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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatggactgtaactgcttgtttccagctataaattgtctgtctttcaacttcaatctcccacttccttaaggctcatgtctacaacctaaacgaagtcacttctgtttattcttttgctctctgggtttttcttttcataatggaagtgtttttgctgtttagcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTATGATTCCCACACTGATACCTTCCAGGCCAG

Basic information

species Vitis vinifera
transcript Vv06s0009g02700.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g02700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g17390.1 (Oryza sativa), 3'ss of exon 1
gtatggactgtaactgcttgtttccagctataaattgtctgtctttcaacttcaatctcccac-ttccttaaggctcatgtctacaacctaaacgaagtcacttctgtttattcttttgctctctgggtttttcttttcataatggaagtgtttttgctgtttagcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTATGATTCCCACACTGATACCTTCCAGGCCAG
                                               |  |    ||       || ||| ||| || | ||| |||             |||| |  ||||  ||  ||   | |      ||||           ||  |||||| |  || ||||  ||| |||||||| || ||| | |||||||| ||||||||||| |||||||||| ||||| |||||||||||  || ||
---------------------------------------------ctagatgagctcatttgtgtttctttaggatcttatcttcaa-------------acttttagttatgtttgagcaaccggaaccaatctt----------gaggctttttgtttgtttgcagCATGGGCATGTTGGATTCATGATGTCATGCTACGATGCAGAGCTCAGCTATGATTTCCACAGTGATACCTTCCGTGCAAG

upper sequence: Vv06s0009g02700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA14G04080.1 (Glycine max), 3'ss of exon 1
gtatggactgtaactgcttgtttccagctataaat---tgtctgtctttcaacttcaatctcccac-ttccttaaggctcatgtctacaacctaaacgaagtcacttctgtttattcttttgctctctgggtttttcttttcataatggaagtgtttttgctgtttagcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTATGATTCCCACACTGATACCTTCCAGGCCAG
                  | |       ||| |||   | | ||  |||     |  |   |  |  ||| || | |||    || | |   | ||  || | | || |   |      | |       | || || | ||        |  |   |||     |  ||||| |||||||||||| ||||||||||||||||||||||| ||||||||||||||| | |||| ||| ||||||||||||||
-----------------gtatcaatgattatgaatccctttgtgctttttggtattgaaaacttatattctttcatgctaccttcaatag--tgaaacaaattagtttttcatggcaactagaatagaagattgttgtgttttctcacaagttacatttttcact--gcagAATGGCCATGTTGGATTTATGTTATCATGCTATGATGCTGAGCTTAGCTATGATCCTCACAATGACACCTTCCAGGCCAG

upper sequence: Vv06s0009g02700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA02G44660.1 (Glycine max), 3'ss of exon 1
gtatggactgtaactgcttgtttccagctataaattgtctgtctttcaacttcaatctcccacttccttaaggctcatgtctacaacctaaacgaagtcacttctgtttattcttttgctctctgggtttttcttttcataatggaagtgtttttgctgtttagcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTATGATTCCCACACTGATACCTTCCAGGCCAG
         ||| |   |  |    | |       ||  | | || | | |  || ||   | |   | | |    |  |  |  |   |||| || |   || |   |  |   | |       | || || | ||  |     ||||    ||  |   | ||||| |||||||||||| |||||||| |||||||||||||| ||||||||||||||| | |||||||| ||||||||||||||
---------gtatcaa-tcatcatgaacccctttgtgctt-ttttcctattgaaaacttatattctatcatg--ctaccttcaatagtgaaacaaattagttttttcatggtaactagaatagacgattattgtgtttttctcacaagttacatttttcact-gcagAATGGCCATGTTGGATTTATGTTGTCATGCTATGATGCTGAGCTTAGCTATGATCCTCACACTGACACCTTCCAGGCCAG

upper sequence: Vv06s0009g02700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA07G36360.1 (Glycine max), 3'ss of exon 1
gtatggactgtaactgcttgtttccagctataaattgtctgtctttcaacttcaatctcccacttccttaaggctcatgtctacaacctaaacgaagtcacttctgtttattcttttg---ctctctgggtt-tttcttttcataatggaagtgtttttgctgttta----gcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTATGATTCCCACACTGATACCTTCCAGGCCAG
|||||   | |   |        ||   | |        ||  |||| | |  ||  |   |  | | |     |  |  ||||||   | |  || ||| || | |  |||    ||   | |  |||||| | | || ||| ||  |     |||||||||||      | ||| ||| ||| |||| ||  ||||||| ||||||||||| || |||||||||||| | || ||||||||||| || |||||
gtatgtgatatgtataaacaaacccttttgtgg------tgcttttctattgaaaatttatatctacct-----tgctagctacaa---atataaaatcagttgtttgaatttcaatggaacacagtgggttgtgttttctcacaa--gttacatttttgctgttggtggtgtagAATGGTCATATTGGATTCTTGTTATCTTGCTATGATGCTGAACTTAGCTATGATCCACAAACTGATACCTTTCAAGCCAG

