGGGAGCTGAATTAGAACCCCTCAACATTTAAGTATGTATTTAGGTTGCACCCTAGGGATAGAGTAACATAGT
                                        tctcttcttttgc  CT-rich tract
                   acaatttataatgt  TA-rich tract