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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATAATGCTCTGTGCAGATCATGGCCCTGCTGTGTCTGGAGCACACAACACTATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTGgtacagtctaaattgcagaagctatgttatgtatgaagctcttgaaatattctttgctattgctaaagcttgccccgttatacttatcagaattgtgtaactgatttatatttttttaatgaatactag

Basic information

species Physcomitrella patens
transcript PP1S46_63V6.1
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S46_63V6.2 (Physcomitrella patens), 5'ss of exon 12
lower sequence: Vv05s0077g00950.t01 (Vitis vinifera), 5'ss of exon 13
ATAATGCTCTGTGCAGATCATGGCCCTGCTGTGTCTGGAGCACACAACACTATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTGgtacagtctaaattgcagaagctatgttatgtatgaagctcttgaaatattctttgctattgctaaagcttgccccgttatacttatcagaattgtgtaactgatttatatttttttaatgaatactag
|| ||| | ||||| |||||||||||   ||| ||||| || |||||||||||||| || ||  | |||||||||||| | ||||| |||||||| || ||||       ||||| || |  ||||||   | |  |  |      |       |    |   |  |  |      | | || |        ||||| |||||||||       | ||||| | ||   
ATCATGTTATGTGCTGATCATGGCCCCTGTGTCTCTGGTGCTCACAACACTATTGTTACAGCAAGGGCAGGAAAGGACCTCGTATCCAGTCTTGTCTCAGgta-------aattgtagcaattatgtttcatttttatttagatggagggatcatatcttcattggaaat------gctgtagtgtgggcttttgtg-aactgattt-------tataatggaaacag-
















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|67574889|gb|BJ947713.1|BJ947713
EST:     TATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTG                         GTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC
genomic: TATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTGgtacagtcta ... tgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC
EST: gi|208366526|gb|DC955602.1|DC955602
EST:     TATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTG                         GTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC
genomic: TATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTGgtacagtcta ... tgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC
EST: gi|162196012|gb|FC372183.1|FC372183
EST:     TATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTG                         GTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC
genomic: TATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTGgtacagtcta ... tgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC
EST: gi|100385297|gb|BY950889.1|BY950889
EST:     TATTGTCACTGCTCGTGCAGGANAGGACTTGGTATTAAGTCTTGTGTCTG                         GTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC
genomic: TATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTGgtacagtcta ... tgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTC

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: 21 (upstream exon), 19 (downstream exon)
Score: 3

ATAATGCTCTGTGCAGATCATGGCCCTGCTGTGTCTGGAGCACACAACACTATTGTCACTGCTCGTGCAGGAAAGGACTTGGTATCAAGTCTTGTGTCTGgtacagtcta ... tgaatactagGTCTTCTCACAATTGGCCCTCGTTTTGGTGGAGCTATTGATGATGCTGCTCGCTATTTTAGAGAAGCCCATGACAACGGATTATCGCCTTACGCATTTGT




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