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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gctgtgttgtgaaagtcagctgacgtatgtgttcaaactatatctttaattccaccctccgctcactcaccgattggtgtgcgatctcatctggatgcagATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACATATACTCTTCTGGTGCTTTTCTGGGCTGAAATCTATCACCAG

Basic information

species Physcomitrella patens
transcript PP1S295_28V6.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S295_28V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: GLYMA07G38920.2 (Glycine max), 3'ss of exon 3
---gctgtgttgtgaaagtcagctgacgtatgtgttcaaactatatctttaattccaccctccgctcactcaccgattggtgtgcgatctcatctggatgcagATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACATATACTCTTCTGGTGCTTTTCTGGGCTGAAATCTATCACCAG
     |  ||| || |  |  | ||  || ||| ||      ||   | |||        | | | || | ||    | |||||   |||  | ||  |  || | |||      || || || |||||||| ||  || |||| ||| |||||||||| ||||| || ||||||||||| ||||| |||||||||
gttagttagttttgcacctgtgttg-tgt-tgtatttgcctaatgattgtaaggttggtatgctcacaatgaca---tagtgtggcttcttgtttgatt--agGTGTTGATTTCGGTGCTATTAGATCTGCCAGGACTACTTTTTTTCTCAACATATACACTTCTTGTCCTTTTCTGGGCAGAAATTTATCACCAG

upper sequence: PP1S295_28V6.1 (Physcomitrella patens), 3'ss of exon 3
lower sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 3
gctgtgttgtgaaagtcagctgacgtatgtgttcaaactatatctttaattccaccctccgctcactcaccgattggtgtgcgatctcatctggatgcagATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACATATACTCTTCTGGTGCTTTTCTGGGCTGAAATCTATCACCAG
   || | |    | ||| |     | |   || || ||   | || | ||      |  |   ||   |  |    | |||  | | ||||   || ||||  |||||||  |  |  | ||| | ||  |  |   ||||||||| || ||| |||||||||| ||||||||||||||||| ||| | |||
---gtttaggatcattcaccatcattgtaattttaatct---tattgacttgtttattgtgtcaaccttctaa---atttgcagtgttatctt--tgtagATTCTGCAACATATCTTGCTTGATATTCCAAGTCTTGCTTTCTTCACCACCTATGCTCTTCTGGTTCTTTTCTGGGCTGAAATTTATTATCAG
















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|100358043|gb|BY965443.1|BY965443
EST:     GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAG                         ATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACA
genomic: GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAGgtatgtcaca ... ctggatgcagATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACA
EST: gi|67716278|gb|BJ966538.1|BJ966538
EST:     GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAG                         ATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACA
genomic: GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAGgtatgtcaca ... ctggatgcagATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACA
EST: gi|208372289|gb|DC936447.1|DC936447
EST:     GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAG                         ATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACA
genomic: GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAGgtatgtcaca ... ctggatgcagATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACA
EST: gi|100377699|gb|BY986358.1|BY986358
EST:     GCGCCGCAGTTTTTTGCTTCCGGGAGGATGTGCAGGCATTATCTCCTGAG                         ACATTGCAACAGGTTCTTTTTGAACTGCCGCGTATAAATTTCTTCACA
genomic: GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAGgtatgtcaca ... ctggatgcagATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACA
EST: gi|100356111|gb|BY946202.1|BY946202
EST:     GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAG                         ATATTGCAGCACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACA
genomic: GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAGgtatgtcaca ... ctggatgcagATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACA
EST: gi|67508414|gb|BJ941281.1|BJ941281
EST:     GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAG                         ATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACA
genomic: GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAGgtatgtcaca ... ctggatgcagATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACA
EST: gi|208355715|gb|DC910613.1|DC910613
EST:     GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAG                         ATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACA
genomic: GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAGgtatgtcaca ... ctggatgcagATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACA
EST: gi|208374316|gb|DC940673.1|DC940673
EST:     GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAG                         ATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACA
genomic: GCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAGgtatgtcaca ... ctggatgcagATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACA

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: 30 (upstream exon), 24 (downstream exon)
Score: 4

TGCGCGCCGCAGTTTTTTGCTTCCGTGAGGATGTGCAGGCATTATCTCCTGAGgtatgtcaca ... ctggatgcagATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACATATACTCTTCTGGTGCTTTTCTGGGCTGAAATCTATCACCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttaattccaccctccgctcactcaccgattggtgtgcgatctcatctggatgcagATATTGCAACACGTTCTTTTGGATCTGCCGGGCATAATTTTCTTCACAACATATACTCTTCTGGTGCTTTTCTGGGCTGAAATCTATCACCAG
                  cactcac  putative branch site (score: 4)
                                       tctcatct  putative PPT