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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGGGCTTCCGGCCAAAAATCTTATGGCTGAGAGGCGGCGGAGGAAGAAGCTTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAGgtaatcaatttctatggcacataatgcttttcccttgaataaatttattaaaaattgcttcataggtttttcttgataatcttcagttagtgtatagatt...

Basic information

species Vitis vinifera
transcript Vv14s0068g01200.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0068g01200.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os01g70310.1 (Oryza sativa), 5'ss of exon 2
GGGGCTTCCGGCCAAAAATCTTATGGCTGAGAGGCGGCGGAGGAAGAAGCTTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAGgtaatcaat---ttctatggcacataatgcttttcccttg--aataaatttattaaaaattgcttcataggtttttcttgataatcttcagttagtgtatagatt
|||| | |||||||| || || ||||| ||| ||||||| ||||||||||| || ||| | |||||||||||  | || || |||||||||||||||||||| || |||    ||  |   |  |  |   | | | |||  ||| | || |||||  |     ||  || || | || ||   | |    ||| |   || || 
GGGGATGCCGGCCAAGAACCTCATGGCGGAGCGGCGGCGCAGGAAGAAGCTCAACGACCGCCTCTACATGCTGCGCTCCGTGGTGCCCAAGATCAGCAAGgtgattaatgacctcatttctattttttcactgttcattgctaattatttaattaatcagcagctc-cagtttctactagactgtatcttattaat---taaat-

upper sequence: Vv14s0068g01200.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: LOC_Os11g32100.1 (Oryza sativa), 5'ss of exon 1
GGGGCTTCCGGCCAAAAATCTTATGGCTGAGAGGCGGCGGAGGAAGAAGCTTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAGgtaatcaatttctatggcacataatgcttttcccttgaataaatttattaaaaattgcttcat---aggtttttcttgataatcttcagttagtgtatagatt-
|||| | |||||||| || || ||||| ||| | || ||  |||||||||| || ||| | |||||||||||  | || ||||||||||||||||||||||| |  | |   | |    | |    |  ||| | ||||   || | | ||||| | ||| ||    |    || | |  |||    | ||   ||  |  || 
GGGGATGCCGGCCAAGAACCTCATGGCGGAGCGCCGCCGCCGGAAGAAGCTCAACGACCGCCTCTACATGCTCCGCTCCGTCGTGCCCAAGATCAGCAAGgtcaggattccttctcctgc-tctcccaattctcatgaa---atctctcaaaaagttcttaattctggcgaattttagggaatgcgtaattttggtcgaatttt

upper sequence: Vv14s0068g01200.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G033356_T01 (Zea mays), 5'ss of exon 1
GGGGCTTCCGGCCAAAAATCTTATGGCTGAGAGGCGGCGGAGGAAGAAGCTTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAGgtaatcaat-ttctatggcacata-atgcttttcccttgaataaatttattaaaaattgcttcataggtttttcttgataatcttcagttagtgtatagatt
|||| | |||||||| || || ||||| ||| | || ||  ||||||||||||||||| |||||||||||||  |||| |||||||||||||||||||||||||  | | | |  | |||  ||  || |  ||  ||      | || |      |   ||    |  || ||    |  ||   ||  | |    |  | 
GGGGTTGCCGGCCAAGAACCTCATGGCAGAGCGCCGTCGCCGGAAGAAGCTTAATGACCGGCTCTACATGCTCCGGTCCGTCGTGCCCAAGATCAGCAAGgtaagaattgtacctttgcatctatgtgttaatcagttactacgaattgtagctcgtaatttagatgaattctccgcgttttcggtagcaatta-gcaact-

