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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gaattatgttttaaggaggaaactgtgtgctgaccaaaactgcttggttgttcatttaaatcatggcttattatgccagctttattcttgtgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGG

Basic information

species Vitis vinifera
transcript Vv13s0067g00710.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G000923_T01 (Zea mays), 3'ss of exon 2
gaattatgttttaaggaggaaactgtgtgctgaccaaaactgcttggttgttcatttaaatcatggcttatta-tgccagctttattcttgtgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGG---------
    | ||   |  | |     |||| || |    |   ||| |  ||    || ||| | ||   || |  | |    |  | ||| |  | ||  ||      ||| | ||| ||||| ||||| | ||||||||| ||| | ||||| ||||||||||||||||| ||| |||||||||| ||||| |||||  | ||         
-tcctgtgcgctttgaatttg-ctgtctgttt-ttatctctggtatgtgaaacaattacaacac--ctgacaagtatttgtctcattttcatctttcgcg-----acaagAAGGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCG

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G000923_T02 (Zea mays), 3'ss of exon 2
gaattatgttttaaggaggaaactgtgtgctgaccaaaactgcttggttgttcatttaaatcatggcttatta-tgccagctttattcttgtgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGG------------
    |  | ||| |    |   |||| || |    |   ||| |  ||    || ||| | ||   || |  | |    |  | ||| |  | ||  ||      ||| | ||| ||||| ||||| | ||||||||| ||| | ||||| ||||||||||||||||| ||| |||||||||| ||||| |||||  | ||            
--tgtgcgctttgaatttg---ctgtctgttt-ttatctctggtatgtgaaacaattacaacac--ctgacaagtatttgtctcattttcatctttcgcg-----acaagaagGGGATGCCAGTGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAGGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGTCAGCCGCGT

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G465333_T01 (Zea mays), 3'ss of exon 2
-gaattatgttttaaggaggaaactgtgtgctgaccaaaactgcttggttgttcatttaaatcatggcttattatgccagctttattcttgtgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGG---
  |  |      |  | |     |||| || |    |   ||| |  ||    || ||  |     |  |||    | ||  ||  | |  | || | |   || ||| | ||| ||||| || || | ||||||||| ||| | ||||| |||||||||||||| || ||| |||||||||| ||||| |||||  | ||   
taacctgcaccctttgaatttg-ctgtctgttt-ttatctctggtgtgtgaaacaattgcagacctg--tatctgacaagtattggtgtcattttcatcttcagGACAAGAAGGGGATGCCAGCGGCAAGTCAAAGCAAAGCAGGAGTGAGAAGAAGAGCCGCAAAGCCATGCTGAAGCTTGGCATGAAGCCCATCACTGGTGT

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G27570.1 (Glycine max), 3'ss of exon 2
-gaatta-tgttttaaggaggaaactgtgtgctgaccaaaactgcttggttgttcatttaaatcatggcttattatgccagctttattcttgtgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGG---
 |  | | ||  ||||    |  | | | |     |   |||||    |          | |||     | |  ||   ||    |||  ||||||     | || ||  | ||| |||||   ||||||||| ||||||| | | |||||||||||||| |||||||||||| | || ||||||||||||||  |  ||||   
tgtctgaatgagttaatattgttattttctttctgcatgaactga--agccacatggacagatc-caattcacaatcttagaggaatt--tgtgttctattgcagGACTAGAAGGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGTGAAAAGAAGAGTCGCAAGGCAATGCTTAAACTTGGAATGAAACCTGTAACAGGTGT

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G30540.1 (Glycine max), 3'ss of exon 2
gaattatgttttaaggaggaaactgtgtgctgaccaaaactgcttggttgttcatttaaatcatggcttattatgccagctttatt-cttgtgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGG---
   || ||| | |  |||  ||   ||   |   ||       |    ||    |  |||  || | |     | | | ||       |||||||     | || ||  | ||| |||||   ||||||||| ||||||| | | |||||||||||||| |||||||||||| | || ||||||||||||||  |  ||||   
---ttctgtctgactgagttaatattgatattttcattgtacatgaactgaagctacaaag-atagttccaattacaatctcaggaatttgtgttctattgcagGACTAGAAGGTGATGCATCTGGTAGGTCGAAGCAGACCAGAAGTGAAAAGAAGAGTCGCAAGGCAATGCTTAAACTTGGAATGAAACCTGTCACAGGTGT

