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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctttatgaatcttcttttccataaacgaaacagagtgatttttttgtttttttttttttaaatttctaatctgatattatttcttaattttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGG

Basic information

species Vitis vinifera
transcript Vv01s0010g01740.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G426306_T01 (Zea mays), 3'ss of exon 2
-tttctttatgaatcttcttttccataaacgaaac-agagtgatttttttgtttttttttttttaaatttctaatctgatattatttcttaattttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGG
 |     | ||| |  |  | |      |||||   |||| |       |||    |        ||||   |||  |   |  ||  ||  | | ||  ||||  || |  |  | ||  | |  || || ||||||||||| ||||| ||||||||||||||||| ||||| || ||||| |||||||| |
gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtccgccgagaattctgaattcgtggtgtttaatt--tctattgtagGTCAAATTAATCAGAATCGAGTGCAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAATGGCG

upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G003076_T05 (Zea mays), 3'ss of exon 1
-tttctttatgaatcttcttttccataaacgaaac-agagtgatttttttgtttttttttttttaaatttctaatctgatattatttcttaattttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGG---------
 |     | ||| |  |  | |      |||||   |||| |       |||    | |      ||||   |||  |   |  ||  ||  | | ||  |||| ||| |  |  | ||  | |  || || ||||||||||| ||||| ||||||||||||||||| ||||| || ||||| ||||| || |         
gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtctgccgagaattctgaattcgcggtgtttaatt--tctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCGGTGAGCCAG

upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G003076_T02 (Zea mays), 3'ss of exon 1
-tttctttatgaatcttcttttccataaacgaaac-agagtgatttttttgtttttttttttttaaatttctaatctgatattatttcttaattttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGG
 |     | ||| |  |  | |      |||||   |||| |       |||    | |      ||||   |||  |   |  ||  ||  | | ||  |||| ||| |  |  | ||  | |  || || ||||||||||| ||||| ||||||||||||||||| ||||| || ||||| ||||| || |
gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcactgtaacgtctgccgagaattctgaattcgcggtgtttaatt--tctattgcagGTCCAATTAATCAGAATCGAGTGTAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG

upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G055462_T01 (Zea mays), 3'ss of exon 2
-tttctttatgaatcttcttttccataaacgaaac-agagtgatttttttgtttttttttttttaaatttctaatctgatattatttcttaattttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGG
 |     | ||| |  |  | |      |||||   |||| |        ||  | |        ||||   |||  |   |  ||  ||  | | ||  |||| ||| |  |  | ||  | |  || || ||||||||||| ||||| ||||||||||||||||| ||||| || ||||| ||||| || |
gtgctggtttgatttgtggtcttgtgggacgaattgagagaggcggcacagtaatgtccgccgagaattctgaattcgcggtgtttaatt--tctattgcagGTCCAATTAATCAGAATCGAGTGCAGGGTGCCAGAGTATGGATGGACAACGCAGAAGGTGTTCCATTTTCTAAACTTCCTTGTGAACGGCG

upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT1G14530.1 (Arabidopsis thaliana), 3'ss of exon 1
-----------------------------------------------------------tttctttatgaatctt---cttttccataaacgaaacagag----tgatttttttgttttttttttttta-------aatttctaatctgat---attatttcttaattttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGG
                                                           ||    |  |||  ||   | |||    | | ||||  |||    |  || || | |    | ||  |||       ||   ||||  ||||   | | |   ||  ||||||  || ||||| ||||  | |||||||||||||| ||||| ||||| ||||| ||||||||||| || || |||||||||||| |||| || || |
gtaccgtttacttgtccttctggttttgaattgggattggaattagggaatgtgttgatttggaatcggaagattaggcatttaaggatatgaaattgaggaaatagttgttgtatggagtgttgattagagaaaaaaaccctaaattgattaaagtttcatttgtttttttgtagATTCAATTGGTAAGAATACAATTGAGAGTTCCAGAATATGGCTGGACGACGCAGAAGGTCTTTCATTTTCTCAATTTCATGGTTAACGGAG

upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AT2G02180.1 (Arabidopsis thaliana), 3'ss of exon 1
tttctttatgaatcttcttttccataaacgaaacagagtgatttttttgtttttttttttttaaatttctaatctgatattatttcttaattttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGG
                        ||             |||||  ||| |  || ||   | || ||    |   || |||| | | | |||  |  || ||||||| ||  | |||||||||||||| || || ||||||||||| ||||| ||||| || ||||||||||||||| | || ||||| |
-----------------------gtacgtttcgtttctggatttgattgatgattcttcgatgaaattggtgtaacatcttatgtttgattttggtttagATTCAACTTGTGAGAATACAATTGAGAGTTCCTGAATATGGTTGGACGACGCAAAAGGTCTTTCACTTTCTCAATTTCGTTGTTAATGGAG

upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EDP05347 (Chlamydomonas reinhardtii), 3'ss of exon 2
tttctttatgaatcttcttttccataaacgaaacagagtgatttttttgtttttttttttttaaatttctaatctgatattatttcttaattttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGG---------
                             |  |      || |  |  |||        |   ||     |  |||| | || ||             |||| |||||| | ||| | ||  || | || ||||||||||| |||||||| ||||||||||||||| |||| || | | |||||  || |          
-----------------------------gtgagtacacgagtcgtcggttccgccaactcggaaggctcacactgagaataattg---------cgcagGTACAACTGCTGCGGCTGCAGCTGCGCGTGCCAGAGTATGGCTGGACCACCCAGAAGGTGTTCCACCTTCTAAACTGCTTGGTGTCTGTGCTGCGCTGCT

upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ23006 (Selaginella moellendorffii), 3'ss of exon 1
tttctttatgaatcttcttttccataaacgaaacagagtgatttttttgtttttttttttttaaatttctaatctgatattatttcttaattttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGG
                        ||   ||| | || |  |||| | || |||| | ||    |||  |     |  ||  |  |    | | |   || | |||||  | |||||  |  |  | ||||| |||||||| ||||||||||||||||| ||||| || || |||||||| || ||||| |
-----------------------gtatg-gaatccgactagttttctggtcttttctatt---gattcttgg---ggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACCACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG

upper sequence: Vv01s0010g01740.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: EFJ30530 (Selaginella moellendorffii), 3'ss of exon 1
tttctttatgaatcttcttttccataaacgaaacagagtgatttttttgtttttttttttttaaatttctaatctgatattatttcttaattttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGG
                           | | ||    |  | ||| ||| | |||| | ||   |||        |  ||  |  |    | | |   || | |||||  | |||||  |  |  | ||||| |||||||| ||||| ||||||||||| ||||| || || |||||||| || ||||| |
-------------------------gtatggaatccggctagtttgttggtcttttctatt--gattctcgg---ggaatcgtggcgatttctctcgcagATACAACTCATCCGGATCGAGATTCGCGTCCCCGAGTATGGCTGGACGACGCAGAAGGTCTTCCATTTGCTGAATTTCCTTGTAAATGGAG

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|349816624|gb|FQ399613.1|FQ399613
EST:     TCTTTCATGTCCTCGCCGCTCTCTATGGAATCGTCGCTGCCGTCGCTCTG                         GTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACG
genomic: TCTTTCATGTCCTCGCCGCTCTCTATGGAATCGTCGCTGCCGTCGCTCTGgtactcttac ... ttttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACG
EST: gi|349823327|gb|FQ402526.1|FQ402526
EST:     TCTTTCATGTCCTCGCCGCTCTCTATGGAATCGTCGCTGCCGTCGCTCTG                         GTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACG
genomic: TCTTTCATGTCCTCGCCGCTCTCTATGGAATCGTCGCTGCCGTCGCTCTGgtactcttac ... ttttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACG
EST: gi|161718299|gb|FC064760.1|FC064760
EST:     TCTTTCATGTCCTCGCCGCTCTCTATGGAATCGTCGCTGCCGTCGCTCTG                         GTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACG
genomic: TCTTTCATGTCCTCGCCGCTCTCTATGGAATCGTCGCTGCCGTCGCTCTGgtactcttac ... ttttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACG
EST: gi|294965642|gb|GW837241.1|GW837241
EST:     TCTTTCATGTCCTCGCCGCTCTCTATGGAATCGTCGCTGCCGTCGCTCTG                         GTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACG
genomic: TCTTTCATGTCCTCGCCGCTCTCTATGGAATCGTCGCTGCCGTCGCTCTGgtactcttac ... ttttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACG
EST: gi|349809177|gb|FQ398950.1|FQ398950
EST:     TCTTTCATGTCCTCGCCGCTCTCTATGGAATCGTCGCTGCCGTCGCTCTG                         GTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACG
genomic: TCTTTCATGTCCTCGCCGCTCTCTATGGAATCGTCGCTGCCGTCGCTCTGgtactcttac ... ttttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttgtttttttttttttaaatttctaatctgatattatttcttaattttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGG
                                     tttcttaatttttt  CT-rich tract
     ttttttttttttaaat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctttatgaatcttcttttccataaacgaaacagagtgatttttttgtttttttttttttaaatttctaatctgatattatttcttaattttttaaagGTTCAACTGGTTCGGATACAATTGAGAGTCCCAGAGTATGGTTGGACCACGCAGAAGGTGTTCCACTTTCTCAATTTCCTGGTGAATGGGG

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