upper sequence: Vv14s0068g01200.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G172297_T01 (Zea mays), 5'ss of exon 1
GGGGCTTCCGGCCAAAAATCTTATGGCTGAGAGGCGGCGGAGGAAGAAGCTTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAGgtaatcaatttctatggcacataatgcttttcccttgaataa-atttattaaaaattgcttcataggtttttcttgataatcttcagttagtgtatagatt---
| || | |||||||| || || ||||| ||| | || ||  ||||||||||||||||| |||||||||||||  | || ||||||||||||||||||||||| |   | || ||             || |   | |  ||  ||  |||  |  | |     ||| |   |  |   ||| ||  | |||    |||  |   
GAGGTTGCCGGCCAAGAACCTCATGGCGGAGCGCCGTCGCCGGAAGAAGCTTAATGACCGGCTCTACATGCTCCGATCCGTCGTGCCCAAGATCAGCAAGgtga--gaattgtaccctttcatccatttgttaatcggctactatgaattgtagctcgtaatttagatgaattctccgaatttt--ggtagcaattagcatctg

upper sequence: Vv14s0068g01200.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GRMZM2G173534_T02 (Zea mays), 5'ss of exon 1
GGGGCTTCCGGCCAAAAATCTTATGGCTGAGAGGCGGCGGAGGAAGAAGCTTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAGgtaatcaatttctatggcacat--aatgcttttcccttgaataaat--ttattaaaaattgcttcataggtttttcttgataatcttcagttagtgtatagatt
 ||| | |||||||| || || ||||| ||| | |||||  | |||||||| |||||| | |||||||||||  | || || ||||| |||||||||||||| |||||      | |  |||  |   | | | | | |  |      |   |    |||  |  |||| |   | | ||  ||  |   || |  ||||    
AGGGATGCCGGCCAAGAACCTCATGGCGGAGCGCCGGCGTCGCAAGAAGCTCAATGACCGCCTCTACATGCTGCGCTCGGTGGTGCCGAAGATCAGCAAGgtgatcaaccagcctcgtccattcatctcctattcgtcgtgtttcccatctgtgcttattagtgtatagttacatatagagtattat-gctttgcctatat---

upper sequence: Vv14s0068g01200.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ28242 (Selaginella moellendorffii), 5'ss of exon 1
GGGGCTTCCGGCCAAAAATCTTATGGCTGAGAGGCGGCGGAGGAAGAAGCTTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAGgtaatcaatttcta-----tggcacataatgcttttcccttgaataaatttattaaaaa----ttgcttcataggtttttcttgataatcttcagttagtgtatagatt-----------
||| ||||||||||| ||||| ||||| ||| |||| ||| ||||||||||||||||  |  | ||||||||| | || || || ||||| || |  ||||| |  | |||| |     | |  ||   ||   ||| || |        | ||   |     || | || |    |  ||| | |     ||| |       | | ||           
GGGCCTTCCGGCCAAGAATCTCATGGCGGAGCGGCGACGGCGGAAGAAGCTTAATGATCGCTTGTACATGCTTCGCTCGGTGGTCCCCAAAATTACAAAGgtgagtactttcaaaccactcgggcaacttggcattcactcgcccgctcctctttccatgcctttacctctttttctcctctcgctctcactcactctcaacttggtttgattttgtcag

upper sequence: Vv14s0068g01200.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ29742 (Selaginella moellendorffii), 5'ss of exon 1
GGGGCTTCCGGCCAAAAATCTTATGGCTGAGAGGCGGCGGAGGAAGAAGCTTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAGgtaatcaatttcta-----tggcacataatgcttttcccttgaataaatttattaaaaattgcttcataggtttttcttgataatcttcagttagtgtatagatt----------------
||| ||||||||||| ||||| ||||| ||| |||| ||| ||||||||||||||||  |  | ||||||||| | || || || ||||| || |  ||||| |  | |||| |     | |  ||   ||   ||| || |        | ||   | |  ||| |    |||||||       ||     |       |  ||                
GGGCCTTCCGGCCAAGAATCTCATGGCGGAGCGGCGACGGCGGAAGAAGCTTAATGATCGCTTGTACATGCTTCGCTCGGTGGTCCCCAAAATTACAAAGgtgagtactttcaaaccactcgggcaacttggcattcactcgcccgctcctctttcca-tgcctttacctctttttctcctctcgctctcactcacactcaacttggtttgattttgtcag