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA19G30550.1 (Glycine max), 3'ss of exon 2
-gaatta-tgttttaaggaggaaactgtgtgctgaccaaaactgcttggttgttcatttaaatcatggcttattatgccagctttattcttgtgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGG---
 |  | | ||  ||||    || | | | |    ||   |||||    | |    |  || |||     |||  ||  |||    |||  ||||||     | || ||  | ||| |||||   ||||||||| ||||||| | | |||||||||||||| |||||||||||| | || ||||||||||||||  |  ||||   
tgtctgactgagttaatattgatattttctttgtacatgaactga--agctacaaagatagatc-caatttacaatctcagaggaatt--tgtgttctattgcagGACTAGAAGGTGATGCATCTGGTAGGTCGAAGCAGACCAGAAGTGAAAAGAAGAGTCGCAAGGCAATGCTTAAACTTGGAATGAAACCTGTCACAGGTGT

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G27580.1 (Glycine max), 3'ss of exon 2
-gaattatgttttaaggaggaaactgtgtgctgaccaaaactgcttggttgttcatttaaatcatggcttattatgccagctttattcttgtgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGG---------
   | |    ||||          |   || |      |  ||  | |  ||| |  | |   ||    |   ||  | |  | |||  | |  ||   |   |  || | ||| |||||   ||||||||| ||||||| | | || ||||||||||| |||||||||||| | || ||||||||||||||  |  ||||         
aatactgcacttta---------tttcatgttatttttacatgaattgaagttaaaatgatggatacaattcaatctctgagtaatttgtattctatttaaatgt-caagAAGGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGCGAAAAGAAGAGTCGCAAGGCAATGCTCAAACTTGGAATGAAACCTGTCACAGGTGTCAGTCG

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA03G27580.2 (Glycine max), 3'ss of exon 2
gaattatgttttaaggaggaaactgtgtgctgaccaaaactgcttggttgttcatttaaatcatggcttattatgccagctttattcttgtgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGG------------
  | |    ||||          |   || |      |  ||  | |  ||| |  | |   ||    |   ||  | |  | |||  | |  ||   |   |  || | ||| |||||   ||||||||| ||||||| | | || ||||||||||| |||||||||||| | || ||||||||||||||  |  ||||            
--actgcacttta---------tttcatgttatttttacatgaattgaagttaaaatgatggatacaattcaatctctgagtaatttgtattctatttaaatgt-caagaagGTGATGCATCTGGTAGGTCCAAGCAGACCAGAAGCGAAAAGAAGAGTCGCAAGGCAATGCTCAAACTTGGAATGAAACCTGTCACAGGTGTCAGTCGTGT

upper sequence: Vv13s0067g00710.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: PP1S122_100V6.1 (Physcomitrella patens), 3'ss of exon 2
-----gaattatgttttaaggaggaaactgtgtgctgaccaaaactgcttggttgttcatttaaat--catggcttattatgccagctttattcttgtgttaagcagGAGAACAGGGAGGAGAT---GCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGG---
     |||     || |||     |     ||    |  ||       |   |     |  ||| |  |||    ||| ||  |    | ||       || | ||   | |   | ||  | |    ||   |||| |||||||||||||||| |||| ||||||||| | ||||| |||   |||||||| ||||||||  | || ||   
gtgaagaagcccattctaactcccatcacttgctgcgttcagtgaatttcaatcaacaagataattttcattttatataatctccaactcatgtgaagtttgaacatctgcagGCGAAGACGGTCTGACTGCAGGTAAGTCAAAGCAGAGCCGTGGTGAGAAGAAGAGCAGGAAGGCCATGCAAAAGCTTGGCATGAAACCAGTCCCCGGCGT

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|30306354|gb|CB983148.1|CB983148
EST:     GGATGAAGATGATGTTGAAG                         GAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAA
genomic: GGATGAAGATGATGTTGAAGgttagctaat ... tgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAA
EST: gi|30253437|gb|CB970988.1|CB970988
EST:     CGAAGGTGACAAGGATGAAGATGATGTTGAAG                         GAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAA
genomic: CGAAGATGACAAGGATGAAGATGATGTTGAAGgttagctaat ... tgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAA
EST: gi|30302985|gb|CB979779.1|CB979779
EST:     TGATGATGATGAGGATGACGAAGATGANANTCATGAAGATGATGTTGAAG                         GAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAA
genomic: TGATGATGATGAGGATGACGAAGATGACAAGGATGAAGATGATGTTGAAGgttagctaat ... tgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggttgttcatttaaatcatggcttattatgccagctttattcttgtgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGG
                                       ttcttgt  CT-rich tract
     ttcatttaaatcat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gaattatgttttaaggaggaaactgtgtgctgaccaaaactgcttggttgttcatttaaatcatggcttattatgccagctttattcttgtgttaagcagGAGAACAGGGAGGAGATGCTAGTGGTAGGTCAAAGCAGAGCCGTAGTGAAAAGAAGAGCCGCAAGGCAATGTTGAAGCTTGGAATGAAACCCATTCCAGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - aggaaac
- - - - - - - - - - - -tgtgtgc
- - - - - - - - - - - - - - - - -ccaaaac
- - - - - - - - - - - - - - - - - - - - tgcttgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tcatggc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tatgcca