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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcggtatctccatcttggcgtacacaatttagcttacgtctattctgcacatggcctcttctcttagctgttacatgccctagtccttgaagttgttcctgcgacttttagagaagcatacagcgctgatacgcaacaccggttgatcagTGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAGCTCTCTTAAAGCCACACGAGCGCATAATGGCCTTAGATCTTCCTCATGG

Basic information

species Physcomitrella patens
transcript PP1S79_54V6.1
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|162179835|gb|FC355906.1|FC355906
EST:     TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAG                         TGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
genomic: TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAGgtcggtatct ... ggttgatcagTGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
EST: gi|162182305|gb|FC357176.1|FC357176
EST:     TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAG                         TGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
genomic: TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAGgtcggtatct ... ggttgatcagTGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
EST: gi|18369273|gb|BJ201358.1|BJ201358
EST:     TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGANAAATGGGGAG                         TGAATGTGCAGTCTCTCTCTGGGTCC
genomic: TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAGgtcggtatct ... ggttgatcagTGAATGTGCAGTCTCTCTCTGGGTCC
EST: gi|100385980|gb|BY951174.1|BY951174
EST:     TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAG                         TGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
genomic: TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAGgtcggtatct ... ggttgatcagTGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
EST: gi|18365567|gb|BJ197644.1|BJ197644
EST:     TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAG                         TGAATGTGCAGTCTCTCTCTGGGTCCCCAGCC
genomic: TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAGgtcggtatct ... ggttgatcagTGAATGTGCAGTCTCTCTCTGGGTCCCCAGCC
EST: gi|208358811|gb|DC935197.1|DC935197
EST:     TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAG                         TGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
genomic: TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAGgtcggtatct ... ggttgatcagTGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
EST: gi|100428360|gb|BY977766.1|BY977766
EST:     CNNNNNNNGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAG                         TGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
genomic: CAAAAAA-GAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAGgtcggtatct ... ggttgatcagTGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
EST: gi|208379665|gb|DC903720.1|DC903720
EST:     TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAG                         TGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
genomic: TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAGgtcggtatct ... ggttgatcagTGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
EST: gi|162155361|gb|FC331767.1|FC331767
EST:     TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAG                         TGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
genomic: TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAGgtcggtatct ... ggttgatcagTGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
EST: gi|18366816|gb|BJ198896.1|BJ198896
EST:     TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAG                         TGAATGTGCAGTCTCTCTCTGGGTCCCCAGCC
genomic: TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAGgtcggtatct ... ggttgatcagTGAATGTGCAGTCTCTCTCTGGGTCCCCAGCC
EST: gi|100392460|gb|BY953374.1|BY953374
EST:     CNNNNNNNGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAG                         TGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
genomic: CAAAAAA-GAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAGgtcggtatct ... ggttgatcagTGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAG
EST: gi|18370401|gb|BJ202003.1|BJ202003
EST:     TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAG                         TGAATGTGCAGTCTCTCTCTGGG
genomic: TCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAGgtcggtatct ... ggttgatcagTGAATGTGCAGTCTCTCTCTGGG

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: 16 (upstream exon), 31 (downstream exon)
Score: 8

GTTCATTGACATGGCTGAAAGACTGTGTCAAAAAAGAGCTCTCGCAGCTTTCCGCCTCGATCCAGAGAAATGGGGAGgtcggtatct ... ggttgatcagTGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAGCTCTCTTAAAGCCACACGAGCGCATAATGGCCTTAGATCTTCCTCATGG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttcctgcgacttttagagaagcatacagcgctgatacgcaacaccggttgatcagTGAATGTGCAGTCTCTCTCTGGGTCCCCAGCCAATTTTCAGGTCTACACAGCTCTCTTAAAGCCACACGAGCGCATAATGGCCTTAGATCTTCCTCATGG
                            cgctgat  putative branch site (score: 8)
        actttta  TA-rich tract