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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tattcttaattagcattaagcaattatacaatggattattgtatcgccgaagctcataatcaaaattatatttcatcaactcttttttggtggtcttcagAATTTTGGCAAACCGGCAATCAGCTCAGAGGTCAAGGGTGAGGAAGCTACAATACATTTCAGAGCTTGAGCGGAGCGTAACATCTTTACAA

Basic information

species Vitis vinifera
transcript Vv19s0014g01780.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g01780.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os02g14910.1 (Oryza sativa), 3'ss of exon 1
tattcttaattagcattaagcaattatacaatggattattgtatcgccgaagctcat-aatcaaaattatatttcatcaactcttttttggtggtcttcagAATTTTGGCAAACCGGCAATCAGCTCAGAGGTCAAGGGTGAGGAAGCTACAATACATTTCAGAGCTTGAGCGGAGCGTAACATCTTTACAA
| | | | |      | ||        |  |  |   |||  |  | | || |   |  |    |  | || |||    |  ||||  |  || | ||||| |||||||||||| |||| || || ||| ||||||||||||| ||| | || ||||| || ||||||||||| ||||| ||  || | || 
tgtgcatgaaccatttgaaattcaccaaagaccgtgaattcgagtgacaaatcgtgttgaatttagctgtaattctggcatgctttgcttctg-ttttcagGATTTTGGCAAACAGGCAGTCGGCGCAGCGGTCAAGGGTGAGAAAGTTGCAGTACATCTCTGAGCTTGAGCGCAGCGTCACCACTCTCCAG

upper sequence: Vv19s0014g01780.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G052102_T01 (Zea mays), 3'ss of exon 1
tattcttaattagcattaagcaattatacaatggattattgtatcgccgaagct-cataatcaa---aattatatttcatcaactcttttttggtggtcttcagAATTTTGGCAAACCGGCAATCAGCTCAGAGGTCAAGGGTGAGGAAGCTACAATACATTTCAGAGCTTGAGCGGAGCGTAACATCTTTACAA
     | | |     |||     |||   |||  ||  |  || | |  | |   ||||    |   | |     |  |||   |  | ||   |||  ||||| || ||||||||| |||| || |||||||||||| | ||||||||||| || ||||| || |||||||| |||||||| ||   | | || 
----atcactcgtgcttagtttcttaattaataaatagtcatagctcatacgtaacatagctgactgagtagcgatcgatcgttttctgttccttgggtttcagGATATTGGCAAACAGGCAGTCGGCTCAGAGGTCACGAGTGAGGAAGCTGCAGTACATCTCGGAGCTTGAACGGAGCGTCACCAGTCTCCAG

upper sequence: Vv19s0014g01780.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G027976_T01 (Zea mays), 3'ss of exon 1
-tattcttaattagcattaagcaattatacaatggattattgtatcgccgaagctcataatcaaaattatatttcatcaactcttttttggtggtcttcagAATTTTGGCAAACCGGCAATCAGCTCAGAGGTCAAGGGTGAGGAAGCTACAATACATTTCAGAGCTTGAGCGGAGCGTAACATCTTTACAA
 |   |    |    ||  ||| |     | |||  |   || |      |  || | ||  |   ||   || |  | | | | ||           ||| ||  | || |||||||| ||||||||||||||  ||||||||||||| || ||||| || ||||| ||||| ||||| ||| |  | || 
gtgagcccggtcg--atcgagctagcccgccatgcgtgcatgcaaaatgcagactga-aacgagcctttgcttgcgccgaatttcttc----------cagGATCCTTGCCAACCGGCAGTCAGCTCAGAGGTCGCGGGTGAGGAAGCTGCAGTACATCTCCGAGCTCGAGCGCAGCGTCACAACACTGCAG

upper sequence: Vv19s0014g01780.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G170079_T02 (Zea mays), 3'ss of exon 1
---------------------------------------tattcttaattagcattaagcaattatacaatggattattgtatcgccgaagctcataatcaaaattatatttc--atcaactcttttttggtggtctt----------cagAATTTTGGCAAACCGGCAATCAGCTCAGAGGTCAAGGGTGAGGAAGCTACAATACATTTCAGAGCTTGAGCGGAGCGTAACATCTTTACAA
                                           | |||||     |  |||   | ||||||  ||  |    |   |  |    ||||| |  ||    |    |   |  |      || || |||          ||| ||  | || |||||||| || |||||||||||  ||||||||||||| || ||||| || ||||| ||||| ||||| ||| |  | || 
gtgagcccgatcgaacgagctagcacaccatgcgtgcgccgcccgtaattg----tgcgcaggcaaacaatgcgtttctcctgcag-gcggtaggtaatccatcttgatctgtggactgaaacgcggccggcgggcttgaaattctggcagGATCCTTGCCAACCGGCAGTCGGCTCAGAGGTCGCGGGTGAGGAAGCTGCAGTACATCTCCGAGCTCGAGCGCAGCGTCACAACACTGCAG