upper sequence: Vv06s0009g02700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA20G08260.1 (Glycine max), 3'ss of exon 1
gtatggactgtaactgcttgtttccagctataaattgtctgtctttcaacttcaatctcccacttccttaaggctcatgtctacaacctaaacgaagtcacttctgtttattcttttgctctctgggtt-tttcttttcataatggaagtgtttttgctgttta----gcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTATGATTCCCACACTGATACCTTCCAGGCCAG
|||||   | |   |        ||   | |      | | | ||  ||    ||| |     | ||||       |    || ||    ||| |  |  |||   |||    |      |  |||||| | | || ||| ||  |  |  |||||||||||      | ||| ||| |||||||| || ||| |||| ||||||||||| || |||||||||||| | |  ||||||||||| || |||||
gtatgtgatatgtataaacaaacccttttgttgtacttttctattgaaaa---aatatatatataccttgctagctacaaatataa----aaccagtttgcttgaattt-caatgggaaacagtgggttgtgttttctcacaa-agttgcatttttgctgttggtggtgtagAATGGTCATGTTGGATTCATGCTATCTTGCTATGATGCTGAACTTAGCTATGATCCGCGAACTGATACCTTTCAAGCCAG

upper sequence: Vv06s0009g02700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G32560.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatggactgtaactgcttgtttccagctataaattgtctgtctttcaacttcaatctcccacttccttaaggctcatgtctacaacctaaacgaagtcacttctgtttattcttttgctctctgggttt--ttcttttcataatggaagtgtttttgctgttt-agcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTATGATTCCCACACTGATACCTTCCAGGCCAG
                                                                             |    |   | |||||  |||  || |         ||||||| | ||| |||  ||    |  |||  |   | |||||| ||    |||||| ||| ||||| || || ||||| |||||||||||||| ||||| ||||||||| | ||||| ||||| ||||| |||||
----------------------------------------------------------------------------gtaatcatttcataaacatagttgctcca-------tttttgctttatggatttgattaaagtactaagaggcttttttttggtgaaagagcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCGGAGCTCAGCTATGATACTCACACGGATACGTTCCAAGCCAG

upper sequence: Vv06s0009g02700.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G26850.1 (Arabidopsis thaliana), 3'ss of exon 1
gtatggactgtaactgcttgtttccagctataaattgtctgtctttcaacttcaatctcccacttccttaaggctcatgtctacaacctaaacgaagtcacttctgtttattcttttgctctctgggtttttcttttcataatggaagtgtttttgctgttt-agcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTATGATTCCCACACTGATACCTTCCAGGCCAG
                                                                    |||   |    |  | || | | |   ||  ||| |  ||||||||||       |||||||  ||     || ||   |  |||||| |||   |||||| ||| ||||| || || ||||| |||||||||||||| ||||| ||||||||  |  ||||| |||| || || || ||
-------------------------------------------------------------------gtaatcatagatttcataaac-atatatagctactccattttattcttta------tgggtttgactaaa-gtagtgagggcttttttggtgtaagagcagAATGGACATGTAGGGTTCATGTTGTCATGCTATGATGCTGAGCTCAGCTATGACACTGACACTAATACTTTTCAAGCTAG

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|22013912|gb|BQ798946.1|BQ798946
EST:     CTCTTGAGACTGGCAGGTTTTGGTTCCCTGCACAGGTTTACAATCGTGAG                         AGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTAT
genomic: CTCTTGAGACTGGCAGGTTTTGGTTCCCTGCACAGGTTTACAATCGTGAGgtatggactg ... tgtttagcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTAT
EST: gi|34542214|gb|CF510446.1|CF510446
EST:     CTCTTGAGACTGGCAGGTTTTGGTTCCCTGCACAGGTTTACAATCGTGAG                         AGTGGCCATGTTGGGTTTATGTTATCATGCTATGATGCTGAGCTTAGCTAT
genomic: CTCTTGAGACTGGCAGGTTTTGGTTCCCTGCACAGGTTTACAATCGTGAGgtatggactg ... tgtttagcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTAT
EST: gi|33409673|gb|CF215300.1|CF215300
EST:     CTCTTGAGACTGGCAGGTTTTGGTTCCCTGCACAGGTTTACAATCGTGAG                         AGTGGCCATGTTGGGTTTATGTTATCATGCTATGATGCTGAGCTTAGCTAT
genomic: CTCTTGAGACTGGCAGGTTTTGGTTCCCTGCACAGGTTTACAATCGTGAGgtatggactg ... tgtttagcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cttttgctctctgggtttttcttttcataatggaagtgtttttgctgtttagcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTATGATTCCCACACTGATACCTTCCAGGCCAG
                                      tttttgct  CT-rich tract
               tttttcttttcataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatggactgtaactgcttgtttccagctataaattgtctgtctttcaacttcaatctcccacttccttaaggctcatgtctacaacctaaacgaagtcacttctgtttattcttttgctctctgggtttttcttttcataatggaagtgtttttgctgtttagcagAGTGGCCATGTTGGCTTTATGTTATCATGCTATGATGCAGAGCTTAGCTATGATTCCCACACTGATACCTTCCAGGCCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT