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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaggccctgatactcaatttttttctttaattcttaggaactagtatcccacatgtttgatttataatcattttccattaccaatgaataatatagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGATGAATCATGGGTCCCG

Basic information

species Vitis vinifera
transcript Vv06s0004g06730.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g01370.1 (Oryza sativa), 3'ss of exon 2
gtaggccctgatactcaatttttttctttaattct-taggaactagtatc--ccacatgtttgattt--ataatcattttccattaccaatgaataatatagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGATGAATCATGGGTCCCG
 | |      |||  ||  ||    | | | | || | | || |  | ||    ||   |  ||| |    |      |   ||||  ||||    ||  |||||||||||||||||||| |||||||| ||||| |||||| | || || || || || |||  ||||
-tggtttaccatag-catcttggaccatcactgctatggtaattcatctcgttgacccatccgatctgagcatctgactgatattattaatgtcatatgcagGAGAATCAGCCACAGAACACACCATCAGAACCACGGTCATATCGAGAAGGACGAGTCCTGGCACCCG

upper sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os11g01340.3 (Oryza sativa), 3'ss of exon 2
gtaggccctgatactcaatttttttctttaattct-taggaactagtatc--ccacatgtttgattta--taatcattttccattaccaatgaataatatagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGATGAATCATGGGTCCCG
 |    |    ||| ||  ||    | | | | || |   || |  | ||    ||   |  ||| |    |     ||   ||||  ||||    ||  ||||| |||||||||||||| |||||||| ||||| |||||| | || |  || || || |||  ||||
-ttaatctatctac-catcttggaccatcactgctatgctaattcatctcgttgacccatccgatctgaccatctgattgatattaataatgtcatatgcagGAGGATCAGCCACAGAACACACCATCAGAACCACGGTCATATCGAGAGGGACGAGTCCTGGCACCCG

upper sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA18G06950.1 (Glycine max), 3'ss of exon 2
---------------------------gtaggccctgatactcaatttttttctttaattcttaggaactagtatcccacatgtttgatttataatcattttccattaccaatgaataat--atagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGATGAATCATGGGTCCCG
                           ||   |  ||    | ||||||||| | |  || |||  || |  |    |  || |   |    ||| ||||||  |  ||  ||| ||  |    |||||||| |||||||| ||||||||||| |||||||| |||||||| || |||||||||||||| || 
ggtcggttccttttagcaacttttcatgttcactttgtccttaaatttttttttatgtttgttaaaaaatctttggtctgatttaacaacc-taaccattttt-acaactcatggattttttgcaGGAGAATTAGCCACAGGACTCACCATCAGAACCATGGCCATGTTGAGAAGGATGAATCATGGGTTCC-

upper sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA11G27190.1 (Glycine max), 3'ss of exon 2
--------------gtaggccctgatactcaatttttttctt--taattcttaggaactagtatcccacatgtttgatttataatcatt----ttccattaccaatgaataa----tatagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGATGAATCATGGGTCCCG
                |     | ||  ||| ||| |   |   || || ||       |  |  |     || |||||| | | | |     ||  | |||  ||| |||     |  |||||||| |||||||| ||||||||||| |||||||| |||||||| || |||||||||||||| |||
gtcgattccttttatcaacttttcatgttcactttgtccttaaatatttttttttgttaaaaaatcttttggtctgatttgtcaacctcaccattttactactcatggatatcttttgcagGAGAATTAGCCACAGGACTCACCATCAGAACCATGGCCATGTTGAGAAGGATGAATCATGGGTTCCG

upper sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA02G39230.1 (Glycine max), 3'ss of exon 2
---gtaggccctgatactcaatttttttctttaattcttaggaactagtatcccacat-gtttgatttataatcatttt-ccattaccaatgaataatatagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGATGAATCATGGGTCCCG
    |||   ||||   | ||  |         |   || |||  | | | |  |  |  ||||||  || |  |         |    ||| ||  |  |||||||| ||||||||||||||||||||||||||||| ||  |||| || ||||| |||||||| || 
ctgttagcttctgag--taaacgtggaaaaaccacattttggatttggaaccaaattttatttgataaatgacaaccaaattgattttgatggattttgcagGAGAATTAGCCACAGAACTCACCATCAAAACCATGGACACATTGAGAAGGATGAGTCATGGGTTCCA

upper sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA14G37350.2 (Glycine max), 3'ss of exon 2
gtaggccctgatactcaatttttttctttaattcttaggaactagtatcccacatg--------tttgatttataatcattttccattaccaatgaataatatagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGATGAATCATGGGTCCCG
    |   | |   | || ||||  ||  | ||   |  | |   | |   |  ||        | ||||||   | |    |  |||    ||| ||  |  |||||||| ||||||||||||||||||||||| ||||| ||  |||| || |||||||| ||||| || 
----gttataactattaacttttgactaaacttgaaaaaatcacatttttgatgtggaaccaaatctgatttgagaaccaagttgatt-ttgatggattttgcagGAGAATTAGCCACAGAACTCACCATCAAAATCATGGACACATTGAGAAGGATGAATCCTGGGTTCCA

upper sequence: Vv06s0004g06730.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT2G29980.2 (Arabidopsis thaliana), 3'ss of exon 2
gtaggccct-gatactcaatttttttctttaattcttaggaactagtatcccacatgtttgatttataa--tcattttccattaccaat-gaataatatagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGATGAATCATGGGTCCCG
 ||       |||  | |   | |  |   ||  |      |   |        || | | |||||  |  | |  |   | ||  ||| |  | ||  |||||||| |||||| | || ||||| || |||||||| ||||||||||| || || |||||||| |||
-taaatttgagattgttagaatctgccccgaaaacgacattatatgacagatgtatttataatttacgaattgaaatgttaatattaattgggttatgcagGAGAATAAGCCACCGGACACACCACCAGAACCATGGCCATGTTGAAAACGACGAGTCATGGGTTCCG

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|352768954|gb|FQ468145.1|FQ468145
EST:     ATAGTGGGGCATCTCCTGCACTCTTGGATTCTTGTTCCCTACCATGGATG                         GAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGA
genomic: ATAGTGGGGCATCTCCTGCACTCTTGGATTCTTGTTCCCTACCATGGATGgtaggccctg ... aataatatagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGA
EST: gi|161712917|gb|FC062390.1|FC062390
EST:     ATAGTGGGGCATCTCCTGCACTCTTGGATTCTTGTTCCCTACCATGGATG                         GAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGA
genomic: ATAGTGGGGCATCTCCTGCACTCTTGGATTCTTGTTCCCTACCATGGATGgtaggccctg ... aataatatagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGA
EST: gi|294966337|gb|GW837588.1|GW837588
EST:     ATAGTGGGGCATCTCCTGCACTCTTGGATTCTTGTTCCCTACCATGGATG                         GAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGA
genomic: ATAGTGGGGCATCTCCTGCACTCTTGGATTCTTGTTCCCTACCATGGATGgtaggccctg ... aataatatagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGA
EST: gi|352773722|gb|FQ472504.1|FQ472504
EST:     ATAGTGGGGCATCTCCTGCACTCTTGGATTCTTGTTCCCTACCATGGATG                         GAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGA
genomic: ATAGTGGGGCATCTCCTGCACTCTTGGATTCTTGTTCCCTACCATGGATGgtaggccctg ... aataatatagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGA
EST: gi|351019690|gb|FQ439507.1|FQ439507
EST:     ATAGTGGGGCATCTCCTGCACTCTTGGATTCTTGTTCCCTACCATGGATG                         GAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGA
genomic: ATAGTGGGGCATCTCCTGCACTCTTGGATTCTTGTTCCCTACCATGGATGgtaggccctg ... aataatatagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tagtatcccacatgtttgatttataatcattttccattaccaatgaataatatagGAGAATCAGCCACAGAACTCACCATCAAAACCATGGTCATGTTGAAAATGATGAATCATGGGTCCCG
             gtttgat  putative branch site (score: 5)
           atgtttgatttataat  TA-rich tract