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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTCGAGCCTAGGCCTCCTTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAGgtcattgataattttcatgcaatgtggccatctttttttttttggggagtgccacctagagtctacggtagagtagcaagagctgatttctgtatggagc...

Basic information

species Physcomitrella patens
transcript PP1S332_45V6.1
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: PP1S332_45V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA01G38120.1 (Glycine max), 5'ss of exon 2
CCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTCGAGCCTAGGCCTCCTTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCC-TTATCAAGgtcattgataattttcatgcaatgtggccatctttttttttttggggagtgccacctagagtctacggtagagtagcaagagctgatttctgtatggagc
||||| ||| | ||  | || || |||||||| ||||||||||||||||| ||||| | |||||| ||||| || || || || ||||| || |||||| | |  |||  |||      |  | ||     | |   | |||| |  || |   || | | || | |  |  | |     |   |  ||||| | |  |  
CCAACCGGTCTAACAGCGAACCTGTTGAAGCTCTTCGAGCCTAGGCCTCCGTTGGAGTACAAGCCGCCTCCGGAGAAACGGAAATGTCCACCGTTATCAGgtt--ttgtaaatgcatccgttaggt-----tttcgctattttcgttgattat-actttgtgttt-caattaatttatttgtttttctttctcttttcaag

upper sequence: PP1S332_45V6.1 (Physcomitrella patens), 5'ss of exon 2
lower sequence: GLYMA11G07200.2 (Glycine max), 5'ss of exon 2
CCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTCGAGCCTAGGCCTCCTTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCC-TTATCAAGgt-cattgataattttcatgcaatgtggccatctttttttttttggggagtgccacctagagtctacggtagagtagcaagagctgatttctgtatggagc
||||| ||| | ||  | || || |||||||| ||||||||||||||||| ||||| | |||||| ||||| || || ||||| || || || |||||| | | | |  || |||    |    | | || || ||  ||  ||         | || | | || |    |  | |   | |   |  ||||| | | ||  
CCAACCGGTCTCACAGCGAACCTGTTGAAGCTCTTCGAGCCTAGGCCTCCGTTGGAGTACAAGCCACCTCCGGAGAAACGAAAATGCCCACCGTTATCAGgtttcgtaaatgattccgttaggttttcgcaattttcgttgatt---------ctactttgtgttt-taattaattgatatgcttttctttctcttttgaag
















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|18355039|gb|BJ187098.1|BJ187098
EST:     TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAG                         GCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
genomic: TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAGgtcattgata ... tgtgttgcagGCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
EST: gi|18342127|gb|BJ174162.1|BJ174162
EST:     TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAG                         GCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
genomic: TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAGgtcattgata ... tgtgttgcagGCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
EST: gi|67718772|gb|BJ969031.1|BJ969031
EST:     TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAG                         GCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
genomic: TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAGgtcattgata ... tgtgttgcagGCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
EST: gi|100452661|gb|CJ975381.1|CJ975381
EST:     TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAG                         GCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
genomic: TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAGgtcattgata ... tgtgttgcagGCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
EST: gi|67712849|gb|BJ966298.1|BJ966298
EST:     TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAG                         GCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
genomic: TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAGgtcattgata ... tgtgttgcagGCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
EST: gi|162156991|gb|FC333353.1|FC333353
EST:     TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAG                         GCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
genomic: TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAGgtcattgata ... tgtgttgcagGCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
EST: gi|100391079|gb|BY953089.1|BY953089
EST:     TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAG                         GCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
genomic: TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAGgtcattgata ... tgtgttgcagGCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
EST: gi|100388050|gb|BY988523.1|BY988523
EST:     TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAG                         GCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
genomic: TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAGgtcattgata ... tgtgttgcagGCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
EST: gi|18373032|gb|BJ204634.1|BJ204634
EST:     TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAG                         GCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG
genomic: TTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAGgtcattgata ... tgtgttgcagGCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATG

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: 27 (upstream exon), 33 (downstream exon)
Score: 12

CCAACTGGTTTGACTACTAATCTTTTGAAGCTTTTCGAGCCTAGGCCTCCTTTGGAATTCAAGCCCCCTCCTGAAAAGCGAAAGTGTCCGCCTTATCAAGgtcattgata ... tgtgttgcagGCATTGGGCAGTTTGTTCAGCATTTTGCAGAGCCTGGGGATCCCGAATATGCCCCTCCTGTTACGAAGGGGGAAACTCCT




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