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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TTCCAGCCTTGTCCCCTTGTGCAACTACACTTCCAGTGTTTCTTGCAGTTGGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatagcatgaatattggaatctaacgcatttttctttccttgattcacttgtttcttgacacttcttctagcaaacatagaacagagcatctgtg...

Basic information

species Vitis vinifera
transcript Vv06s0009g01580.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g01580.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os01g17020.1 (Oryza sativa), 5'ss of exon 2
TTCCAGCCTTGTCCCCTTGTGCAACTACACTTCCAGTGTTTCTTGCAGTTGGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatagcatgaatattggaatctaacgcatttttctttccttgattcact-tgtttcttgacacttcttctagcaaacatagaacagagcatctgtg
| || || || || || |||||||| || ||||||||||||||||| ||||| ||||| |||||||||||| | ||||| || || ||||| || || ||||    |   | |    | ||   ||    |||||  |  ||   |     ||  |   |    | |||| || |   |  |  |  |||        | |
TACCTGCATTATCACCCTGTGCAACAACTCTTCCAGTGTTTCTTGCTGTTGGCAATTCATCCTCCATGATGATCCTTGCGATCATTGTGCTCCTCTTTAGgtgggtacccctttc-cactgttttcagttgcattgcttgttttctaccgaacaataaattgctatacttttttttatagccgcaacacattatgaaagag

upper sequence: Vv06s0009g01580.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G078895_T02 (Zea mays), 5'ss of exon 2
TTCCAGCCTTGTCCCCTTGTGCAACTACACTTCCAGTGTTTCTTGCAGTTGGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatagcatgaatattggaatctaacgcatttttctttccttgattcac-ttgtttcttgacacttc-ttctagcaaacatagaac-agagcatctgtg---
| || || || || ||||||||||| || |||||||| |||||||| ||||| || |||||||| |||||| | ||||| || || ||||| || ||||||| |  |         | ||  | || |  |  ||||| ||   ||  ||     |     || | | | | || |  |   | |      |  |  | |||    
TACCTGCATTATCACCTTGTGCAACAACTCTTCCAGTTTTTCTTGCTGTTGGCAACTCTTCCTCAATGATGATTCTTGCAATCATTGTGCTCCTCTTCAGgtcttcaccc------tctttcactccactgtttttttattgtatttgttggtactaccaattcaaattgcattatcacgtcctttctgttattgggtttgttaac

upper sequence: Vv06s0009g01580.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA02G44180.1 (Glycine max), 5'ss of exon 2
TTCCAGCCTTGTCCCCTTGTGCAACTACACTTCCAGTGTTTCTTGCAGTTGGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatagcatgaatattggaatctaacgcatttttctttccttgattcacttgtttcttgacacttcttctagcaaacatagaaca-gagcatctgtg-
| || || ||||| |||||||| || ||||| ||||| |||||||| ||||| ||||| || ||||||||||||||||| || ||||| || || |||||||||  ||    |   |   | ||| | |    |||| ||     |  ||   |  |||    ||     | ||      |      || | |||| | || 
TCCCTGCATTGTCTCCTTGTGCTACAACACTCCCAGTATTTCTTGCTGTTGGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtatttatcaatttccttaagcaatatgatt--ttttcctcctgctattttgttctttttcaaacgtgcatacttttcttctgcttccatgtgcatgtttgg

upper sequence: Vv06s0009g01580.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA14G04600.1 (Glycine max), 5'ss of exon 2
TTCCAGCCTTGTCCCCTTGTGCAACTACACTTCCAGTGTTTCTTGCAGTTGGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatagcatgaatattggaatctaacgc-atttttctttccttgattcacttgtttcttgacacttcttctagcaaacatagaacagagcatctgtg
|||| || ||||| |||||||| || ||||| || || |||||||| ||||| ||||| || ||||||||||||||||| || ||||| || || |||||||||  ||     |  |||    || ||| |  || | |  ||  ||| |  |   || ||  |  | |     ||  ||| ||      |   | ||   
TTCCTGCATTGTCTCCTTGTGCTACAACACTCCCGGTCTTTCTTGCTGTTGGAAATTCCTCTTCCATGATGGTGCTTGCCATCATAGTACTACTATTCAGgtattaatcaatggcctatgattatttaaagtgatatgttatttgttggtaaaacggtgtca-gtgattatcaataataaaaattctgatgttgaccttaa

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|71866987|gb|DT016042.1|DT016042
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|33407593|gb|CF213220.1|CF213220
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|110387190|gb|EC951840.1|EC951840
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|351036192|gb|FQ464037.1|FQ464037
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|33408182|gb|CF213809.1|CF213809
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|30256230|gb|CB972073.1|CB972073
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CCCCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|110724908|gb|EE101145.1|EE101145
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|351013366|gb|FQ425071.1|FQ425071
EST:     GGAAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|161721045|gb|FC069647.1|FC069647
EST:     GGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCA
genomic: GGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTG-CTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCA
EST: gi|30128699|gb|CB914038.1|CB914038
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACG
EST: gi|110389090|gb|EC953903.1|EC953903
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|110693601|gb|EE069985.1|EE069985
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|351031955|gb|FQ460212.1|FQ460212
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|161717560|gb|FC066258.1|FC066258
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|161716448|gb|FC064936.1|FC064936
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CAC-ATTACTGTGATGAC-TCACTGGTG-CTCTCTCAT-CTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|110370920|gb|EC934542.1|EC934542
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|352795616|gb|FQ480204.1|FQ480204
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|351026323|gb|FQ428335.1|FQ428335
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|161715249|gb|FC064867.1|FC064867
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|351018509|gb|FQ424616.1|FQ424616
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCCCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|351024928|gb|FQ433345.1|FQ433345
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|110388694|gb|EC953471.1|EC953471
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|33407504|gb|CF213131.1|CF213131
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|33408270|gb|CF213897.1|CF213897
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTTTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|349824308|gb|FQ417719.1|FQ417719
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|351033350|gb|FQ446582.1|FQ446582
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCCCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|110723263|gb|EE100373.1|EE100373
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|110686866|gb|EE063774.1|EE063774
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGGCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
EST: gi|349833056|gb|FQ416434.1|FQ416434
EST:     GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAG                         CACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG
genomic: GGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatag ... gattttgcagCACCATTACTGTGATGACCTCACTGGTGGCTCTCTCATTCTACGGTGCCAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TTCCAGCCTTGTCCCCTTGTGCAACTACACTTCCAGTGTTTCTTGCAGTTGGGAATTCTTCCTCCATGATGGTGCTTGCTATTATAGTGCTGCTTTTCAGgtatcgatagcatgaatattggaatctaacgcatttttctttccttgattcacttgtttcttgacacttcttctagcaaacatagaacagagcatctgtg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gcaaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaacaga