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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcccctcctttgtttctctctgatgagaatagattaggtgcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt...

Basic information

species Vitis vinifera
transcript Vv09s0002g04810.t01
intron # 12
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os06g05180.2 (Oryza sativa), 5'ss of exon 12
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcccctcctttgtttctctctgatgagaatagattaggtgcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt----
||| ||||| || |||||||| ||||| ||||||||||| || || |||||| |||| |||||||||||||   | ||||||||||||||    || ||||||||   | | |   ||||  |  |    |    ||  ||| | | || || |  | ||    | ||| | |             |||  |||  ||      
GTCATTTGGATCTGCATTGGAGTTTGTTTGGTCATCAGAAGGAGAGTATGCTATCAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtttggcccacattgattgtagcctttcctttt--atgaatttgat-cagtaaaactgtagtgtttcatttcttcaatcac-cactctggagaatgcaccatct

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os02g11840.1 (Oryza sativa), 5'ss of exon 3
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcccctcctttgtttctctc--tgatgagaatagattaggtgcaatatatatatatatatgca-tgtgtgtgtgtgtgtgtgctgctgaaaacatt-
 || || || || ||| | |||||||| ||||||   ||||| |||||||||||||||||||| || || | | | ||||| | |||||| |||||||||||||||    || |  |   |||| |   | ||     || || ||    | ||    |   |  ||||| |||||| |   |       |  ||         
ATCATTCGGGTCTGCACTTGAATTTGTTTGGTCAGTTGATGGAGAATATGCTGTCAGAGAAAGCACGTCGAGGATAAAGATATACAGTAAAAATTTCCAGgtttgtactaccactgtcccttcttttaattatctttgtacatcag----agtaggggtccttcaatgcaatgtgtgggctagaaaaatttattgggtgtgcac

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: LOC_Os02g11830.2 (Oryza sativa), 5'ss of exon 12
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcccctcctttgtttctctctgatgagaatagattaggtgcaatatatatatatatatgca-tgtgtgtgtgtgtgtgtgctgctgaaaacatt-
 || || || || ||| | |||||||| ||||||   ||||| ||||| |||||||||||||| || || | | | ||||| | |||||| |||||||||||||||    ||  ||     |   | | || |   | |   |   | | ||    |   |  ||||| |||||| |  |        |   | |    |  
ATCATTCGGGTCTGCACTTGAATTTGTTTGGTCACTTGATGGAGAATACGCTGTCAGAGAAAGCACCTCGAGGATAAAGATATACAGTAAAAATTTCCAGgtttgtactgcccactgccccttcttttaattatcgttgtacatcag-agtaggggtccttcaatgcaatgtgtggggctagaaaaatt-tagtaggtgtgc

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G124886_T02 (Zea mays), 5'ss of exon 12
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcc------cctcctttgtttctctctgatgagaatagattaggtgcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt
 || ||||| || ||| | |||||||| |||||| | ||||| ||||||||  |||||||||| || |||| | | ||||||| |||||| ||||||||||||||| ||       | |  |    ||||| ||| | | ||| | || | |    ||||| ||||    || | |  ||| | |       |  ||| |      
ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCAAGGATAAAGATTTACAGTAAAAATTTCCAGgtttgtttcaatataacatattccccttctccctggt-acaat-gttttgtttagttatatctataccgctgtaggcctgtctcta-acaaacacctgtaggg---

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G095348_T03 (Zea mays), 5'ss of exon 12
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgt--gtcccctcctttgtttctctctg-atgaga-atagattaggtgcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt
||| ||||| || ||| |||||||||| ||||||||||| || ||||||||  | || |||||||||||||   | ||||||||||||||    || ||||| |    ||    |   ||||||||||||  || |||   |  ||          |  |||  ||  |  |  | |   | ||  |  ||  ||| ||||   
GTCATTTGGATCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAGTAAATCATTTCAGgtattctagtttagtttattgtttctctctctatcagatgcaagtttctcatttcttccataattacgtaaacct-tacctctggtttggcatctgtaaac---

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G000645_T01 (Zea mays), 5'ss of exon 12
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcccctcct------ttgtttctctctg-atgag--aatagattaggtgcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt
 || ||||| || ||| |||||||||| ||||||||||| || ||||||||  | || |||||||||||||   | |||||||||| |||    || |||||   ||  |     |      |||||| ||| |  || |     |  || || |||||  |    || | | | |||   |   |     | |||  |||        
ATCATTTGGGTCTGCACTGGAATTTGTTTGGTCATCAGAAGGAGAATATGCAATTAGGGAAAGTACATCAAGAATAAAGATTTTCAATAAATCGTTTCAGgtacatggtctgctttagtttattgtttttctatatattaattgcttaatcagatgcaaatttctcatttct-tccatagttacctaaacat-tgcctctgg-------

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GRMZM2G141587_T05 (Zea mays), 5'ss of exon 12
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcc------cctcctttgtttctctctgatg-agaatagattaggtgcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt
 || ||||| || ||| | |||||||| |||||| | ||||| ||||||||  |||||||||| || || | | | ||||| | |||||| ||||||||||||||  ||       | |  ||   ||||  |||  | | |||   |||  || |    || | |  |                                      
ATCATTTGGGTCTGCACTTGAATTTGTTTGGTCAACTGATGGAGAATATGCCATCAGAGAAAGCACCTCGAGGATAAAGATATACAGTAAAAATTTCCAGgtttgcctcgatataacatatttcacttcttcctggagcataatctgttaactggagctgatcttttcag-------------------------------------

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA13G43680.2 (Glycine max), 5'ss of exon 12
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcccctc-----ctttgtttc-tctctgatgagaatagattaggtgcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt
||| |||||||| ||| |||||||||| ||||| || || || |||||||||||||||||||||||||||||| |||| |||||||| || |||||||||||||||      |      |||  |||| ||||| ||       |||   || |  | | || ||  |    || ||   ||  | | | |      |||||    
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttttaaacttcatttcctctctaatcttgtgtgatcttgttctttgtgta-atgaaccaacaagttcttgc-tatttcttaaaaggaaaa----

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA15G01680.1 (Glycine max), 5'ss of exon 12
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcccctc-----ctttgtttc-tctctgatgagaatagattaggtgcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt
||| |||||||| ||| |||||||||| ||||| || || || |||||||||||||||||||||||||||||| |||| |||||||| || |||||||||||||||      |      ||||||||| ||||| ||        ||   || |  | | || ||  |    || ||   ||  | | | |      |||||    
GTCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCTGAGGGAGAATATGCTGTCAGAGAAAGTACATCAAAGATTAAAATTTTCAGCAAAAATTTCCAGgtttgtacttttttaaaaactttgtttcctctctaatctcgtgcaatcttgttctgtgtgta-atgaaccaacaagttcttgc-tatttcttaaaaggaaaa----

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA08G22140.1 (Glycine max), 5'ss of exon 12
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcccctcctttgtttctctctgatgagaatagattaggt---gcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt
 || |||||||| ||| |||||||||| ||||| |||||||| || |||||||| |||||||||||||| |||||||| |||||||| || |||||||||||| |||   |    |  ||| ||||   || |   || | |  ||      |   |  |     |    |  |     | |   |    || | |||  || 
ATCATTTGGTTCAGCACTGGAATTTGTTTGGTCTTCAGATGGGGAGTATGCTGTAAGAGAAAGTACATCGAAGGTTAAAATTTTCAGCAAAAATTTCCAGgtt-gtgcttcactttcagttactctt--atcattttatactttgtcttatgacgaaagtgatggtgacaacctacaattctaaataatttgttaaaaggata

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA07G03890.1 (Glycine max), 5'ss of exon 12
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcccctcctttgtttctctctgatgagaatagattaggtgc-aatatatatatatatatgcatgtgtgtg---tgtgtgtgtgctgctgaaaacatt
 || |||||||| ||  |||||||||| ||||| |||||||| || |||||||| |||||||||||||| ||||| || |||||||| || |||||||||||| |||   | |  |  ||| ||||   || |   || | |  ||   || |   |  |     ||   |  |      | |   |    || | |||  || 
ATCATTTGGTTCAGCTCTGGAATTTGTTTGGTCTTCAGATGGGGAGTATGCTGTAAGAGAAAGTACATCGAAGGTCAAAATTTTCAGCAAAAATTTCCAGgtt-gtgcttcattatcagttactctt--atcattttatactttgtattaagacgaaagtgatggtgacagcctacaaattctaaataatttgttaaaaggat-

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: GLYMA07G03890.2 (Glycine max), 5'ss of exon 1
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcccctcctttgtttctctctgatgagaatagattaggtgc-aatatatatatatatatgcatgtgtgtg---tgtgtgtgtgctgctgaaaacatt
                         || ||||| |||||||| || |||||||| |||||||||||||| ||||| || |||||||| || |||||||||||| |||   | |  |  ||| ||||   || |   || | |  ||   || |   |  |     ||   |  |      | |   |    || | |||  || 
-------------------------GTTTGGTCTTCAGATGGGGAGTATGCTGTAAGAGAAAGTACATCGAAGGTCAAAATTTTCAGCAAAAATTTCCAGgtt-gtgcttcattatcagttactctt--atcattttatactttgtattaagacgaaagtgatggtgacagcctacaaattctaaataatttgttaaaaggat-

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT3G15980.2 (Arabidopsis thaliana), 5'ss of exon 12
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttg-tgtcccctcctttgttt--------ctctctgatgagaata-gatt----aggtgcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt---------------------
 |||||||| || |   |||||||||| |||||||| || || |||| ||| || ||||||||  |||||||| | ||||| |||||||| |||||||||||||| | | | |    | |  |        || | |  |  || || ||||     | || |  |  |  | ||   ||||  |         | |     ||| |  | |||                     
ATCTTTTGGGTCTGGCCTGGAATTTGTTTGGTCATCTGAGGGGGAATGTGCGGTTAGAGAAAGCTCATCAAAGATAAAGATATTCAGTAAAAATTTCCAGgtttgctattctcattatggccttactcatactattttgttggagtatgattctagggttgaagaaattgcagatgcttgca-atagagacagctattactggcttattatattaataaaaggtggtgttttcag

upper sequence: Vv09s0002g04810.t01 (Vitis vinifera), 5'ss of exon 12
lower sequence: AT1G79990.1 (Arabidopsis thaliana), 5'ss of exon 16
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcccctcctttgtttctctctgatgagaatagattaggtgcaatatatatatatat-atgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt-------------------------
||| ||||| || ||  | |||||||| |||||||| ||||| ||  |||||||||| |||||  |  ||||| | ||||| ||||| ||||||||||||||||||    |||  ||||   |  ||   |    |  |||||  |  ||    | | | | |  ||  |   | ||| | | ||   | |   || |  |                         
GTCATTTGGCTCTGCGCTAGAATTTGTTTGGTCATCTGATGGGGAGCATGCTGTCAGGGAAAGCTCGACAAAGATCAAGATCTTCAGCAAGAATTTCCAGgtttgtaattcct--tttggcacgttccttttccgactgattaactctaaagcttttgttttttgtgtcttattctgt-tatctgaaatacactaacctatgctgatacccttgtttaatttgcag

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|351030017|gb|FQ430759.1|FQ430759
EST:     CTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAG                         GAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGA
genomic: CTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcc ... catctttcagGAAAAGAGGAGTGTCCGACCAACATTTTCAGCTGAGCATATTTTTGGAGGA




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GTCTTTTGGTTCGGCATTGGAATTTGTATGGTCATCAGATGGTGAATATGCTGTCAGAGAAAGTACATCAAAGGTTAAGATTTTCAGTAAGAATTTCCAGgtttgtgtcccctcctttgtttctctctgatgagaatagattaggtgcaatatatatatatatatgcatgtgtgtgtgtgtgtgtgctgctgaaaacatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tttctctc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaataga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaaaca