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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTACCTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggactttatcataattgctattgtttcatgcatcatttcttgcaaatgtgataatcatatttagaatgtttttcttttcatgattttcag

Basic information

species Vitis vinifera
transcript Vv05s0094g01380.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os01g23680.3 (Oryza sativa), 5'ss of exon 3
CAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTACCTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggactttatcataattgctattgtttcatgcatcatttcttgcaaatgtgataatcatatttagaatgtttttcttttcatgattttcag-------------
| | |||||  |||| || || || |||||| |||| |||||||| |||||||| ||| | |||| |||||||||||| || ||||| ||  | ||||||||| || || || ||| |  | | |     ||  |||||||||| |   |   ||  | ||    | ||| |||| ||    | | | | ||              
CCGGGGTGCTTTAAGGGCTGAAAAGCCAGAGTTGCTCACTGTAATTTTACCTCAAAGTCTAAAGAAGCAACCTCCTGAAAGTCAAGAGCTTTTATCTAAAgtaagatttcatgatatt--ccagtcccgaattgatcatttcttacctgttccatttttat---caaaatcttttactagaga-gctctacatggaccagtttctc

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G022090_T02 (Zea mays), 5'ss of exon 2
CAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTACCTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggactttatcataattgctattgtttcatgcatcatttc----ttgcaaatgtga--taatcatatttagaatgtttttcttttcatgattttcag---
||| ||||| |||||||| || ||||||||||||||||||||||| |||||||| ||  | |||| ||| |||||||| |||||||||||  ||||||||||| || ||  |  || || ||||| |   ||| | | |       || | | | |||  |  |||| |||  | | |  ||  || ||   || |      
CAGGGGTGCTCTAAGAGCTGAAAAACCAGAGCTGCTTACTGTAATTTTACCTCAAAGCCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaattcctggtattt-ctattctgaaatgaaacttcctgacgtttctattatgaattggtcat-tttctagtctacttagttccagacttgttgctat

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G081653_T02 (Zea mays), 5'ss of exon 4
CAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTACCTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggactttatcataattgctattgtttcatgcatcatttc----ttgcaaatgtga--taatcatatttagaatgtttttcttttcatgattttcag---
 || || ||  ||||||| || || |||||| ||||||||||||| |||||||| ||| | |||| ||| |||||||| |||||||||||  ||||||||||| || |  || ||| || || || |    ||   | |||     || | | | | |  |  |||| |||  | |     | || ||  ||  |       
TAGGGGCGCTTTAAGAGCTGAAAAGCCAGAGTTGCTTACTGTAATTTTACCTCAAAGTCTAAAGAAGCAGCCTCCTGAAAGCCAAGAACTGTTGTCTAAAgtaagaatccatgatattt-ctgttctgaagtgagactttttgatatttctattataaactggtcat-tttgtagtcaaacttttctcccgacctgttactt

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA17G00330.1 (Glycine max), 5'ss of exon 4
CAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTACCTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggactttatcataattgc---tattgtttcatgcatcatttcttgcaaatgtgataatcatatttagaatgtttttcttttcatgattttcag----
  |||||||  |||| ||||||||||||||| ||||||| || || |||||||| ||||| |  |  || ||||||||||| || |||||| |||| |||||| |  || |   |  ||     |||  ||||    |   ||   |  || |||    ||  | |||  ||     || ||    || ||| ||     
TCGAGGTGCTTTAAGGGCAGAGAAACCAGAGTTGCTTACAGTTATATTACCTCAAAGTTTAAGCAAACAGCCTCCTGAGAGTCAGGAACTATTGTCCAAAgtaaggtttaaaagtttttatatatatgctttctcaaaggtttgaatataagtgtttatatactttttgaaaaaaggtttttcatttgctttacatattg

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GLYMA07G40350.2 (Glycine max), 5'ss of exon 4
CAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTACCTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggactttatcataa----ttgctattgtttcatgcatcatttcttgcaaatgtgataatcatatttagaatg----tttttcttttcatgattttcag
| |||||||  |||| ||||||||||| ||| |||||||||| || |||||||| ||||| |  |  || ||||| ||||| || || ||| |||| |||||| |  || |   | |    ||  |||  |||| |  |   ||   |  || |||    ||  | |||  ||      ||||  ||||| | |  |    
CCGAGGTGCTTTAAGGGCAGAGAAACCGGAGTTGCTTACTGTTATATTACCTCAAAGTTTAAGAAAACAGCCTCCAGAGAGTCAGGAGCTATTGTCCAAAgtaaggtttaagtttgaagtttttatatgctttcttaaaggtttggatataagtgtttatatactttttgaaaaaaggattttcattttctttacatatt-

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT3G59870.1 (Arabidopsis thaliana), 5'ss of exon 4
CAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTACCTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggacttta---tcataattg-ctattgtttcatgcatcatttcttgcaaat-gtgataatcatatttagaatgtttttcttttcatgattttcag----------------------------------------------------
 |||||||| || |||||||||| ||||||||| ||||| || ||||||||||| |||||||| | |||||||||||| ||||| ||||||||||| |||||| ||   ||   |||  |||  || ||  | ||       | ||||  | || |  ||  |||  | ||   || | |   | | |  ||  ||                                                      
AAGAGGTGCACTTAGAGCAGAGAGACCAGAGCTTCTTACAGTTATCTTACCTCAAAGTTTGAAAAAGCAACCTCCTGAAAGCCAGGAACTACTGTCAAAAgtaagagactagtttcaagattttcttttactccaactgcattgtcttaaatatcgaaatgttcacttctatc-tgctataaatctgaatatcatccattcttggctatgctatagttcaactgagtctcctttgtaatgtctgcaacag

upper sequence: Vv05s0094g01380.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: AT2G43945.1 (Arabidopsis thaliana), 5'ss of exon 4
CAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTACCTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggactttatcataattgctattgtt----tcatgcatcatttcttgcaaatgtgataatcatatttagaatgtttttcttttcatgattttcag
|||||||||  | |||||||||| ||||||||||||||| |||||  |||| || |||||||| |  |||||||||||||||||||||||| ||||||||||| |     |    |  | | |  ||     || ||   | | |||     ||   ||    |  | | |  ||| || || |     |||| |||
CAGAGGTGCATTGAGAGCAGAGAGACCAGAGCTGCTTACAGTAATTCTACCCCAAAGTTTGAAAAAACAACCTCCTGAGAGCCAAGAACTATTGTCTAAAgtaagcaaaaactgcatgttcaaaagtcagaatcttgttgcgtctctgatttattacatctgaaactcttgtctgtattgctatggtcaatttacag

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|18459061|gb|BM437339.1|BM437339
EST:     CTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAA                         GTGAAAAATGTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAA
genomic: CTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggacttt ... tgattttcagGTGAAAAATGTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAA
EST: gi|71870474|gb|DT019529.1|DT019529
EST:     CTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAA                         GTGAAAAATGTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAA
genomic: CTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggacttt ... tgattttcagGTGAAAAATGTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAA
EST: gi|30320624|gb|CD003886.1|CD003886
EST:     CTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAA                         GTGAAAAATGTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAA
genomic: CTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggacttt ... tgattttcagGTGAAAAATGTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAA
EST: gi|110420391|gb|EC986663.1|EC986663
EST:     CTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAA                         GTGAAAAATGTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAA
genomic: CTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggacttt ... tgattttcagGTGAAAAATGTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAA
EST: gi|30321162|gb|CD004424.1|CD004424
EST:     CTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAA                         GTGAAAAATGTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAA
genomic: CTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggacttt ... tgattttcagGTGAAAAATGTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAA
EST: gi|110374681|gb|EC939602.1|EC939602
EST:     CTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAA                         GTGAAAAATGTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAA
genomic: CTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggacttt ... tgattttcagGTGAAAAATGTAATAGAGAAGCCTTACAATGATCATCTTCCTTTGATAGAA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CAGAGGTGCGCTAAGAGCAGAGAAACCAGAGCTGCTTACTGTAATCTTACCTCAGAGTTTGAAGATGCAACCTCCTGAGAGCCAAGAACTACTGTCTAAAgtaggactttatcataattgctattgtttcatgcatcatttcttgcaaatgtgataatcatatttagaatgtttttcttttcatgattttcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAC