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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaagaggcagttgttgaatgtcatgacacataagggattggtggatctagtgcattaatgtccctgtgaaatattttgttcatatatgagtattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT

Basic information

species Vitis vinifera
transcript Vv11s0016g00900.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os09g26880.3 (Oryza sativa), 3'ss of exon 12
gaagaggcagttgttgaatgtcatgacacataagggattggtggatc---tagtgcattaatgtccctgtgaaatattttgttcata-tatgagtattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT
  | |      | ||  | |   | | |  |     | ||      |   ||   ||| ||  |  || ||  |  |  ||||| |  | |   |  | |||||||| ||||| ||||||||||| ||||| ||||||||||| || |||||||| ||||| ||||||||||||||||| |||||||| || ||||||||||| 
--acacctttcttttacacgctctcagatttcttttactgccatgccccataagacatgaa-atgactatggta-gtgatgttcttgctcttcttgctgtacagGCCTCATGGTAGTGACTGTGGCATTGTTAATGTAAATATTCCCACAAATGGTGCTGAAATTGGTGGAGCTTTTGGTGGAGAAAAAGCTACTGGTGGTGGA

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G130440_T02 (Zea mays), 3'ss of exon 12
--gaagaggcagttgttgaatgtcatgacacataagggattggtggatctagtgcattaatgtccctgtgaaatattttgttcatatatgagtattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT
  ||| |   | |     ||| ||    |   |  ||| |   | ||  ||     ||    | ||  | |       ||||  |       |||||| |||||| ||||| ||||| |||||||| |||||||| || |||||||| ||||| ||||| ||||||||||| ||||| |||||||| |||||||||||||| 
ttgaatacttattgcaaaaatttctcatcttttgtggggtccttcgagttatattttttgattgccaataagcctcactgtttgttctct--tattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAACTGGTGGTGGA

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM5G820733_T01 (Zea mays), 3'ss of exon 4
--gaagaggcagttgttgaatgtcatga-cacataagggattggtggatctagtgcattaatgtccctgtgaaatattttgttcatatatgagtattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT
  ||| |   | |||   || ||  | | |   |  ||| |   | |   ||     ||    | ||  | |       ||||  |       |||||| |||||| ||||| ||||| |||||||| |||||||| || |||||||| ||||| ||||| ||||||||||| ||||| |||||||| ||| |||||||||| 
ttgaatattta-ttgcaaaaagttctcatcttttgtggggtcctttgggttatattttttgattgccaataagtctcactgtttgttctct--tattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G070514_T02 (Zea mays), 3'ss of exon 5
--gaagaggcagttgttgaatgtcatga-cacataagggattggtggatctagtgcattaatgtccctgtgaaatattttgttcatatatgagtattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT
  ||| |   | |||   || ||  | | |   |  ||| |   | |   ||     ||    | ||  | |       ||||  | |     |||||| |||||| ||||| ||||| |||||||| |||||||| || |||||||| ||||| ||||| ||||||||||| ||||| |||||||| ||| |||||||||| 
ttgaatattta-ttgcaaaaagttctcatcttttgtggggtcctttgggttatattttttgattgccaataagcctcactgtt--tgttctgttattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM5G828253_T01 (Zea mays), 3'ss of exon 1
--gaagaggcagttgttgaatgtcatga-cacataagggattggtggatctagtgcattaatgtccctgtgaaatattttgttcatatatgagtattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT
  ||| |   | |||   |||||  | | |   |  ||| |   |     ||     ||    | ||  | |       ||||  |       |||||| |||||| ||||| ||||| |||||||| |||||||| || |||||||| ||||| ||||| ||||||||||| ||||| |||||||| ||| |||||||||| 
ttgaatattta-ttgcaaaatgttctcatcttttgtggggtcctttcggttatattttttgattgccaataagcctcactgtttgttctct--tattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G382159_T01 (Zea mays), 3'ss of exon 3
--gaagaggcagttgttgaatgtcatgacacataagggattggtggatctagtgcattaatgtc-cctgtgaaatattttgttcatatatgagtattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT
  ||| |   | |||   || ||  | |    |   ||  |  |     |  |   ||  | |  ||  | |       ||||  |       |||||| |||||| ||||| ||||| |||||||| |||||||| || |||||||| ||||| ||||| ||||||||||| ||||| |||||||| ||| |||||||||| 
ttgaatattta-ttgcaaaaagttctcatcttttgtggggtcctttgcgttatatttttttattgccaataagcctcactgtttgttctct--tattatgcagGCCCCATGGTAGTGATTGTGGTATAGTGAATGTGAACATACCTACTAATGGTGCTGAAATTGGTGGAGCATTTGGTGGAGAAAAAGCAGCTGGTGGTGGA

