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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aaaattattagttgcttgctttcaattgtctaggaagtattatagtaaattactaaatcctgactgattcacatttggtgtgtgtaaaacccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC

Basic information

species Vitis vinifera
transcript Vv05s0124g00360.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os09g33860.1 (Oryza sativa), 3'ss of exon 5
aaaattattagttgcttgctt---tcaattgtctaggaagtattatagtaaattactaaatcctgactgattcacatttggtgtgtgtaaaacccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC
|| |  | |||||   ||  |   | || |  | |  |  | |||   |   ||  |||    | ||| | |||  | |  | |||    |  || |    |||||||| |||||||| || ||||||||||| |||||||| ||||||||||||||||||||  ||||||||||||| || || ||||| || ||||| || 
aagaccaatagttctatgaataactgaagttcccattatttgttaccatgc-ttgttaatcattcactcagtcatgtatcctttgttctcactccatgc--agGTATGCCATGACTGGCCAGTTGACTCAGAAAAGTGATGTATATAGTTTTGGAGTTGTTCTTCTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCACACA

upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os01g67340.3 (Oryza sativa), 3'ss of exon 5
aaaattattagttgcttgctttcaattgtctaggaagtat-tatagtaa-attactaaatcctgactgat-tcacatttggtgtgtgtaaaacccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC
     |||  |    || ||    | |    | ||  ||| | ||  |   ||  ||       | |||| |||   |  |      ||       | |  |||||||||||||| || ||  |||| ||||| |||||||||||||| || ||||||||||| || || ||||| || || |||||||| || |||||||| 
---tctatatgacattttctgatgaataatcaagatatatatgtaacactgtttttatgcttgaaatgatatcattatctgacccaatatgtgaactttgcagGTATGCAATGACCGGTCAGCTGACACAGAAAAGTGATGTGTATAGCTTCGGAGTTGTTCTCTTGGAACTTCTGACAGGAAGAAAACCAGTAGATCATACA

upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: LOC_Os03g62700.1 (Oryza sativa), 3'ss of exon 5
--aaaattattagt-tgcttgctttcaattgtctaggaagtattatagtaaattactaaatcctgactgattcacatttggtgtgtgtaaaacccttctt----tagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC
  |  |  || ||| | ||||   | | ||||   |||| || |    | |     |  ||  | |   |||  |  |       | || |||||| |||     || ||||| |||||||| ||  |||| ||||||||||||||||| |||||||| || ||||| || || || || ||||| || ||||| || || || || 
aaatgaggataagtgttcttggcatgagttgt---ggaaatact----tgatgccgtgtatttttatgcatttcctctcttaacttatataaccctacttgccgcagATATGCTATGACTGGCCAGCTGACGCAGAAGAGTGATGTGTACAGTTTTGGTGTAGTTCTTTTGGAACTCCTGACTGGAAGGAAACCAGTGGACCACACA

upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G153945_T03 (Zea mays), 3'ss of exon 5
aaaattattagttgcttgctttcaattgtctaggaagtattatagtaaattactaaatcctgactgat---tcacatttggtgtgtgtaaaacccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC
  ||| ||   ||   |  |||  |     |      | |   | |  ||   |    |    |||||   | ||||  |   | | | | ||  |||   |||||||| |||||||| ||| ||||||| || |||||||| ||||||||||| ||||| || ||||||||||| ||||| || |||||||| |||||||| 
ctaataatcttttcactattttgcacgagatgaatgttttggaactttatctttgttcctcatctgatcagtgacataagagatctattatacatttc---agGTATGCTATGACTGGCCAACTGACTCAAAAAAGTGATGTATATAGTTTTGGGGTTGTCCTTTTAGAGCTTCTTACTGGAAGGAAACCTGTAGATCATACA

upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G029530_T01 (Zea mays), 3'ss of exon 5
aaaattattagttgcttgctttcaattgtctaggaagtattatagtaaattactaaatcctgactgattcacatttggtgtgtgtaaaacccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC
  |||||||     |      |  ||  |      ||  | ||  |  ||||    | |   |   | | | | |   | | | |          |  |||||||| |||||||| ||  | ||||||||||||||||| ||||| ||||| |||||||| |||||||||||||| || || ||||| || |||||||| 
gtaattattcaactcaaatccttgatcatgatttcagcttcatgattgattataccaac--aatcaacttaaactaaatttttctttgtttaaaatgcagGTATGCCATGACTGGCCAGCTAACTCAGAAGAGTGATGTATATAGCTTTGGGGTTGTTCTTTTAGAGCTTCTAACAGGAAGGAAACCAGTAGATCATACA

upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA10G44210.1 (Glycine max), 3'ss of exon 6
---aaaattattagttgcttgctttcaattgtctaggaagtattatagtaaattactaaatcctgactgattcaca-tttggtgtgtgtaaaacccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC
   ||| | ||| ||| ||   | |||    | | |    |  | |   |  | | |   |  | | ||||||  |  ||  | |||||        | |  || |||||||||||||| || |||||||| || |||||||| ||||||||||| || |||||  | |||||||| ||||| |||||||||||||| ||||||
tttaaattaatttgtttctca-tctcatcccttttgcc--tcctttgagatttgattttgtttt-attgattcttagcttcttctgtgttgccaaactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGGTGTGGTTCTTCTTGAGCTTCTTACTGGCAGAAAACCTGTTGACCATACC

upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA20G38980.1 (Glycine max), 3'ss of exon 6
---aaaattattagttgcttgctttcaattgtctaggaagtattatagtaaattactaaatcctgactgattcaca-tttggtgtgtgtaaaacccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC
   ||| | ||| ||| ||   | |||  | | | |  | |  | |   |  ||| |   |  | | ||||||  |  ||  | |||||        | |  || |||||||||||||| || |||||||| || |||||||| ||||||||||| ||||||||  | |||||||| || || |||||||||||||| ||||||
tttaaattaatttgtttctca-tctcatctcttttg--actcctttgagattttattttgtttt-attgattcttagcttcttctgtgttgccaaactttacagATATGCAATGACTGGGCAGTTGACTCAAAAAAGTGATGTCTATAGTTTTGGTGTTGTTCTTCTTGAGCTTCTTACAGGAAGAAAACCTGTTGACCATACC

upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT2G43230.1 (Arabidopsis thaliana), 3'ss of exon 4
aaaattattagttgcttgctttcaat-tgtctaggaagtatta--tagtaaattactaaatcctgactgattcacatttggtgtgtgtaaaacccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC
                     | ||| ||  |    | |  ||  | | || || ||  || || | | | | | |    ||   | |        | |  || ||||| ||||| ||||| ||||| |||||||||||||| || |||||||||||||| || || || ||||| || ||||||||||| ||||||||||| 
--------------------gtaaatatgcttcaacattgatagctcggaattttcttgattcttagtaactgaaagaatgtaactttggg-----tttgcagATATGCGATGACAGGACAGTTGACACAGAAGAGTGATGTTTACAGTTTTGGAGTTGTGCTTTTGGAACTTCTTACCGGGAGAAAACCGGTTGATCATACT

upper sequence: Vv05s0124g00360.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: AT3G59350.1 (Arabidopsis thaliana), 3'ss of exon 3
aaaattattagttgcttgctttcaattgtctaggaagtattatagtaaattactaaatcctgactgattcacatttggtgtgtgtaaaacccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC
  ||| | |  ||      |   | |||   |   |||||| | |   |     | ||  | |||| | ||  || | |||              |  |||||||| |||||||| ||| |||| |||||||||||||| ||||||||||| || || || || |||||  | ||||| || ||||| || |||||||| 
gtaatgaatgcttctgaaataatagttgatcacacagtattcttgaggaaggaaagattgtaactg-tacattttcgctgt--------------tgcagGTATGCGATGACTGGTCAACTGACACAGAAGAGTGATGTTTATAGTTTTGGTGTGGTGCTTTTGGAGCTCTTGACTGGTAGGAAACCCGTCGATCATACG

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|110730792|gb|EE108276.1|EE108276
EST:     CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGA                         GTATGCAATGACTGGACAATTGACTCAAAAGAGTGATGTGTATAGTTTTGG
genomic: CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGAgtaatgattc ... ccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
EST: gi|110361162|gb|EC924615.1|EC924615
EST:     CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGA                         GTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
genomic: CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGAgtaatgattc ... ccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
EST: gi|110418740|gb|EC984911.1|EC984911
EST:     CGCCTTCATTCTACTCGAGTCCTAGGAACCTTTGGCTATCATGCACCAGA                         GTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
genomic: CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGAgtaatgattc ... ccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
EST: gi|110363425|gb|EC927009.1|EC927009
EST:     CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGA                         GTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
genomic: CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGAgtaatgattc ... ccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
EST: gi|110400981|gb|EC967571.1|EC967571
EST:     CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGA                         GTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
genomic: CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGAgtaatgattc ... ccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
EST: gi|110702439|gb|EE081155.1|EE081155
EST:     CGCCTTCATTCTACTCGAGTCCTGAGGACCTTTGGCTATCATGCACCAGA                         GTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
genomic: CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGAgtaatgattc ... ccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
EST: gi|110720824|gb|EE097082.1|EE097082
EST:     CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGA                         GTATGCGATGACTGGACAATTGACTCANAAGAGTGATGTGTATAGTTTTGG
genomic: CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGAgtaatgattc ... ccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
EST: gi|110686851|gb|EE063746.1|EE063746
EST:     GCCTTCATTCTACTCGAGTCCTGAGGGAC-TTTGGCTATCATGCACCAGA                         GTATGCAATGACTGGA
genomic: GCCTTCATTCTACTCGAGTCCTG-GGGACCTTTGGCTATCATGCACCAGAgtaatgattc ... ccttctttagGTATGCAATGACTGGA
EST: gi|156738849|gb|EV242970.1|EV242970
EST:     CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGA                         GTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
genomic: CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGAgtaatgattc ... ccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
EST: gi|110380468|gb|EC945736.1|EC945736
EST:     CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGA                         GTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
genomic: CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGAgtaatgattc ... ccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
EST: gi|30302005|gb|CB978799.1|CB978799
EST:     CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGA                         GTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
genomic: CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGAgtaatgattc ... ccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
EST: gi|161714633|gb|FC064223.1|FC064223
EST:     CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGA                         GTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG
genomic: CGCCTTCATTCTACTCGAGTCCTGGGGACCTTTGGCTATCATGCACCAGAgtaatgattc ... ccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

taaattactaaatcctgactgattcacatttggtgtgtgtaaaacccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC
                                            cccttcttt  CT-rich tract
     tactaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aaaattattagttgcttgctttcaattgtctaggaagtattatagtaaattactaaatcctgactgattcacatttggtgtgtgtaaaacccttctttagGTATGCAATGACTGGACAATTGACTCAGAAGAGTGATGTGTATAGTTTTGGAGTTGTTCTGTTAGAGCTTCTAACTGGGAGAAAACCTGTTGATCATACC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA
aaaatta
- - - - - - -gcttgct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tgactga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tggtgtg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gtaaaac