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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gcaagtttgattactcctcaaattgtttcattcacgaacatgacattccacgcttttcttttgtttagttctttatctttttgtgccaactttcaatattcaatttttttaagcatcaagtagtgtccaaacatgtgaggctctactaatatttgacatttagaacttgcgggtgcagCTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAGCAGTTGGGGCTGAAATTGTTGTATGTCATGAACACCCATGTACACGCAG

Basic information

species Physcomitrella patens
transcript PP1S99_229V6.1
intron # 3
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|208392227|gb|DC929488.1|DC929488
EST:     CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCC---                         CTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
genomic: CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTGgcaagtttga ... gcgggtgcagCTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
EST: gi|18364447|gb|BJ196520.1|BJ196520
EST:     CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTG                         CTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
genomic: CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTGgcaagtttga ... gcgggtgcagCTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
EST: gi|18360987|gb|BJ193051.1|BJ193051
EST:     CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTG                         CTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
genomic: CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTGgcaagtttga ... gcgggtgcagCTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
EST: gi|208362752|gb|DC950552.1|DC950552
EST:     CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTG                         CTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
genomic: CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTGgcaagtttga ... gcgggtgcagCTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
EST: gi|18346675|gb|BJ178720.1|BJ178720
EST:     CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTG                         CTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
genomic: CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTGgcaagtttga ... gcgggtgcagCTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
EST: gi|208394362|gb|DC904182.1|DC904182
EST:     CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTG                         CTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
genomic: CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTGgcaagtttga ... gcgggtgcagCTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
EST: gi|100422429|gb|BY976369.1|BY976369
EST:     CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTG                         CTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
genomic: CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTGgcaagtttga ... gcgggtgcagCTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
EST: gi|162167044|gb|FC342506.1|FC342506
EST:     CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTG                         CTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
genomic: CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTGgcaagtttga ... gcgggtgcagCTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
EST: gi|100411668|gb|BY992279.1|BY992279
EST:     CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTG                         CTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
genomic: CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTGgcaagtttga ... gcgggtgcagCTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
EST: gi|100391246|gb|BY971560.1|BY971560
EST:     CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTG                         CTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG
genomic: CTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTGgcaagtttga ... gcgggtgcagCTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAG

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: 33 (upstream exon), 30 (downstream exon)
Score: 13

AGCCCAGCCCTCCTTGCTCTTTCGGCAACTATTTGAGAAAGAGTCATCAACTTACACTTACTTGCTGGCAGATACTGCGCATTCGGATCGACCTGCCGTGgcaagtttga ... gcgggtgcagCTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAGCAGTTGGGGCTGAAATTGTTGTATGTCATGAACACCCATGTACACGCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tgtccaaacatgtgaggctctactaatatttgacatttagaacttgcgggtgcagCTTGTGGATCCTGTGGACAAGACCGCAGAGAGGGATGTCGCTCTTGTGGAGCAGTTGGGGCTGAAATTGTTGTATGTCATGAACACCCATGTACACGCAG
                       taatatttgacattta  TA-rich tract