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA15G19670.1 (Glycine max), 3'ss of exon 12
--------------------------------------------------------------gaagaggcagttgttgaatgtcatgacacataagggattggtggatctagtgcattaatgtccctgtgaaatatttt----gttcata--tatgagtattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT
                                                               |     ||||  |||| |  ||   |  |||||   || ||||   |  |  ||   ||      |   |||||||    ||||||   | ||| |||  | ||||||||  || ||||| |||||||| ||||||| ||| ||||||||||||||||||||||||||||| || ||||| ||||||||||| || |||||||| 
gtaagtacttacaaacttatttttgtcctatcctttcgatctctgctgatgagtttggcctacacacttcagtacttgactaacactcc-tataagatgtttgtgg---tgatttatagttgcataaatagtatattttacttgttcatgggtgtgaatatggtgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAGATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACCGGTGGTGGC

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA15G19670.4 (Glycine max), 3'ss of exon 12
----------------------------------------------------------gaagaggcagttgttgaatgtcatgacacataagggattggtggatctagtgcattaatgtccctgtgaaatattt----tgttcata--tatgagtattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT--------
                                                           |     ||||  |||| |  ||   |  |||||   || ||||   |  |  ||   ||      |   ||||||    |||||||   | ||| |||  | ||||||||  || ||||| |||||||| ||||||| ||| ||||||||||||||||||||||||||||| || ||||| ||||||||||| || ||||||||         
gtacttacaaacttatttttgtcctatcctttcgatctctgctgatgagtttggcctacacacttcagtacttgactaacactcc-tataagatgtttgtgg---tgatttatagttgcataaatagtatattttacttgttcatgggtgtgaatatggtgcaggccacgagGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAGATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACCGGTGGTGGCCGTGAGGC

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA09G08150.2 (Glycine max), 3'ss of exon 11
--------------------------------------------------------------gaagaggcagttgttgaatgtcatgacacataagggattggtggatctagtgcattaatgtccctgtgaaatattttgttcatatatgagtat--------tatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT
                                                               |     ||||  |||| |  ||   |  |||||   || ||||   |  |  ||   ||  |   |   |||||||  |  |  ||| || |        |   ||||||||  || ||||| |||||||| ||||||| ||| |||||||||||||||||||| |||||||| || ||||| ||||||||||| || |||||||| 
gtaagtactcacaaacttatttttgtcctatcctttggatctctgctaatgagtttggcctacacacttcagtacttgactaaca-atcctataagatgtttgtgg---tgatttatagttgcacaaatagtatattttacttgttcatgggtgtaaatatggtgcgcagGCCACGAGGTAGTGATTGTGGTATAGTGAATGCAAACATACCTACAAATGGAGCTGAAATTGGTGGTGCCTTTGGTGGAGAAAAGGCGACAGGTGGTGGC