upper sequence: Vv14s0068g01200.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ15029 (Selaginella moellendorffii), 5'ss of exon 1
GGGGCTTCCGGCCAAAAATCTTATGGCTGAGAGGCGGCGGAGGAAGAAGCTTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAGgtaatcaatttctatggcacataatgcttttcccttgaataaatttattaaaaattgcttcataggtttttcttgataatcttcagttagtgtatagatt
     | |||||||| ||| |  |||| |||||||||||| |||||||||| || ||  | |||||||||||| | || || ||||||||||||| ||||||  ||   || | ||  ||     | || |     ||||     |  ||| |       |    | |||  ||   |                      
----ATGCCGGCCAAGAATTTGCTGGCGGAGAGGCGGCGGCGGAAGAAGCTCAACGATCGCCTCTACATGCTTCGATCGGTGGTGCCCAAGATCACCAAGgttctct-cttgtctgctacg----gtttatgggaagaatgtgggtgctaacatcgatcgc----gctttgattcgcag---------------------

upper sequence: Vv14s0068g01200.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ37663 (Selaginella moellendorffii), 5'ss of exon 1
GGGGCTTCCGGCCAAAAATCTTATGGCTGAGAGGCGGCGGAGGAAGAAGCTTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAGgtaatcaatttctatggcacataatgcttttcccttgaataaatttattaaaaattgcttcataggtttttcttgataatcttcagttagtgtatagatt
     | |||||||| ||| |  |||| |||||||||||| ||||||| || || ||  | |||||||||||| | || || ||||||||||||| ||||||      ||||| | |      | | |||    | | |  ||| |        |     ||| | |    |||  | ||   |||              
----ATGCCGGCCAAGAATTTGCTGGCGGAGAGGCGGCGGCGGAAGAAACTCAACGATCGCCTCTACATGCTTCGATCGGTGGTGCCCAAGATCACCAAGgt------tttctcttgtctgctacggttt---atgggaagaatgtg-----ggtgctaacatcgatcgcgctt--tgattcgcag--------------

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|110419904|gb|EC986158.1|EC986158
EST:     CAAGATCAGCAAG                         ATGGATAGAGCTTCTATCCTTGGGGATGCTATTGAGTACTTGAAGGAGCTT
genomic: CAAGATCAGCAAGgtaatcaatt ... aaatttgcagATGGATAGAGCTTCTATCCTTGGGGATGCCATTGAGTACTTGAAGGAGCTT
EST: gi|351026770|gb|FQ436423.1|FQ436423
EST:     TTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAG                         ATGGATAGAGCTTCTATCCTTGGGGATGCCATTGAGTACTTGAAGGAGCTT
genomic: TTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAGgtaatcaatt ... aaatttgcagATGGATAGAGCTTCTATCCTTGGGGATGCCATTGAGTACTTGAAGGAGCTT
EST: gi|71869310|gb|DT018365.1|DT018365
EST:     TTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAG                         ATGGATAGAGCTTCTATCCTTGGGGATGCTATTGAGTACTTGAAGGAGCTT
genomic: TTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAGgtaatcaatt ... aaatttgcagATGGATAGAGCTTCTATCCTTGGGGATGCCATTGAGTACTTGAAGGAGCTT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GGGGCTTCCGGCCAAAAATCTTATGGCTGAGAGGCGGCGGAGGAAGAAGCTTAATGACAGGCTCTACATGCTTAGGTCTGTCGTGCCCAAGATCAGCAAGgtaatcaatttctatggcacataatgcttttcccttgaataaatttattaaaaattgcttcataggtttttcttgataatcttcagttagtgtatagatt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGATCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - attaaaa