Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   		9  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...attaatgctcacatgtgtgtttcttttgtaattgaaacattacttattcttattcatcaaaaaaaaataaaacattacttattcttgttcttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCTGGTGATTTGGTTGGGGTGAACAAAGATAGCTACTTAATCTTAGATACTT

Basic information

species Vitis vinifera
transcript Vv14s0060g02260.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os06g07630.1 (Oryza sativa), 3'ss of exon 3
---attaatgctcacatgtgtgtttcttttgtaattgaaacattacttattcttattcatcaaaaaaaaataaaacattacttattcttgttcttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCTGGTGATTTGGTTGGGGTGAACAAAGATAGCTACTTAATCTTAGATACTT
   | || |  | |    |  |  |   || || || ||| |  |   |     ||  | |  |      ||||| ||   || ||| | || | || || |||| || || || ||||| |||||||| ||||||||||||||  | |||||||||||||||||||| || |||||||| |||||| | ||  | || ||  
cataatattttttaggcttaagcatgacttatagttcaaaaaaaaaagagaa--atcaaactcatttttgtaaaatatcctttgttcctatt-tcgattgcagACTATATTCCTTCCTGTGGTTGGGCTAGTTGACCCTGATAAACTCAAGCCTGGTGATTTGGTTGGAGTAAACAAAGACAGCTACCTTATACTGGACACAC

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os02g56000.2 (Oryza sativa), 3'ss of exon 3
--------attaatgctcacatgtgtgtttcttttgtaattgaaacattacttattcttattcatcaaaaaaaaataaaacattacttattcttgttcttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCTGGTGATTTGGTTGGGGTGAACAAAGATAGCTACTTAATCTTAGATACTT
        | || | ||  ||||  | |  | ||| | ||   ||    | |||||  |||| ||        |     |      | |||       || | || ||||||| || || |||||  | ||||| ||||||||||| ||| | |||||||| ||||||||||| || |||||||| |||||||| ||  |||| ||  
agttgtgtaatactcctaccatgcatataccgtttctcatctcaattaaatttatttgtattgat--------acctgcatgggtttaattgactactttaattgcagACAATATTCCTTCCTGTAATCGGGCTTGTTGACCCTGAAAAGCTCAAGCCTGGGGATTTGGTTGGAGTCAACAAAGACAGCTACTTGATACTAGACACGC

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G032505_T02 (Zea mays), 3'ss of exon 3
-attaatgctcacatgtgtgtttcttttgtaattgaaacattacttattcttattcatcaaaaaaaaataaaacattacttattcttgttcttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCTGGTGATTTGGTTGGGGTGAACAAAGATAGCTACTTAATCTTAGATACTT
 ||  |     |        |  ||||| |   ||   | | | ||    | ||  |   ||      |||||  ||| ||  |  | ||  ||| || |||| || || || |||||||||||||| || |||||||| ||| |||||||||||||| ||||||| || || |||||||||||| | ||  ||||||| |
aatctaaagcaatgaaaaactgccttttatgcatggt-cttgagtttaagtaatcaaattaactgctgtaaaatcttagtttcttgtcttgatgattgcagACTATATTCCTTCCTGTTGTTGGGCTAGTGGACCCTGACAAGCTAAAGCCTGGTGATCTGGTTGGAGTCAATAAAGATAGCTACCTTATACTAGATACAT

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA10G29250.1 (Glycine max), 3'ss of exon 3
--------attaatgctcacatgtgtgtttcttttgtaattga--aacattacttattcttattcatcaaaaaaaaataa----aacattacttattcttgttcttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCTGGTGATTTGGTTGGGGTGAACAAAGATAGCTACTTAATCTTAGATACTT
            ||| |  ||| |    || || | | |  ||  || |   || | |   ||    || |      |||     |  ||| ||||  ||  | ||||||| ||||||||||||| |||||||||||||| ||||||||||| |||||||| ||||||||| ||||||| || ||||| ||||| ||||||||||| ||||| |
gtgacatggacgatgatttcatattatcttattcttttagcgaggaaaagctctcagtacaatagtacatatttctttaatcttgagcttaattatgttttcttttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCTGGTGATCTGGTTGGTGTTAACAAGGATAGTTACTTAATCTTGGATACCT

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G39500.1 (Glycine max), 3'ss of exon 3
attaatgctcacatgtgtgtttcttttgtaattgaaacattacttattcttattcatcaaaaaaaaata--aaacattacttattcttgttct----tgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCTGGTGATTTGGTTGGGGTGAACAAAGATAGCTACTTAATCTTAGATACTT
     |||     | |  | | |||    ||   |||      ||    ||| |   |||| ||||      || |||| | | |  |||| |    |||||||||||||||||||| |||||||||||||| ||||||||||  |||||||| ||||||||| ||||||| || ||||||||||| |||||| |||| ||| |  
-----tgcatttcttttggatccttggaaaagcaaaatgg-gtttggagttagttggcaaagaaaagccctcaatattaataaattatgttttcatttgactgtagACAATCTTTCTTCCTGTTGTTGGGCTTGTTGACCCTGCCAAGTTAAAACCTGGTGATCTGGTTGGTGTTAACAAAGATAGTTACTTAGTCTTGGATGCCC

