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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCGCTCGGCTAAGATTATTGGGGGATTATCATCACTCAACTCGGATTGCGTTTGTCGAGTTCGTGATGgtgagtttttattctcttttgggagaccttgtgttgattggatttgtgctgggactaattgttaagcatcgacaatgacgtgaattctgtgtgagtcctg...

Basic information

species Physcomitrella patens
transcript PP1S196_50V6.1
intron # 9
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|162272247|gb|FC448756.1|FC448756
EST:     TGGGGGATTATCATCACTCAACTCGGATTGCGTTTGTCGAGTTCGTGATG                         GCGGAAAGTGCAATGGCAGCTTTGAATTGCAGTGGCGCAATATTAGGTTCT
genomic: TGGGGGATTATCATCACTCAACTCGGATTGCGTTTGTCGAGTTCGTGATGgtgagttttt ... ctctttgcagGCGGAAAGTGCAATGGCAGCTTTGAATTGCAGTGGCGCAATATTAGGTTCT
EST: gi|67575157|gb|BJ947981.1|BJ947981
EST:     GGATTGCGTTTGTCGAGTTCGTGATG                         GCGGAAAGTGCAATGGCAGCTTTGAATTGCAGTGGCGCAATATTAGGTTCT
genomic: GGATTGCGTTTGTCGAGTTCGTGATGgtgagttttt ... ctctttgcagGCGGAAAGTGCAATGGCAGCTTTGAATTGCAGTGGCGCAATATTAGGTTCT
EST: gi|162272246|gb|FC448755.1|FC448755
EST:     TGGGGGATTATCATCACTCAACTCGGATTGCGTTTGTCGAGTTCGTGATG                         GCGGAAAGTGCAATGGCAGCTTTGAATTGCAGTGGCGCAATATTAGGTTCT
genomic: TGGGGGATTATCATCACTCAACTCGGATTGCGTTTGTCGAGTTCGTGATGgtgagttttt ... ctctttgcagGCGGAAAGTGCAATGGCAGCTTTGAATTGCAGTGGCGCAATATTAGGTTCT
EST: gi|67698614|gb|BJ958847.1|BJ958847
EST:     TCATCACTCAACTCGGATTGCGTTTGTCGAGTTCGTGATG                         GCGGAAAGTGCAATGGCAGCTTTGAATTGCAGTGGCGCAATATTAGGTTCT
genomic: TCATCACTCAACTCGGATTGCGTTTGTCGAGTTCGTGATGgtgagttttt ... ctctttgcagGCGGAAAGTGCAATGGCAGCTTTGAATTGCAGTGGCGCAATATTAGGTTCT

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: 19 (upstream exon), 34 (downstream exon)
Score: 9

GTCGCTCGGCTAAGATTATTGGGGGATTATCATCACTCAACTCGGATTGCGTTTGTCGAGTTCGTGATGgtgagttttt ... ctctttgcagGCGGAAAGTGCAATGGCAGCTTTGAATTGCAGTGGCGCAATATTAGGTTCTCTTCCAATCAG




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