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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctgcatacatctccatctcatcacactaactgaaaagaagatagaaaattctcttcttggagttcctgtgataattatttttcttcctttattttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTTGGATGGTTTCCGCGTGGCAAGATGGCTGGTCCATTTCAGGATGTTGCCT

Basic information

species Vitis vinifera
transcript Vv17s0000g06430.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g06430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os09g24540.1 (Oryza sativa), 3'ss of exon 2
ctgcatacatctccatctcatcacactaactgaaaagaagatagaaaattctcttcttggagttcctgtgat-aattatttttcttcctttattttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTTGGATGGTTTCCGCGTGGCAAGATGGCTGGTCCATTTCAGGATGTTGCCT
|  | ||||| |   |  |          || |        |  | ||  | ||        |   | |     | |  | ||  |  |||  |    ||| ||||   |||||| || ||||||||||| || ||||| ||||| || ||||||||||| |||||||| || |||||||| || |||||||||||||| |
ccacttacatgttgcttgctgtctgtaggctcaggctgctttc-ataacccactagacactatgtatatatccgactgatattactattttgatactgcagATAGCCCAAGAATACTCTGAATGTCCATCTGGAAAGAAAGGTGGAGATCTTGGATGGTTCCCGCGTGGAAAAATGGCTGGCCCTTTTCAGGATGTTGCAT

upper sequence: Vv17s0000g06430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G048277_T03 (Zea mays), 3'ss of exon 2
ctgcatacatctccatctcatcacactaactgaaaagaagatagaaaattctcttcttggagttcctgtgataattattt-ttcttcctttattttct------cagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTTGGATGGTTTCCGCGTGGCAAGATGGCTGGTCCATTTCAGGATGTTGCCT
     |   |  | |  || ||  | |   |   |      | |    | |  || || ||  | |  |||| || ||   | ||  ||||||||| |      ||| |||||  ||| ||||| ||||| |||||||||||||| ||||| || ||||| ||||| ||||||||||||||||||||||| || ||||| ||||| |
-aatctgactaactacttcgtcgaagtttttctcatattttttg----tgccattattaga--taccatgatgataatagatcctgactttattttttgtactacagGTAGCACAAGAGTATTCTGAATGCCCATCAGGGAAGAAAGGTGGAGATCTTGGTTGGTTCCCGCGTGGCAAGATGGCTGGTCCTTTCCAGGAGGTTGCTT

upper sequence: Vv17s0000g06430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G21080.1 (Glycine max), 3'ss of exon 3
-----ctgcatacatctccatctcatcacactaa-ctgaaaagaagatagaaaattctcttcttggagttcctgtgataattatttttcttcctttattttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTTGGATGGTTTCCGCGTGGCAAGATGGCTGGTCCATTTCAGGATGTTGCCT
       | ||| ||    ||||  ||||   ||  | |     ||| | || ||| | | |     |||  | | |  | |||||  ||  ||| |      ||| |||||  ||| |||||||||||||||||||| ||||||||||| ||||||||||||||||| || || ||||||||||| ||||||||||| |||||||
ttgaaaaggataaataagaatctgttcacttgaaattaacctagagacaaaatattttgtccaattggttattatcaatagtatttcactgacttca------cagGTAGCACAAGAGTATTCAGAATGTCCATCAGGAAAGAAGGGTGGAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGAAGTTGCCT

upper sequence: Vv17s0000g06430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G33180.2 (Glycine max), 3'ss of exon 3
ctgcatacatctccatctcatcacactaactgaaaagaagatagaa--aattctcttcttggagttcctgtgataattatttttcttcctttattttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTTGGATGGTTTCCGCGTGGCAAGATGGCTGGTCCATTTCAGGATGTTGCCT
 || |   ||    |            |  |||||  ||  ||||   ||   | || ||  | ||  |||  | || | |    || |  |   ||| ||| ||||   ||| |||||||||||||| ||||| ||||||||||| ||||||||||||||||| || || ||||||||||| |||||||||||||||||||
ttgaaaggataaataagaatctggttcatttgaaatcaatctagagacaaacatttttttccaatt--tgttgttatcaataacttttcactgacttcacagATAGCTCAAGAGTATTCAGAATGTCCTTCAGGAAAGAAGGGTGGAGACCTTGGATGGTTTCCCCGAGGAAAGATGGCTGGGCCATTTCAGGATGTTGCCT