upper sequence: Vv19s0014g01780.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G170079_T01 (Zea mays), 3'ss of exon 1
---------------------------------------tattcttaattagcattaagcaattatacaatggattattgtatcgccgaagctcataatcaaaattatatttc--atcaactcttttttggtggtctt----------cagAATTTTGGCAAACCGGCAATCAGCTCAGAGGTCAAGGGTGAGGAAGCTACAATACATTTCAGAGCTTGAGCGGAGCGTAACATCTTTACAA---------
                                           | |||||     |  |||   | ||||||  ||  |    |   |  |    ||||| |  ||    |    |   |  |      || || |||          ||| ||  | || |||||||| || |||||||||||  ||||||||||||| || ||||| || ||||| ||||| ||||| ||| |  | ||          
gtgagcccgatcgaacgagctagcacaccatgcgtgcgccgcccgtaattg----tgcgcaggcaaacaatgcgtttctcctgcag-gcggtaggtaatccatcttgatctgtggactgaaacgcggccggcgggcttgaaattctggcagGATCCTTGCCAACCGGCAGTCGGCTCAGAGGTCGCGGGTGAGGAAGCTGCAGTACATCTCCGAGCTCGAGCGCAGCGTCACAACACTGCAGGTACGTATA

upper sequence: Vv19s0014g01780.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA13G34770.1 (Glycine max), 3'ss of exon 2
tattct--taattagcattaagcaattatacaatggattattgtatcgccgaagctcataatcaaaattatatttcatcaactcttttttggtggtcttcagAATTTTGGCAAACCGGCAATCAGCTCAGAGGTCAAGGGTGAGGAAGCTACAATACATTTCAGAGCTTGAGCGGAGCGTAACATCTTTACAA
|| |    | |||    |||   |  || |  |   |   |||| | |    |   || | | || || || ||| ||        |||   ||     |||||||||||| ||| ||||||||||||||||||||||||| || ||||| ||||||||||| ||||||||  ||||||||||| |||| || 
taattaagtgattgattttatatacgtacaagaattaaacttgtgtagatata--ccaaactaaatataattttttattgttatgatttgtttgcaaaccagAATTTTGGCTAACAGGCAATCAGCTCAGAGGTCAAGGGTAAGAAAGCTGCAATACATTTCTGAGCTTGAAAGGAGCGTAACAACTTTGCAG

upper sequence: Vv19s0014g01780.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA12G35650.1 (Glycine max), 3'ss of exon 3
-tattcttaattagcattaagcaattatacaatggattattgtatcgccgaagctcataatcaaaattatatttcatcaactcttttttg-gtggtcttcagAATTTTGGCAAACCGGCAATCAGCTCAGAGGTCAAGGGTGAGGAAGCTACAATACATTTCAGAGCTTGAGCGGAGCGTAACATCTTTACAA
 ||| | | |||    |||   |  || |  |   |    || |  |   |    |  ||  |||  ||  || |      | || ||||  ||     |||||||||||| ||| ||||||||||||||||||||||||| || ||||||||||||||||| || || ||  ||||||||||| |||| || 
gtatacgtgattgattttatatacgtagaagaattaaacgtgcagtgtgtatataccaaactaaatctaatttgctattgttattatttgtatgcaaaccagAATTTTGGCTAACAGGCAATCAGCTCAGAGGTCAAGGGTAAGAAAGCTACAATACATTTCTGAACTCGAAAGGAGCGTAACAACTTTGCAG

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|30129365|gb|CB914704.1|CB914704
EST:     TCCACCGCCTCTAACGGCGATTCCATCATCGATCCAAAGCGGGTTAAGAG                         AATTTTGGCAAACCGGCAATCAGCTCAGAGGTCAAGGGTGAGGAAGCTACA
genomic: TCCACCGCCTCTAACGGCGATTCCATCATCGATCCAAAGCGGGTTAAGAGgtaaaaaaaa ... tggtcttcagAATTTTGGCAAACCGGCAATCAGCTCAGAGGTCAAGGGTGAGGAAGCTACA
EST: gi|30134000|gb|CB919338.1|CB919338
EST:     TCCACCGCCTCTAACGGCGATTCCATCATCGATCCAAAGCGGGTTAAGAG                         AATTTTGGCAAACCGGCAATCAGCTCAGAGGTCAAGGGTGAGGAAGCTACA
genomic: TCCACCGCCTCTAACGGCGATTCCATCATCGATCCAAAGCGGGTTAAGAGgtaaaaaaaa ... tggtcttcagAATTTTGGCAAACCGGCAATCAGCTCAGAGGTCAAGGGTGAGGAAGCTACA
EST: gi|161720173|gb|FC065488.1|FC065488
EST:     TCCACCGCCTCTAACGGCGATTCCATCATCGATCCAAAGCGGGTTAAGAG                         AATTTTGGCAAACCGGCAATCAGCT
genomic: TCCACCGCCTCTAACGGCGATTCCATCATCGATCCAAAGCGGGTTAAGAGgtaaaaaaaa ... tggtcttcagAATTTTGGCAAACCGGCAATCAGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gccgaagctcataatcaaaattatatttcatcaactcttttttggtggtcttcagAATTTTGGCAAACCGGCAATCAGCTCAGAGGTCAAGGGTGAGGAAGCTACAATACATTTCAGAGCTTGAGCGGAGCGTAACATCTTTACAA
                                                tcttc  CT-rich tract
                aaaattatatttcatc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tattcttaattagcattaagcaattatacaatggattattgtatcgccgaagctcataatcaaaattatatttcatcaactcttttttggtggtcttcagAATTTTGGCAAACCGGCAATCAGCTCAGAGGTCAAGGGTGAGGAAGCTACAATACATTTCAGAGCTTGAGCGGAGCGTAACATCTTTACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - -ttaagca
- - - - - - - - - - - - - - caatgga
- - - - - - - - - - - - - - - - - - - - - - - - - -gctcata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaatta
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatcaa