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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCATAACCAACCCCACAGATAGCGGGAAGCCGgtgagtgagtacgttgctgtctgtctctgtctctgtctctctgtctctgtttctctgtgtctctgtgtgactcccattcttcctcttctcctttttgcga...

Basic information

species Physcomitrella patens
transcript PP1S84_134V6.5
intron # 1
splice site 5'
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|100415782|gb|BY993001.1|BY993001
EST:     ATAACCAACCCCACAGATAGCGGGAAGCCGGTGAGTG                   
genomic: ATAACCAACCCCACAGATAGCGGGAAGCC-------Ggtgagtgagt ... ctct
EST: gi|100415782|gb|BY993001.1|BY993001
EST:     ATAACCAACCCCACAGATAGCGGGAAGCCGGTGAGTG                   
genomic: ATAACCAACCCCACAGATAGCGGGAAGCC-------Ggtgagtgagt ... ctct
EST: gi|162199322|gb|FC373702.1|FC373702
EST:     GATAGCGGGAAGCCG                         GTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
genomic: GATAGCGGGAAGCCGgtgagtgagt ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
EST: gi|18372495|gb|BJ204097.1|BJ204097
EST:     CTCATAACCAACCCCACAGATAGCGGGAAGCCG                         GTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
genomic: CTCATAACCAACCCCACAGATAGCGGGAAGCCGgtgagtgagt ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
EST: gi|100384294|gb|BY969425.1|BY969425
EST:     ATAACCAACCCCACAGATAGCGGGAAGCCG                         GTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
genomic: ATAACCAACCCCACAGATAGCGGGAAGCCGgtgagtgagt ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
EST: gi|100436515|gb|BY961256.1|BY961256
EST:     CTCATAACCAACCCCACAGATAGCGGGAAGCCGGTGAGTG                   
genomic: CTCATAACCAACCCCACAGATAGCGGGAAGCC-------Ggtgagtgagt ... ctct
EST: gi|100436515|gb|BY961256.1|BY961256
EST:     CTCATAACCAACCCCACAGATAGCGGGAAGCCGGTGAGTG                   
genomic: CTCATAACCAACCCCACAGATAGCGGGAAGCC-------Ggtgagtgagt ... ctct
EST: gi|18329966|gb|BJ161972.1|BJ161972
EST:     ATAACCAACCCCACAGATAGCGGGAAGCCG                         GTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
genomic: ATAACCAACCCCACAGATAGCGGGAAGCCGgtgagtgagt ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
EST: gi|18345682|gb|BJ177725.1|BJ177725
EST:     CTCATAACCAACCCCACAGATAGCGGGAAGCCGGTG                       
genomic: CTCATAACCAACCCCACAGATAGCGGGAAGCC---Ggtgagtgagt ... ctctgtgt
EST: gi|18345682|gb|BJ177725.1|BJ177725
EST:     CTCATAACCAACCCCACAGATAGCGGGAAGCCGGTG                       
genomic: CTCATAACCAACCCCACAGATAGCGGGAAGCC---Ggtgagtgagt ... ctctgtgt
EST: gi|162185457|gb|FC362552.1|FC362552
EST:     GCGGGAAGCCG                         GTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
genomic: GCGGGAAGCCGgtgagtgagt ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
EST: gi|162176115|gb|FC351883.1|FC351883
EST:     CACAGATAGCGGGAAGCCG                         GTATACCACAGCACGGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCC
genomic: CACAGATAGCGGGAAGCCGgtgagtgagt ... ctctgtgtagGTATACCACAGCAC-GGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCC
EST: gi|18325297|gb|BJ157293.1|BJ157293
EST:     ATAACCAACCCCACAGATAGCGGGAAGCCG                         GTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG
genomic: ATAACCAACCCCACAGATAGCGGGAAGCCGgtgagtgagt ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCG

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: 13 (upstream exon), 35 (downstream exon)
Score: 6

CTCATAACCAACCCCACAGATAGCGGGAAGCCGgtgagtgagt ... ctctgtgtagGTATACCACAGCACGGGTTGCATTAACAGCCTCCTCCCCTTCCTGTACCCGCGGTCGTTTTTGGCTAAGGACTAGATCGGACAAGCGAAGATGGCAACAC




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