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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acttgtcattagcacatgcattgctgatacttgagctgtaaaaagactatgtgctgataaattgtcaattgatcactgcgttattgcttttctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCATTTTGCACATAAAATAAACAGCTTTGACACAGCTCCTAGGAAGTTGTTGG

Basic information

species Vitis vinifera
transcript Vv06s0004g04930.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GRMZM2G174644_T01 (Zea mays), 3'ss of exon 8
------------------------acttgtcattagcacatgcattgctgatact--tgagctgtaa-aaagactatgtgctgataaattgtcaattgatcactgcgttattgcttttctg-ttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCATTTTGCACATAAAATAAACAGCTTTGACACAGCTCCTAGGAAGTTGTTGG
                           | |   || |   ||   |    ||||   | || || ||    |   |  |  |     ||     ||  |       | |  | |||   ||  ||||| | |||   ||||||  ||  ||  |||||||||| | ||||||||| || || ||||| |||||||||||||| ||||| || |||| |||| ||||||
gtcgtactttctttcactttctgctactatggataacgtgtgttatatatatacccataagatgcaatggtggtcacatatttgcggatgactgatgcactgaactggtcatacttgattgactgcagATCTGGAGAGTTGCTCCTGCCCCACAGGGCGACAAGTATCAGTACACACACTTCGCACACAAAATAAACAGCTTCGACACGGCACCTAAGAAGCTGTTGG

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA12G06690.1 (Glycine max), 3'ss of exon 8
-----acttgtcattagcacatgcattgctgatacttgagctgtaaaaagactatgtgctgataaattgtcaattgatcactgcgttattgcttttctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCATTTTGCACATAAAATAAACAGCTTTGACACAGCTCCTAGGAAGTTGTTGG
     | |  |  ||  |  || | |||||||||  |  |   | |    ||||  | |    || ||    ||  ||       |  |    ||| |  ||||||||||||||||||||||||||||  ||   |||||||||||||| || |||||||| ||||||||||||||||||||||| || ||||| ||||||||||
aataaagtaatttttctcttatactttgctgatatattgg---tgaggtcacta-ataccttaaagttccttatc-attgtcatttcctctgatttattatgcagGTTTGGCATGTTGCTGATGTTCCCCAGAATGACAAATTTCAGTATACACATTTTGCTCATAAAATAAACAGCTTTGACACTGCCCCTAGAAAGTTGTTGG

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA11G14770.1 (Glycine max), 3'ss of exon 8
--acttgtcattagcacatgcattgctgatacttgagctg-taaaaagactatgtgctgataaattgtcaattgatcactgcgttattgcttttctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCATTTTGCACATAAAATAAACAGCTTTGACACAGCTCCTAGGAAGTTGTTGG
  | |  |  ||  |  || | |||||||||  | | ||| | | || |||| || |    || ||    ||   |  |        || |||| |  ||||||||||||||||||||||||||||  ||   |||||||||||||| || |||||||| ||||||||||||||||||||||| || ||||  ||||||||||
gaagtaattttt--cttatactttgctgatatattaactggtgacaacacta-gtaccttaaagttccttatcattgtcatttcctctgattttattctgcagGTTTGGCATGTTGCTGATGTTCCCCAGAATGACAAATTTCAGTATACACATTTTGCTCATAAAATAAACAGCTTTGACACTGCCCCTAAAAAGTTGTTGG

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA15G04210.1 (Glycine max), 3'ss of exon 8
acttgtcattagcacatgcattgctgatacttgagct-gtaaaaagacta-tgtgctgataaattgtca--attgatcactgcgttattgcttttctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCATTTTGCACATAAAATAAACAGCTTTGACACAGCTCCTAGGAAGTTGTTGG
  ||  | ||   || |   |||||||||| | |  | || ||   | ||      | ||  ||  |    |||| | | |   |   |  |||| |  ||||||||||||||||||||||||||||  ||   || ||||| ||||| ||  | ||||||||||||||||||||||||||||| || ||||  || |||||||
--tttacttttatactttt-ttgctgatacatcaattagtgaaggcattaacaaagttatttataattgttattggt-attttatctgtaattttattctgcagGTTTGGCATGTTGCTGATGTTCCAAAGAATGATAAATTCCAGTATACATACTTTGCACATAAAATAAACAGCTTTGACACTGCCCCTAAAAAATTGTTGG

upper sequence: Vv06s0004g04930.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT5G59420.1 (Arabidopsis thaliana), 3'ss of exon 8
--------------------------------------------------acttgtcattagcacatgcattgctga--tacttgagctgtaaaaagactatgtgctgataaattgtcaattgatcactgcgttattgcttttctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCATTTTGCACATAAAATAAACAGCTTTGACACAGCTCCTAGGAAGTTGTTGG
                                                     ||| ||||     ||||    ||   || |   |    | |  |  |   |  | |    |||   ||   |  |   | | || ||| | |  | ||||| |||||| | |||||||| ||  |   |||||| |||||||||||||| ||||| || || ||||||||||| |||||||| |||   ||| | ||||
gtatgtcgtttcttttccgttttacatttttactggcctttgctagggttctgtgtgattatactttgcaaccttgggttattgttgaccaacattgtttgactttttagcggttgcttatgcttgtcgttggtttttcttgttttcttcagGTGTGGCATTTGGCTGATGTCCCCAAAAACGACAACTTTCAGTACACTCACTTTGCTCACAAGATAAACAGCTTCGACACAGCGCCTGCTAAGCTCTTGG

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|22012903|gb|BQ797937.1|BQ797937
EST:     AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAG                         GTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
genomic: AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAGgttaatctca ... tctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
EST: gi|33405066|gb|CF210693.1|CF210693
EST:     AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAG                         GTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
genomic: AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAGgttaatctca ... tctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
EST: gi|110716660|gb|EE091846.1|EE091846
EST:     AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAG                         GTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
genomic: AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAGgttaatctca ... tctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
EST: gi|33405148|gb|CF210775.1|CF210775
EST:     AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAG                         GTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
genomic: AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAGgttaatctca ... tctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
EST: gi|110688435|gb|EE066987.1|EE066987
EST:     AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAG                         GTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
genomic: AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAGgttaatctca ... tctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
EST: gi|110378376|gb|EC943506.1|EC943506
EST:     AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAG                         GTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
genomic: AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAGgttaatctca ... tctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
EST: gi|110705363|gb|EE082145.1|EE082145
EST:     AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAG                         GTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
genomic: AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAGgttaatctca ... tctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
EST: gi|30252533|gb|CB970084.1|CB970084
EST:     AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAG                         GTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT
genomic: AACCATGTGACATTGAAGGGGAGCCTCTTACAGGCACAGATCTGAAGGAGgttaatctca ... tctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

actatgtgctgataaattgtcaattgatcactgcgttattgcttttctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCATTTTGCACATAAAATAAACAGCTTTGACACAGCTCCTAGGAAGTTGTTGG
                                      ttgcttttct  CT-rich tract
           ataaattgtcaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acttgtcattagcacatgcattgctgatacttgagctgtaaaaagactatgtgctgataaattgtcaattgatcactgcgttattgcttttctgttgcagGTTTGGCATGTTGCTGATGTTCCTGAGGGCGACAAATTTCAGTACACTCATTTTGCACATAAAATAAACAGCTTTGACACAGCTCCTAGGAAGTTGTTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - - cacatgc
- - - - - - - - - - -tgctgat
- - - - - - - - - - - - - - - - - - - -aaaaaga
- - - - - - - - - - - - - - - - - - - - - - - -tatgtgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcactgc