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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attttggtgcctgtacctttccttcacttcattaggtaccatacagagcttaatttcaacactgtttttaatgaatttttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC

Basic information

species Vitis vinifera
transcript Vv07s0005g06490.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA09G02790.1 (Glycine max), 3'ss of exon 1
-attttggtgcctgtacctttccttcacttcattaggtacc-atacagagcttaatttcaacactgtttttaatgaatttttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC
| | | | | | |||| | | ||| ||| | | | ||| | | | | || |||||| ||||| ||||| || |||||||| |||||||| | ||| || ||||| || ||||||| |||||| ||||||||||| |||||||| |||| ||||| |||||
cagggagagggagagatagataaagagaaataagaggtgttgagagggagtttagaatttgtgggtgtctaaatataatcactcgtttgtgtttt--tgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTT

upper sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA15G13670.1 (Glycine max), 3'ss of exon 1
--attttggtgcctgtacctttccttcacttcatt--aggtaccatacagagcttaatttc----aacactg----tttttaatgaatttttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC
| | || || | || | | ||||| | ||| | || || | |||||| || || |||| || || | || | ||| || |||||| ||||| || |||||||| |||||||| | ||| || ||||| || ||||||| |||||| ||||||||||| |||||||| |||| ||||| |||||
gtctgtctgtcactttttgttattattatttcatctcatgtataaaacctagttcaatttcttaaaaagttgggaactttttgtgttttaatctgttgttgggtttttgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCTGCTCTTGCTCGTTTGAAGGTTTATGAAGGAATCCCTCCTCCATATGACAAGACCAAGAGAATGGTT

upper sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA16G13580.1 (Glycine max), 3'ss of exon 1
-attttggtgcctgtacctttccttcacttcattaggtaccatacagagcttaatttcaacactgtttttaatgaatttttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC
| ||| | | | ||| | ||| || | || | || ||| | ||| || | ||| | || ||||| ||||| || |||||||| |||||||| | ||| || || || || ||||||| |||||||||||| ||||| |||||||| ||||| ||||| |||||
gagattgattgaagaatttttgtat-actatatctatctgaaggtaggatggatttaatttgttgtgggaagggaaggttctgaaatttctgtttctgtagAATGATACCACACAAGACAAAGCGTGGGGAAGCCGCTCTCGCTCGTTTGAAGGTTTATGAGGGAATTCCTCCTCCATATGACAAGATAAAGAGAATGGTT

upper sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G46860.1 (Glycine max), 3'ss of exon 1
attttggtgcc--tgtacctttccttcacttcattaggtaccatacagagcttaatttcaacactgtttttaatgaatttttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC
||||| || ||| | | || || | || | | | | || ||| | ||| | | | || | | | | ||| |||||||| || |||||||| ||||| || | ||| || ||||| |||||||||| |||||||| || ||||| || ||||| |||| |||||||||||
-atttggggctaatgtgtttatggttgacattatgaacttgta-atgaagattactggtgttgttgtggaaagttttctaagacggatgtttgtgtttgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCGCGATTGAAGGTGTATGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT

upper sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA08G46850.1 (Glycine max), 3'ss of exon 1
--attttggtgcc--tgtacctttccttcacttcattaggtaccatacagagcttaatttcaacactgtttttaatgaatttttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC
| ||| || ||| | | || | | || | | | | || ||| | ||| | | | || | | | | || |||||||| || |||||||| ||||| || | ||| || ||||||||| |||||| || ||||| || ||||| || ||||| |||| |||||||||||
attatatggggctaatgtgtttatggttggcattatgaacttgta-atgaagattact---ggtgttgtggaaagttttctgagaaggatgtttgtgtctgcagGATGATACCACACAAGACAAAGCGCGGGGAAGCTGCTCTTGCACGACTGAAGGTGTACGAGGGCATTCCTCCTCCTTATGACAAGACCAAGAGGATGGTT

upper sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT4G13170.1 (Arabidopsis thaliana), 3'ss of exon 1
attttggtgcctgtacctttccttcacttcattaggtaccatacagagcttaatttcaacactgtttttaatgaatt---tttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC
| || ||| | | | | | | ||| | || || || ||| ||||| |||| ||||||| ||| | | ||| ||||||||||| ||||||||||||||||| || || || ||||| || ||||||| || |||||||||||| || || || || ||||| ||||| |||||
-tctttgtgaagattcagtgatgtagcgtt-ttaataaagatgaagtctttctttttttttgagttttggtgaaattgaatttttggcttt-tgtggttgcagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCACTTGCTCGCTTGAAGGTTTTTGAGGGAATCCCACCTCCTTACGACAAGATTAAGAGAATGGTT

upper sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT3G24830.1 (Arabidopsis thaliana), 3'ss of exon 1
attttggtgcctgtacctttccttcacttcattaggtaccatacagagcttaatttcaacactgtttttaatgaatttt--tttggttttgttttatt-gtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC
|||| | | | | | | || | || || | | ||| | | || || | || | | | | ||| ||||||||||| ||||||||||||||||| || || || |||||||| ||||||| | ||||||| | || || || ||||| ||| | ||||| ||||||
---atggtcagcttttgatctttgtgcaatgatgtctgtgttaggaattgtatgtttgatagtgtgatggaggatttgaaatgtgatcatttgtcatttacagGATGATTCCACACAAGACCAAGCGTGGTGCTGCTGCTCTTGCACGTTTGAAGGTGTTTGAGGGAGTACCACCTCCTTATGACAAGGTCAAGAGAATGGTC

upper sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S80_110V6.1 (Physcomitrella patens), 3'ss of exon 2
-attttggtgcctgtacctttccttcacttcattaggtaccatacagagcttaatttcaacactgtttttaatgaatttttttggttttgttt-tattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC
| || || | | | | || | | || | || || ||| | || | | | | | | | ||| || ||||||||||||||||||||| | ||||| || ||||||| || ||||||| | || ||| | ||| |||| || ||||||||||||||||||||
agtattagtttcctgatttagagtaagaggcagaacaatctatctttattttcataccaaagataccttcg--ggttctgatcaactccgaccatgttgcagTATGATTCCGCACAAGACCAAGAGAGGAGCTGCTGCCCTTGAGCGCCTGAAGGCCTTCGAAGGAGTTCCTGCACCTTACGATAAGATGAAGAGGATGGTT

upper sequence: Vv07s0005g06490.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: PP1S63_162V6.1 (Physcomitrella patens), 3'ss of exon 2
------attttggtgcctgtacctttccttcacttcattaggtaccatacagagcttaatttcaacactgttttt-aatgaatttttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC
||| ||| | | | ||||| | ||||| | | |||||| | || ||| ||||||| ||| | | | || ||||| || |||||||||||| | || || || ||||||| || || || || | || || ||||| |||| |||||||||||||||||||||||
tcatacattgcggtacaattgaaaccacagt-cttcaggtctttccata-aaatattaattctgggattgaatttgaatgaat-----gggtgcaaatatgattcagAATGATCCCACACAAGACCAAGAGGGGCGCTGCTGCCCTTGAGCGCTTAAAAGCATTCGAAGGTGTCCCTGCACCTTATGATAAGATGAAGAGGATGGTT

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|294965121|gb|GW836952.1|GW836952
EST:     CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGG                         GATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTGGCACGATTGAA
genomic: CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGGgtgagttatt ... tttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
EST: gi|37188674|gb|CF608023.1|CF608023
EST:     CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGG                         GATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
genomic: CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGGgtgagttatt ... tttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
EST: gi|32456523|gb|CD797697.1|CD797697
EST:     CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGG                         GATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
genomic: CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGGgtgagttatt ... tttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
EST: gi|37185713|gb|CF605066.1|CF605066
EST:     CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGG                         GATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
genomic: CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGGgtgagttatt ... tttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
EST: gi|110384420|gb|EC948855.1|EC948855
EST:     CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGG                         GATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
genomic: CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGGgtgagttatt ... tttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
EST: gi|87584078|gb|DY473371.1|DY473371
EST:     CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGG                         GATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
genomic: CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGGgtgagttatt ... tttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
EST: gi|26262092|gb|CA813155.1|CA813155
EST:     CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGG                         GATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
genomic: CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGGgtgagttatt ... tttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
EST: gi|26262033|gb|CA813096.1|CA813096
EST:     CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGG                         GATGATTCCGCACAAGA
genomic: CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGGgtgagttatt ... tttattgtagGATGATTCCGCACAAGA
EST: gi|37187763|gb|CF607116.1|CF607116
EST:     CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGG                         GATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
genomic: CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGGgtgagttatt ... tttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
EST: gi|71856679|gb|DT005734.1|DT005734
EST:     CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGG                         GATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA
genomic: CCCATCCACTTCCGCGCCCCCTCCAAGATCCTCTGGCGTACCATCCGTGGgtgagttatt ... tttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagcttaatttcaacactgtttttaatgaatttttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC
                    ttttaat  putative branch site (score: 3)
 ttttgtttt  putative PPT
 tttttaatgaattttt  TA-rich tract
















Putative cis-regulatory sequences

 atgc intron ATGC exonic elements by Pertea et al.
 ATGC exon atgc putative intronic elements
 ATGC putative exonic elements identified for retained introns
        10        20        30        40        50        60        70        80        90        100       110       120       130       140       150       160       170       180       190       200       210       220 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attttggtgcctgtacctttccttcacttcattaggtaccatacagagcttaatttcaacactgtttttaatgaatttttttggttttgttttattgtagGATGATTCCGCACAAGACCAAGCGTGGAGCAGCAGCCCTTGCACGATTGAAGGCTTATGAGGGAATCCCTCCACCATATGATAAGATGAAGAGGATGGTC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- - - -tgcctgt
- - - - - - - -cctttcc
- - - - - - - - - - - - cacttca
- - - - - - - - - - - - - - - - - - - ccataca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - caacact