upper sequence: Vv17s0000g06430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G26550.1 (Arabidopsis thaliana), 3'ss of exon 3
ctgcatacatctccatctcatcacactaactgaaaagaagatagaaaattctcttcttggagttcctgtgataattatttttcttcctttatt-----ttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTTGGATGGTTTCCGCGTGGCAAGATGGCTGGTCCATTTCAGGATGTTGCCT
      |||||| ||  |        |   | | |   |  | || |  | | |  |  || ||   | ||   |||      ||  | | |       |||||| | |||||||| || || || |||||||||||||| || || || || ||||||||||| || || || |||||||| |||||||| || ||||| ||||
-----gacatctacaagtttcagttttcggttagatatatttcgatagatgtgtgttatgaattgtggagaatcttaacacgatttgtgtgtggaacgatctcagATTGCAGCAGAGTACTCTGAGTGTCCATCAGGGAAAAAAGGAGGAGATCTTGGATGGTTCCCTCGAGGAAAGATGGCAGGTCCATTCCAAGATGTCGCCT

upper sequence: Vv17s0000g06430.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S217_91V6.1 (Physcomitrella patens), 3'ss of exon 3
--ctgcatacatctccatct-catcacactaactgaaaagaagatagaaaattctcttcttggagt-tcctgtgataattatttttcttcctttattttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTTGGATGGTTTCCGCGTGGCAAGATGGCTGGTCCATTTCAGGATGTTGCCT
  |   | | ||  |||    | |  ||  || |        ||   |      | |   |||||  |    | ||   || |||  ||  | || |    |||||||| |||||||| ||||||||||||||||| ||||| || || ||||| || |||||||| ||||||||||||||||| || || ||||| || ||||
accataaaatattgccacgagcgttgcataaatttctgcatcga---atggcgttttcagtggagcatttcataatttgtagtttggttt-tgtactcatgcagCTAGCGGCAGAATACTCAGAATGTCCATCAGGCAAGAAAGGAGGAGACCTCGGGTGGTTTCCTCGTGGCAAGATGGCTGGACCTTTCCAGGAGGTGGCCT

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|26267741|gb|CA818804.1|CA818804
EST:     ATGGCTGGCTTAGTAATGGAGCCAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|110707849|gb|EE084714.1|EE084714
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAAGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|26263377|gb|CA814440.1|CA814440
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|110427246|gb|EC993681.1|EC993681
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|110380044|gb|EC945280.1|EC945280
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|110399434|gb|EC965939.1|EC965939
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|110725994|gb|EE103039.1|EE103039
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|30128488|gb|CB913827.1|CB913827
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|110386205|gb|EC950785.1|EC950785
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|110416664|gb|EC982660.1|EC982660
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|26262167|gb|CA813230.1|CA813230
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|71875713|gb|DT024768.1|DT024768
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|26265537|gb|CA816600.1|CA816600
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGCTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|110404457|gb|EC969543.1|EC969543
EST:     TGGCTGGCTTAGTAAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: TGGCTGGCTTAGT-AATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|110702518|gb|EE081322.1|EE081322
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|110409580|gb|EC975246.1|EC975246
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|110695358|gb|EE073287.1|EE073287
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
EST: gi|110369228|gb|EC933382.1|EC933382
EST:     ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAG                         CTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT
genomic: ATGGCTGGCTTAGTAATGGAGACAAGGTTCCACCAGCTGAGTTTGCGAAGgtaaattcct ... attttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaattctcttcttggagttcctgtgataattatttttcttcctttattttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTTGGATGGTTTCCGCGTGGCAAGATGGCTGGTCCATTTCAGGATGTTGCCT
                          taattatttttcttcc  CT-rich tract
                       tgataattatttttct  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctgcatacatctccatctcatcacactaactgaaaagaagatagaaaattctcttcttggagttcctgtgataattatttttcttcctttattttctcagCTAGCAGCAGAATATTCAGAATGTCCATCAGGGAAGAAGGGTGGTGACCTTGGATGGTTTCCGCGTGGCAAGATGGCTGGTCCATTTCAGGATGTTGCCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGATG
- gcataca
- - - - - - ccatctc
- - - - - - - - - - - -cactaac
- - - - - - - - - - - - - - - - aaaagaa
- - - - - - - - - - - - - - - - - - - - - agaaaat
- - - - - - - - - - - - - - - - - - - - - - - - - - -ttcttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - ttcctgt