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: AT1G54100.2 (Arabidopsis thaliana), 3'ss of exon 12
gaagaggcagttgttgaatgtcatgacacataagggattgg-tggatctagtgcattaatgtc-cctgtgaaatattttgttcatatatgagtatta-tac-agGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT
              | | ||  || | | | ||    ||   |  ||||     |  ||| |   ||    ||  |  | || || |    || ||| ||| || ||||  |||||||||||||| ||||||||||| || ||||| || ||||||||||||||||||||||||||||| || || || || ||||||||||||
-------------gtaagtgctataaaa-acaacaacttaactcaatctttccgaccaatataatctactgaaattaattttaatgtgatggttttactactagACCACTGGGAAGTGACTGTGGCATTGTGAATGTGAACATACCGACGAATGGAGCTGAGATTGGTGGAGCTTTTGGAGGCGAGAAAGCGACTGGTGGTGGT

upper sequence: Vv11s0016g00900.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: PP1S237_29V6.1 (Physcomitrella patens), 3'ss of exon 13
-gaagaggcagttgttga--atgtcatgacacataagggattgg-tggatctagtgcattaatgtccctgtgaaatattttgttcatatatgagtattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT
   || | || |    ||  | |  |   ||   |    |||   |  || | |    || |  |    |||| |          || | |   |  | | ||| ||    || ||||| ||||||||||| ||||| || ||||| || |||||||| |||||||| ||||| || || ||||| |||||||| || || || 
attagtgacaatgtacgaggaagctacttcatgcacctcatttacttcatttcgaatttttacattttagtgacaagcaag----atgtttctctcgtttgcagACCTACAGGCAGTGATTGTGGTATTGTCAATGTGAACATACCAACCAATGGAGCGGAGATTGGGGGAGCATTCGGTGGAGAGAAGGCAACAGGGGGCGGA

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|349820814|gb|FQ404199.1|FQ404199
EST:     AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGG                         GCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
genomic: AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGGgtgagtactg ... tattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
EST: gi|33405776|gb|CF211403.1|CF211403
EST:     AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGG                         GCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
genomic: AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGGgtgagtactg ... tattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
EST: gi|351015872|gb|FQ431827.1|FQ431827
EST:     AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGG                         GCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
genomic: AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGGgtgagtactg ... tattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
EST: gi|349816247|gb|FQ403743.1|FQ403743
EST:     AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGG                         GCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
genomic: AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGGgtgagtactg ... tattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
EST: gi|349819677|gb|FQ402614.1|FQ402614
EST:     AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGG                         GCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
genomic: AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGGgtgagtactg ... tattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
EST: gi|351019460|gb|FQ429595.1|FQ429595
EST:     AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGG                         GCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
genomic: AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGGgtgagtactg ... tattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
EST: gi|349817443|gb|FQ405447.1|FQ405447
EST:     AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGG                         GCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
genomic: AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGGgtgagtactg ... tattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
EST: gi|351027458|gb|FQ444707.1|FQ444707
EST:     AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGG                         GCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
genomic: AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGGgtgagtactg ... tattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
EST: gi|351033661|gb|FQ462191.1|FQ462191
EST:     AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGG                         GCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG
genomic: AGTAGTTCAATCTTCACTCGCAAACCTGAAGTTATCTTCAAATGGATTGGgtgagtactg ... tattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctagtgcattaatgtccctgtgaaatattttgttcatatatgagtattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT
       cattaat  putative branch site (score: 3)
                       aaatattttgttcata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaagaggcagttgttgaatgtcatgacacataagggattggtggatctagtgcattaatgtccctgtgaaatattttgttcatatatgagtattatacagGCCACATGGAAGTGACTGTGGTATTGTGAATGTAAATATACCTACAAATGGAGCTGAGATTGGTGGAGCTTTTGGGGGAGAAAAGGCAACTGGTGGTGGT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGTGG
- - - - - - - - - - tcatgac
- - - - - - - - - - - - - - - - - - - tggtgga
- - - - - - - - - - - - - - - - - - - - - - - - -gtgcatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgtcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgaaata