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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attcaggagcaataaggtgaatcctcatggaattgcactgatgacgagcaatcgacgatcgtcagtatgttagtgtattgatggatatgctgtatgacagGCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGT

Basic information

species Physcomitrella patens
transcript PP1S491_11V6.1
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S491_11V6.1 (Physcomitrella patens), 3'ss of exon 2
lower sequence: AT1G15120.1 (Arabidopsis thaliana), 3'ss of exon 3
-------------at-tcaggagcaataaggtgaatcctcatggaattgcac-tgatgacgagcaat-cgacgatcgtcagtatgttagtgtattgatggatatgctgtatgacagGCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGT
             || |   ||  ||| | |       | ||    ||  ||    || |  |   |  || |||| |   |    |  |  |  | | | | ||  || |  |||||||| || ||| | ||  | |  |||||   ||| || ||||||||||||||||||||||| ||||| |||   ||||||||  |||||
gtgaaactggttgatgttgtgactaattatgaattgtgttataagttttgacacagtgccatgttttgtgaagatcattgtttgactgatacaaggcttgtt-tgtggt-tctcagGCATGTGTCAAGAGAATCCAAGGTGATGATTCTGGCCACAAGCATTGCACTGGCCAGTATTTTGACTACTGGCAATGCATTGACAAATGT
















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|208397291|gb|DC920645.1|DC920645
EST:     TTGAGGACTCGTGTAAGCCTAGATGTGTGAAGCAACTTATATCTTATGAG                         GCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACT
genomic: TTGAGGACTCGTGTAAGCCTAGATGTGTGAAGCAACTTATATCTTATGAGgtatgggatt ... tgtatgacagGCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACT
EST: gi|37838829|gb|BJ596837.1|BJ596837
EST:     TTGAGGACTCGTGTAAGCCTAGATGTGTGAAGCAACTTATATCTTATGAG                         GCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACT
genomic: TTGAGGACTCGTGTAAGCCTAGATGTGTGAAGCAACTTATATCTTATGAGgtatgggatt ... tgtatgacagGCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACT
EST: gi|208376115|gb|DC906774.1|DC906774
EST:     TTGAGGACTCGTGTAAGCCTAGATGTGTGAAGCAACTTATATCTTATGAG                         GCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACT
genomic: TTGAGGACTCGTGTAAGCCTAGATGTGTGAAGCAACTTATATCTTATGAGgtatgggatt ... tgtatgacagGCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACT
EST: gi|7147932|gb|AW509854.1|AW509854
EST:     TTGAGGACTCGTGTAAGCCTAGATGTGTGAAGCAACTTATATCTTATGAG                         GCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACT
genomic: TTGAGGACTCGTGTAAGCCTAGATGTGTGAAGCAACTTATATCTTATGAGgtatgggatt ... tgtatgacagGCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACT
EST: gi|18360940|gb|BJ193004.1|BJ193004
EST:     TTGAGGACTCGTGTAAGCCTAGATGTGTGAAGCAACTTATATCTTATGAG                         GCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACT
genomic: TTGAGGACTCGTGTAAGCCTAGATGTGTGAAGCAACTTATATCTTATGAGgtatgggatt ... tgtatgacagGCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACT
EST: gi|162229029|gb|FC405064.1|FC405064
EST:     TTGAGGACTCGTGTAAGCCTAGATGTGTGAAGCAACTTATATCTTATGAG                         GCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACT
genomic: TTGAGGACTCGTGTAAGCCTAGATGTGTGAAGCAACTTATATCTTATGAGgtatgggatt ... tgtatgacagGCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACT

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), 35 (downstream exon)
Score: 8

GGCTTCAGTTGAGGAGGAGGTGGTCGAGGCTATGGATCCAAAGCCCGAGATTGAGGACTCGTGTAAGCCTAGATGTGTGAAGCAACTTATATCTTATGAGgtatgggatt ... tgtatgacagGCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGT




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcaatcgacgatcgtcagtatgttagtgtattgatggatatgctgtatgacagGCATGCGTGAAGCGCATTGAGGAGGATGAGAATGGTCAAAAGCATTGCACTGGCCAGTATTTCGACTATTGGGGCTGCATTGATCAATGT
                              tattgat  putative branch site (score: 8)
                    tatgtta  TA-rich tract