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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gggttgtttcgaattctgagcaattagcaatttactgccactgtaattgtgtatatgttgattttgaagattgagctttgtttgaaatgtctttgtgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG

Basic information

species Vitis vinifera
transcript Vv08s0040g00320.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os03g20420.3 (Oryza sativa), 3'ss of exon 2
gggttgtttcgaattctgagcaattagca-atttactgccactgtaattgtgtatatgttgat--tttgaagattgagctttgtttgaaatgtctttgtgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG
 || | ||||  |   |||  |   | |   |  | |     ||| ||    |   | ||  |  ||| |||||  || ||  || | |||||   | |||||||| |||||||||| || |||||||||||||||||||||||||| ||||||||||
cggct-tttcagaccatgacaacaaaacttgtagaatagacttgtgatctacttagttttagtacttttaagatgaagattc-ttggtaatgttact-tgtagGAGCTCAACCATGCCGGGGCTGGTGGACTGTGGGCAGAGCTTGTAAGCAACAGAG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g48750.1 (Oryza sativa), 3'ss of exon 3
--gggttgtttcgaattctgagcaattagcaatttactgccactgtaattgtgtatatgttgattttgaagattgagctttgtttgaaatgtctttgtgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG
        ||||  ||    || |  |    ||  | ||    ||        | |||       | | || ||||  | | ||||   | |||   ||||||||||||||||||| || ||||||||  |||||||||||||||| || |||||||
tgcaacattttcctatatatagtacctgcatatcaaatgaggttgcttcgacttctattccatgctgggagcttgaa-tatatttgtggt-tctacttgtagGAGATCAACCATGCTGGGGCTGGTGGGTTGTGGGCAGAGCTTGTAAGTAACAGAG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g03470.5 (Oryza sativa), 3'ss of exon 2
------------------------------------------gggttgtttcgaat--tctgagcaattagcaatttactgccactgtaattgtgtatatgttgattttgaagattga----gctttgtttgaaatgtctttg-------tgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG
                                          |  || | ||   |  ||    |   | ||| |||  |  ||     |   |   |  | |    |  | | || |    |   || | | ||| |||| |       ||||||| |||||||||||||||||||||||| | ||||| || ||||| || |||||||
gtaaaccgtaagatacatatagtaattttgttttgcacaattgcattatatcactttgtcctttcctctggcactttgttagcatgtctagaataagtcaggtagactacatgtttcactatgtcctgatggcaatttcttggctaatattgtagGAAATCAACCATGCAGGAGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os11g03730.2 (Oryza sativa), 3'ss of exon 2
--------------------------------------------------------------------gggttgtttcgaattctgagcaattagcaatttactgccactgtaattgtgtatatgttgattttgaagattgagctttgtt----tga-aatgtctttg--------tgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG
                                                                     ||   |||    ||  ||      ||    |||      |   |||  |  |  |   |||| |  |  ||   |  |||     ||| ||||   |||        ||||||| |||||||||||||| ||||||||| | ||||| || ||||| || |||||||
gtaagccgtgagacatatacagtaattctgtttttcacaattgcactgtatcactatatcctttcctctggcacttttttgttaggatgctcaagtgcattagcatgcccagaataatccaggta--gattatacatgttccaccatgtcctgatgataatgatcttggctaatattgtagGAAATCAACCATGCAGGGGCTGGTGGAATATGGGCTGAACTTGTTAGTAACAGAG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os11g03780.2 (Oryza sativa), 3'ss of exon 2
---gggttgtttcgaattctgagcaattagcaatttactgccactgtaattgtgtatatgttgattttgaagattgagctttgtttgaaatgtctttgt-gtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG
     ||||   |   || |   || |||    ||  |||| | |  |||  | || ||    ||  |  | | | |   |   | ||   ||     |   |||| || |||||||| |||||||||||  | ||||| ||||||||||| |||||||
cttttgttggcccttgttatattca-ttacatgttcgctgcaatttgaatattctagatt---atcctcgacagtcatgataactggatcggtgaacatcacagGAAATTAACCATGCCGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os12g03530.1 (Oryza sativa), 3'ss of exon 2
--gggttgtttcgaattctgagcaattagcaatttactgccactgtaattgtgtatatgttgattttgaagattgagctttgtttgaaatgtctttgtgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG-------------------------------------
   | | |       ||   |   ||||    || ||||| |    |||  | || ||  || |  | |    |||    |   | |     | || |  |||| || |||||||| |||||||||||  | ||||| ||||||||||| ||||||                                      
tttgttagcgcttgctttatattcattatgtgttcactgcaatctgaatattctagattatgctcgtcagtcatgataactagatcagtgaacattat--agGAAATTAACCATGCTGGAGCTGGTGGGATATGGGCGGAGCTTGTCAGTAACAGAAGTAACTCTCAGTTTGATAAACATTCCTCATGGAAGCT

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G006130_T06 (Zea mays), 3'ss of exon 2
gggttgtttcgaattctgagcaattagcaatttactgccactgtaattgtgtatatgttgattttgaagattgagct--ttgtttgaaatgtctttgtgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG
        |       |     ||  | |  |    |   || |  ||    | || |  ||    |||| | | |    | |     ||| | |  |||||||||||||||||||||||||||||||  | ||||||||||||||||| |||||||
-------gtgaggcagtagtttatcggtagatgctagttcctatgttttaccacatat-aatcagaaagaataatccaaatatactgcatggcctactgtagGAGATCAACCATGCAGGAGCTGGTGGCATATGGGCAGAGCTTGTCAGTAACAGAG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G097277_T01 (Zea mays), 3'ss of exon 1
-----------------------------------------------------------gggttgtttcgaattctgag--caattagcaattt-actgccactgtaattgtgtatatgttgattttgaagattgagctttgtttgaa-atgtctttg--------tgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG
                                                                  ||| ||||||||   |||||     |||   |  |  ||   |  ||  |||  |||     ||||||| |  |   | |   | || ||||        | ||||||||||||||||| |||||||||||  ||||| ||||||| || ||||||||||
gtgcgagtcagattacaattgtgctatcagttagaagcagcagttcatctgctggcacatcaacagttcaaattctgaaaccaatttttgtttttgatttctatgctctgatggttatcctgaga--aaagattgtgggtaactcggttaagtttttggttgtacctatagGAGATCAACCATGCTGGAGCTGGTGGGTTGTGGTCAGAGCTCGTAAGCAACAGAG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G077299_T01 (Zea mays), 3'ss of exon 2
gggttgtttcgaattctgagcaattagcaat-ttactgccactgtaa----ttgtgtatatgt------tgattttga-agattgagctttgtttgaaa----------tgtctttg-tgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG
| |       || ||||  | |   | ||   ||| ||    |  ||    ||||  || |        || |    | | | |  |   ||||   |           ||  ||   || ||||||||||||||||||| ||||||||  | ||||| || ||||| || |||||||
gtgagacagtgatttcttggtacacaccagccttattgatcttacaaggatttgtccatgtaagcggaatggtccaaacacacttggtcgtgttctcagataaccaggttgctttcactgcagGAGATCAACCATGCAGGGGCTGGTGGCATATGGGCTGAACTTGTTAGTAACAGAG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G27490.1 (Glycine max), 3'ss of exon 1
-gggttgtttcg-aattctgagcaattagcaatttactgccactgtaattgtgtatatgttgat---tttgaagattgagctttgtttgaaatgtctttgtgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG
 |  |  ||||  ||| |   |  |||   || |   ||  |   |  ||   ||| |||| |    ||| || | ||| |   |||| |||     ||||| |||||||||||||||| || ||||||||| |||||||||||||||| | ||||||||
agtttcctttcacaatgcatggttatttttaactagatgatatctttttttattat-tgttaaaatgtttcaaaagtgatcaaagttttaaac----ttgtgcagGAGATCAACCATGCCGGTGCTGGTGGATTGTGGGCAGAGCTTGTTAACAACAGAG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA03G00630.1 (Glycine max), 3'ss of exon 1
-------------gggttgtttcg--aattctgagcaattagcaatttactgccactgtaattgtgtatatgttgattttgaagattgagctttgtttgaaatgtctttgtgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG
               ||||||| |   ||| | |   || |    |||   | |  |  | || |   | ||||       |      |   |||||  |    |||||  | |||||||||| |||||||||||||| ||| ||||||| |||||||| || || ||||
gtagtctactaaattgttgttttgtagatttttaagtatgatttttttgaagtccattaagtttttagtctgttttagcgcatttcaaaaaattgttcaa----tcttt-cgcagGAGATCAATCATGCAGGAGCTGGGGGATTGTGGGCTGAGCTTGTGAGGAATAGAG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA19G30150.1 (Glycine max), 3'ss of exon 2
-------------------gggttgtttcgaat---tctgagcaattagcaatttactgccactgtaattgtgtatatgttgattttgaagattgagctttgtttgaaatgtctttgtgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG
                      |||||| | ||   | | ||     || ||  |  |   | ||| ||| |    |||||   |||| | ||  ||||    |||     |||||| | |||| ||||| |||||||||||||| ||| ||||||| |||||||| || || ||||
gtataatttaattaattactttttgtttggtatatttttaagagtccaggaagattttag-agtgtgattctagg-atgttttgtttgca-ataaagct--aattgttggatctttg-gcagGAAATCAATCATGCAGGAGCTGGGGGATTGTGGGCTGAGCTTGTGAGGAATAGAG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G10740.1 (Arabidopsis thaliana), 3'ss of exon 2
gggttgtttcgaattctgagcaattagcaatttactgccactgtaattgtgtatatgttgattttgaagattgagctttgtttgaaatgtctttgt-gtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG
 | |||||   |||  |  |   | |   |  |  |  || ||||       || |||| |  |  |  ||  | |||| | ||   | | ||  |  ||||||||||||||||| || || |||||| | ||||| || ||||| ||||||||||
-gtttgtt---aatgttacggtctcaaatagatctttgcaatgtacgca---atgtgttcaaatcaatcat-aaactttatatgctctatgttcattatagGAGATCAACCATGCTGGTGCCGGTGGATTATGGGCCGAACTTGTTAGCAACAGAG

upper sequence: Vv08s0040g00320.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S317_21V6.1 (Physcomitrella patens), 3'ss of exon 1
-----------------------------------------------------------gggttgtttc-gaattctgagcaattagcaatttactgccactg-taa---ttgtgtat-atgttgattttgaagattga---gctttgtttgaaatgtc--tttg---tgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG
                                                              |  |||| ||| |   |  |  |      | | | | | || | |   |    ||| ||| |  | || | |  | |   || | |||  | || |   ||||   |  |||||||||| ||||| |||| |||||| || ||||||||||||||    ||  |||
gtacgacgaacattcgatgatcacacctccaaatcagttctcaaaacatttttttcctgaaatcatttctgaaattgaattacctcatgcataaattcaattgatgaggctcacatatcatgcttgtatttagggctaataagcctcgttgaatatttacatttgctttacagGAGATCAATCATGCGGGAGATGGTGGCCTTTGGGCAGAGCTTGTTCAGAATCGAG

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|294965127|gb|GW836958.1|GW836958
EST:     AAGGGCTTGGCCGGAAGATGCCAGAAACATTGTTTGGATTATTCTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAAC
genomic: AAGGGCCTGGCCGGAAGATGCCAGAAACATTGTTTGGATTATTCTTTGAGgtgaattttt ... ctttgtgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAAC
EST: gi|161718771|gb|FC066348.1|FC066348
EST:     AAGGGCTTGGCCGGAAGATGCCAGAAACATTGTTTGGATTATTCTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAAC
genomic: AAGGGCCTGGCCGGAAGATGCCAGAAACATTGTTTGGATTATTCTTTGAGgtgaattttt ... ctttgtgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAAC
EST: gi|161712575|gb|FC062177.1|FC062177
EST:     AAGGGCTTGGCCGGAAGATGCCAGAAACATTGTTTGGATTATTCTTTGAG                         GAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAAC
genomic: AAGGGCCTGGCCGGAAGATGCCAGAAACATTGTTTGGATTATTCTTTGAGgtgaattttt ... ctttgtgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

attgtgtatatgttgattttgaagattgagctttgtttgaaatgtctttgtgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG
          tgttgat  putative branch site (score: 4)
                                          tgtcttt  putative PPT
      tatatgttgatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gggttgtttcgaattctgagcaattagcaatttactgccactgtaattgtgtatatgttgattttgaagattgagctttgtttgaaatgtctttgtgtagGAGATCAACCATGCAGGAGCTGGTGGACTGTGGGCAGAGCTTGTCAGCAACAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGGTGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCTT
gggttgt
- - - - - - - - - - - - - - - - -actgcca