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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttccctaatatctcaccatctcatactaacgtttgaacctctttaggagccctttttgacaaattgtttccatctctaatttattgttattgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGT

Basic information

species Vitis vinifera
transcript Vv13s0156g00180.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os11g33240.2 (Oryza sativa), 3'ss of exon 15
tttccctaatatctcaccatct-catactaacgt-ttgaacctctttaggagccctttttgacaaattgtttccatctctaatttattgttattgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGT
  |     || ||| |  |||| |||||     |     |  | ||   || |     |||| || ||      |          |  |   |  | || ||||||||||||| || || ||||||||| | ||||| || |||||| ||||||  ||||| ||||||||||| |||||| |||||||||| |||||||| |
--tattggatctctaatgatctgcatacagttttaccttattttttgttgaacatgaattgagaatttagaattactaaggtcacagcgcattcatttgtagGTTGTTCCTGGCTTCGGTCATGGAGTTCTACGTAAGACCGATCCACGATATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os02g10070.1 (Oryza sativa), 3'ss of exon 15
--tttccctaatatctcaccatctcatactaacgtttgaacctctttaggagccctttttgacaaattgtttccatctctaatttattgttattgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGT
        | || ||| |  ||||   |  ||| ||    | | ||   || | ||   ||| |||||         | |    |       |  |  | ||||||||||||| ||||| ||||||||| | ||||| || |||||| | ||||  ||||| ||||||||||| |||||| |||||||||| |||||||| |
caaacaaatgatttctaatgatctggaataaacattct--ctttttgttgaactctaactgaaaaattcacagatagtatgccatgacacattcattcgtagGTTGTTCCTGGCTTTGGTCATGGAGTTCTACGTAAGACCGATCCACGGTATACATGTCAGAGGGAGTTTGCTTTGAAGTACTTGCCTGAGGATCCACTTT

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GRMZM2G064023_T01 (Zea mays), 3'ss of exon 16
------------------------------------------------------------------tttccctaatatctcacc-atctcatactaacgtttgaacctctttaggagccctttttg-----acaaattgtttccatctc-taatttat---tgttattgtgtgca-----gGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGT
                                                                     |  ||  |  ||||  |  |   | | | ||       |||    ||    | ||||       || |  | || ||||  | || | |    | | |||  ||||     |||||||||||| ||||| ||||||||| ||||||| ||||| ||| | |||   |||||||||||||||||  ||||||| ||||| || |||||||| |
gtatatcgtttcactgaggtctagtgtttatgttcatgctcgaacacggttttgtttcccataggaaagctatatcagttcactgagatttgaatgatgtgcagtagtctgatagatttgtctttgtttatgaaagtgatatctatctgatgatctgtgttcgctgttgcttgcattatagGTTGTTCCTGGATTTGGTCATGGAGTTCTGCGTAAGACAGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCGAGGATCCACTTT

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GRMZM2G063851_T05 (Zea mays), 3'ss of exon 1
tttccctaatatctcaccatctcatactaacgtttgaacctctttaggagccctttttgacaaattgtttccatctctaatttattgttattgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGT
 |    |    |    |      | | |    |||||   | | | | ||     |||  |  || ||||   |      ||  ||    |       ||||||||||||||||||| ||||||||| ||||||| || || ||| | |||   |||||||||||||||||  ||||||| |||||  | |||||||| |
atgatgtgcagtaggtctgatagagagttgtctttgactgtttatggaagtgacatttctctgatggtttgtgtgcactgttgcttacattcaatcatagGTTGTTCCTGGGTTTGGTCATGGAGTTCTGCGTAAGACCGACCCACGGTATTCATGTCAAAGGGAGTTTGCCCTGAAGCATTTGCCCAAGGATCCACTTT

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA08G16770.1 (Glycine max), 3'ss of exon 15
-tttcccta-atatctcaccatctcatactaacgtttgaacctctttaggagccctttttgacaaattgtttccatctctaatttattgttattgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGT
 ||    || ||||||   || |  ||  |   |   |||  |   |   | |   |      | || |  |    || |  |  | | ||    | |||||||||| ||||| | ||| ||||| ||||| ||  | |||||||||||||| |  ||||| ||||||||||| |||||||| |||||| ||||||||   |
tttaatatacatatcttttcaccaaatgatttagagggaatattactgccaacttctcagataatataggctttggctgt--tgcactttttggatttgcagGTTGTGCCTGGATATGGACATGGGGTTTTACGCCAGACAGATCCAAGATACACATGTCAGAGGGAGTTTGCTTTGAAGCATTTGCCTAATGATCCATATT

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA15G42300.2 (Glycine max), 3'ss of exon 15
-tttcccta-atatctcaccatctcatactaacgtttgaacctctttaggagccctttttgacaaattgtttccatctctaatttattgttattgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGT
 ||    |  ||||||   || |  ||  |   |   |||  ||  |   | |   |      | ||    |     | |  | |  | ||    | |||||||||| ||||| | ||| ||||| ||||| ||  | |||||||||||||| |  ||||| ||||||||||| |||||||| |||||| ||||||||   |
attaatatgcatatctgttcaccaaatgatgtagagagaatatcactgccaacttctcagataatataagctttggttgt--tgtgctttttggatttgcagGTTGTGCCTGGATATGGACATGGGGTTTTACGCCAGACAGATCCAAGATACACATGTCAGAGGGAGTTTGCTTTGAAGCATTTGCCTAATGATCCATATT

upper sequence: Vv13s0156g00180.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: AT3G60100.1 (Arabidopsis thaliana), 3'ss of exon 14
----------------------------------------------------------------------------tttccctaatatctcaccatctcatactaacgtttgaacctctttag-----gagccctttttgacaa-attgtttccatctctaatttattgttattgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGT
                                                                            ||    || | | | |  |    |||  | | |  ||   | ||| |     | |   |   ||  ||  ||||    |    ||| | |   ||  | | ||||||||||||| || | ||| ||||| |||||||||||||| |||||||||||||| || ||||| |||||||| ||||||||  | ||||||||||| || |
gttgacaaaattatgctctgctttgccttttgaaactatccatatgtattgcatgctaatcatgacaggccataacttgaattattgtataaataatgaataaaagcttcggattatgttttgattatggggtttgcctgtgaatgttgtcaggaaacttaaataaacatttgtct-tgcagGTTGTTCCAGGATATGGCCATGGTGTTTTGCGTAAAACGGATCCAAGATATATATGCCAAAGAGAGTTTGCCTTGAAGCATCTACCTGATGATCCTCTTT

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|110391493|gb|EC956472.1|EC956472
EST:     GCACAGAACAGTTGAAAGACTATGTCTGGAAAACATTAAAAAGTGGCAAG                         GTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATAT
genomic: GCACAGAACAGTTGAAAGACTATGTCTGGAAAACATTAAAAAGTGGCAAGgtaatttgga ... ttgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATAT
EST: gi|110361418|gb|EC924886.1|EC924886
EST:     GCACAGAACAGTTGAAAGACTATGTCTGGAAAACATTAAAAAGTGGCAAG                         GTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATAT
genomic: GCACAGAACAGTTGAAAGACTATGTCTGGAAAACATTAAAAAGTGGCAAGgtaatttgga ... ttgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATAT
EST: gi|110429398|gb|EC995889.1|EC995889
EST:     GCACAGAACAGTTGAAAGACTATGTCTGGAAAACATTAAAAAGTGGCAAG                         GTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATAT
genomic: GCACAGAACAGTTGAAAGACTATGTCTGGAAAACATTAAAAAGTGGCAAGgtaatttgga ... ttgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATAT
EST: gi|29785895|gb|CB343236.2|CB343236
EST:     GCACAGAACAGTTGAAAGACTATGTCTGGAAAACATTAAAAAGTGGCAAG                         GTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATAT
genomic: GCACAGAACAGTTGAAAGACTATGTCTGGAAAACATTAAAAAGTGGCAAGgtaatttgga ... ttgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATAT
EST: gi|110372355|gb|EC936513.1|EC936513
EST:     GCACAGAACAGTTGAAAGACTATGTCTGGAAAACATTAAAAAGTGGCAAG                         GTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATAT
genomic: GCACAGAACAGTTGAAAGACTATGTCTGGAAAACATTAAAAAGTGGCAAGgtaatttgga ... ttgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATAT
EST: gi|110362967|gb|EC926531.1|EC926531
EST:     GCACAGAACAGTTGAAAGACTATGTCTGGAAAACATTAAAAAGTGGCAAG                         GTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATAT
genomic: GCACAGAACAGTTGAAAGACTATGTCTGGAAAACATTAAAAAGTGGCAAGgtaatttgga ... ttgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATAT
EST: gi|77577886|gb|DV217693.1|DV217693
EST:     GCACAGAACAGTTGAAAGACTATGTCTGGAAAACATTAAAAAGTGGCAAG                         GTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATAT
genomic: GCACAGAACAGTTGAAAGACTATGTCTGGAAAACATTAAAAAGTGGCAAGgtaatttgga ... ttgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggagccctttttgacaaattgtttccatctctaatttattgttattgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGT
                             ctctaat  putative branch site (score: 3)
                              tctaatttattgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttccctaatatctcaccatctcatactaacgtttgaacctctttaggagccctttttgacaaattgtttccatctctaatttattgttattgtgtgcagGTTGTTCCTGGGTTTGGGCATGGAGTTTTGCGTAAAACAGATCCAAGATATATGTGTCAAAGGGAGTTTGCATTGAAGCACTTGCCTGATGATCCACTGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- tccctaa
- - - - - - - - ccatctc
- - - - - - - - - - - - - - - - - - - - - - - - -gcccttt