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA20G38030.1 (Glycine max), 3'ss of exon 3
-------------------------------------------------------------attaatgctcacatgtgtgtttcttttgtaattgaaac-attacttattctta-ttcatcaaaaaaaaataa-aacattacttattcttgttcttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCTGGTGATTTGGTTGGGGTGAACAAAGATAGCTACTTAATCTTAGATACTT
                                                              ||| |  | | |  | |  || | || |  ||  ||| |  ||    ||||| | |||        ||     |  ||| | ||  ||  | ||||||| ||||||||||||| |||||||||||||| ||||||||||| |||||||| || |||||| ||||||| || ||||| ||||| ||||||||||| |||||  
gtgacatggactaggatttcatattgtcatctgatgttcctatatcatagtttaagattgttttatttgttatagttattgttatcttatgcttttaacgaggacaagctcttagtacatttttcggtaaccttgagcttaataatgttttcttttgactgcagACAATCTTTCTACCTGTTGTTGGGCTTGTTGACCCTGACAAGTTAAAACCCGGTGATCTGGTTGGTGTTAACAAGGATAGTTACTTAATCTTGGATACCC

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G42110.1 (Glycine max), 3'ss of exon 1
attaatgctcacatgtgtgtttcttttgtaattgaaac---attactta-ttcttattcatcaaaa-aaaaataaaacattacttattcttgttcttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCTGGTGATTTGGTTGGGGTGAACAAAGATAGCTACTTAATCTTAGATACTT
                 ||   ||     | || ||||    |||  |   |  | || | ||| | |   |   ||  ||   || | |   |  ||| | |     ||  ||      |   | | | | | |||       | |    |      |||  | | |||  |  | ||  |                       
-----------------tgaccctgaca-agttaaaacctggttatctggctggtgttaaccaagatagttacttaatcttggatactttgccttctgagtatgattcatgatttaag-

upper sequence: Vv14s0060g02260.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G05530.1 (Arabidopsis thaliana), 3'ss of exon 3
attaatgctcacatgtgtgtttcttt--tgtaattgaaacattacttattcttattca----tcaaaaaaaaataaaacattacttattcttgttcttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCTGGTGATTTGGTTGGGGTGAACAAAGATAGCTACTTAATCTTAGATACTT
  | |  ||  ||      ||  ||   | |  ||   ||||    | |||   |||     |||      |  |||   ||   | ||| |  | | ||||| |||| |||||||| || |||||||| ||||| || |||||||  || || |||||||| |||||||| || ||||||||||||||||| || || ||||| |
-gtgagacttccaaacccattctttagatatgttttctacatcttctcttccgtttcccgtttcatgtctgagcaaatacttttgttttcgttatgtggactgcagACCATCTTTCTACCAGTTGTTGGACTCGTGGATCCTGATAGTTTGAAACCTGGTGACTTGGTTGGAGTTAACAAAGATAGCTACTTGATTTTGGATACCT

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|71864441|gb|DT013496.1|DT013496
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|71860997|gb|DT010052.1|DT010052
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAATTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|110724320|gb|EE100046.1|EE100046
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAATTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|71859210|gb|DT008265.1|DT008265
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|71858458|gb|DT007513.1|DT007513
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAATTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|110711112|gb|EE087285.1|EE087285
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAATTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|71857850|gb|DT006905.1|DT006905
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|110685213|gb|EE063376.1|EE063376
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|294964455|gb|GW838258.1|GW838258
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|71859776|gb|DT008831.1|DT008831
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAATTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|71863186|gb|DT012241.1|DT012241
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAATTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|110724441|gb|EE100272.1|EE100272
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAATTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|110722856|gb|EE099502.1|EE099502
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|71861858|gb|DT010913.1|DT010913
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAATTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|30252235|gb|CB969786.1|CB969786
EST:     TGTTGTTTTG-GANCATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAATTAAAGCCT
genomic: TGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|110732813|gb|EE108430.1|EE108430
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|34549827|gb|CF518059.1|CF518059
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAATTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|34544589|gb|CF512821.1|CF512821
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAATTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|30252226|gb|CB969777.1|CB969777
EST:     TGTTGTTTTG-GANCATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAATTAAAGCCT
genomic: TGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|37184438|gb|CF603792.1|CF603792
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAATTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT
EST: gi|71879123|gb|DT028178.1|DT028178
EST:     ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAG                         ACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAATTAAAGCCT
genomic: ACTCTCAGAGGAAGGGAAAATGTGTTGTTTTGAAAACATCTACACGCCAGgtacaccagc ... ttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attcttattcatcaaaaaaaaataaaacattacttattcttgttcttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCTGGTGATTTGGTTGGGGTGAACAAAGATAGCTACTTAATCTTAGATACTT
                                           tcttgac  putative branch site (score: 3)
                                cttattcttgttctt  CT-rich tract
     tattcatcaaaaaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
attaatgctcacatgtgtgtttcttttgtaattgaaacattacttattcttattcatcaaaaaaaaataaaacattacttattcttgttcttgactgtagACAATCTTTCTGCCTGTTGTTGGGCTCGTTGACCCTGATAAGTTAAAGCCTGGTGATTTGGTTGGGGTGAACAAAGATAGCTACTTAATCTTAGATACTT

- - - gctcaca
- - - - - - -tgtgtgt
- - - - - - - - - - - - - - - - -gaaacat
- - - - - - - - - - - - - - - - - - - - - - - - - - -tcatcaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaacat