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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATCATCCTACACCAACAAGGGCCGAAGTTTCTGATATTGCAATTGCTGTAAGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaagtcgccctggctagcatttagtcgcatcaataccaaatttgaatttgtttatgctagcagtactaacttttttctttagtttcttagttaaaacag...

Basic information

species Vitis vinifera
transcript Vv02s0012g01170.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os10g42100.1 (Oryza sativa), 5'ss of exon 8
ATCATCCTACACCAACAAGGGCCGAAGTTTCTGATATTGCAATTGCTGTAAGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaag---tcgccctggc-----tagcatttagt-----------cgcatcaataccaaatttgaatttgtttatgctagcagtactaac-ttttttctttagtttcttagttaaaacag----------------------------
| ||||| || |||||||| || |||||||||||||| |||||||| ||  | |||||| |||||||  | ||||| ||||| ||||||||||||||||||||||   ||  |||| |     |  | ||| ||           |   |  || | | |  |  |||| |||| |||     |         |    ||  | ||   | ||| |                                
ACCATCCCACTCCAACAAGAGCAGAAGTTTCTGATATAGCAATTGCAGTTCGTGAAGGTTCTGATGCCATCATGCTGTCTGGTGAAACTGCCCATGGAAAgtaagatttcaacctgacacaggttactttttgtttatgttcctccatgtgcatccaagaaatttatttctttaagctcttgctgtgggtgcatagaattctgctttccaattagacttaccttgattgtgcatcttactgtgtttag

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G144730_T01 (Zea mays), 5'ss of exon 8
ATCATCCTACACCAACAAGGGCCGAAGTTTCTGATATTGCAATTGCTGTAAGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaagtcgccctggctagcattta-gtcgcatcaataccaaatttgaatttgtttatgctagcagtactaacttttttctttagtttcttagttaaaacag-
| |||||||| ||||| ||||| ||||||||||| || || ||||| || || ||||||||||||||  | ||| | ||||| |||||||| |||||||||||||   |      |    |||| ||   || |    |||   | | ||  || ||  ||| || | |   | ||     ||    |   | |    ||  
ACCATCCTACTCCAACTAGGGCAGAAGTTTCTGACATAGCTATTGCAGTCAGGGAAGGTGCTGATGCCATCATGTTATCTGGTGAAACTGCTCATGGAAAgtaaggttcaacatttgttgtttatgtaagattaggcacaagaat-agttgattgattataggagaaatgg-tgttacaaatataggcaatgatggcccaat

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G033526_T02 (Zea mays), 5'ss of exon 8
ATCATCCTACACCAACAAGGGCCGAAGTTTCTGATATTGCAATTGCTGTAAGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaagtc---gccctggctagcatttagtcgcatcaata-ccaaatttgaatttgtttatgctagcagtactaacttttttctttagtttcttagttaaaacag
| |||||||| || || ||||| ||||||||||| || || ||||| ||  | ||||||||||||||  | ||| | ||||| |||||||| |||||||||||||      | || | |    ||||   | |    || || ||     |  ||   |      | ||         |||    | | | |  ||||||    
ACCATCCTACTCCCACTAGGGCAGAAGTTTCTGACATAGCTATTGCAGTTCGGGAAGGTGCTGATGCCATCATGTTATCTGGCGAAACTGCTCATGGAAAgtaaggttcaacacttgttgctgtttaaatgtagtgttatcctaaacgctaaatggcaaaatagtcggtcacctgcagtttagccattatttgggttaaa----

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA01G40860.1 (Glycine max), 5'ss of exon 7
ATCATCCTACACCAACAAGGGCCGAAGTTTCTGATATTGCAATTGCTGTAAGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaagtcgccctggctagcatttagtcgcatcaataccaaatttgaatttgtttatgctagcagtactaacttttttc-----tttagtttct--tagttaaaacag-
||||||| |||||||||||||| |||||||| || || |||||||| |||||| |||||||||||||  | |||||||| ||||||||||| |||||||||| |||     | |||     || ||  |     | || |  ||  ||||  ||||  |||| || | |||||||||      || | ||| |  || || |||    
ATCATCCCACACCAACAAGGGCAGAAGTTTCAGACATCGCAATTGCAGTAAGACAAGGTGCTGATGCTATCATGCTTTCAGGAGAAACTGCACATGGAAAgtgagt-----ttgctgttccttggtgaccatggttcctatattttattt--ttat-ttagctgttcaaactttttttcaatattcaatttttactatttgaaatgca

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA11G04490.1 (Glycine max), 5'ss of exon 4
ATCATCCTACACCAACAAGGGCCGAAGTTTCTGATATTGCAATTGCTGTAAGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaagtcgccctggctagcatttagtcgcatcaataccaaatttgaatttgtttatgctagcagtactaacttttttct----ttagtttcttagttaaaacag--------
||||||| ||||| |  ||||| ||||| || || ||||||||||| |||||| |||||||||||||  | |||||||| ||||||||||| |||||||||| | |     | |||     || ||  | |   | |  |  ||  ||||  || |  |||| || | |||||||||      ||  ||| ||| |      |         
ATCATCCCACACCGAGGAGGGCAGAAGTCTCAGACATTGCAATTGCAGTAAGACAAGGTGCTGATGCTATCATGCTTTCAGGAGAAACTGCACATGGAAAgtgatt-----ttgctgttccttggtgacctttgttcttatattttattt--ttgttttagctgttcaaactttttttcaatattcattttttactatttgtaatgcataag

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: AT1G32440.1 (Arabidopsis thaliana), 5'ss of exon 8
ATCATCCTACACCAACAAGGGCCGAAGTTTCTGATATTGCAATTGCTGTAAGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaagtcgccctggctagcatttagtcgcatcaataccaaatttgaatttgtttatgctagcagtactaacttttttc--tttagtttcttagttaaaacag
||||||| || || ||||| || ||||| ||||| ||||||||||| ||| | ||||| || |||||  | ||||||||||| ||||| || ||||||||||  ||    ||   ||     |   |   |  |   ||| | | | ||    | |  |   |     ||  || ||   |||   ||||  | |   |   
ATCATCCAACGCCTACAAGAGCTGAAGTCTCTGACATTGCAATTGCAGTACGTGAAGGCGCAGATGCTATCATGCTTTCTGGTGAAACCGCACATGGAAAgttcgtatttctaattaaagccttacctt-ttgacgtcaa-tataacttaccatgtcatgtgatcttgaatgttctttggttttaattctcggatgtcag--

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: PP1S318_21V6.1 (Physcomitrella patens), 5'ss of exon 7
ATCATCCTACACCAACAAGGGCCGAAGTTTCTGATATTGCAATTGCTGTAAGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaagt-cgccctggctagcatttagtcgcatcaataccaaatttgaatttgtttatgctagcagtactaacttttttctttagtttcttagttaaaacag---
 ||| ||||| || ||| | || ||||| || || || || || |||||  | |||||||| |||||| |||||||||| || ||||| || |||||||||||||  ||      | ||       || | || | |     |||   | || ||    ||  | |  |   |||    | | || |    ||| |    |   
CTCACCCTACGCCCACACGAGCAGAAGTCTCAGACATAGCCATCGCTGTCCGTGAAGGTGCGGATGCAATTATGCTTTCAGGGGAAACCGCTCATGGAAAgtaagcgcgattaaaccagtgcactatctc-tcgacagt--ttttttttctgcttgaagtaa-atttttgtgtttcgaatatcgtattactgttgaggacgatc

upper sequence: Vv02s0012g01170.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: PP1S205_25V6.1 (Physcomitrella patens), 5'ss of exon 7
ATCATCCTACACCAACAAGGGCCGAAGTTTCTGATATTGCAATTGCTGTAAGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaagtcgccctggctagcatt--tagtcg-catcaataccaaatttgaatttgtttatgctagcag-tactaactttttt---ctttagtttcttagttaaaacag
 ||| || || || ||| | || || ||||| || || || ||||| ||  | |||||||| || ||||||||||||||||| ||||| || || |||||||||||  |  |||      ||  |||||  | | |||| |  || | |  |    ||  | || |  | | ||  ||||    | | ||  |  | || |      
CTCACCCCACTCCCACACGAGCAGAGGTTTCAGACATAGCTATTGCCGTCCGTGAAGGTGCGGACGCAGTTATGCTTTCTGGTGAAACCGCTCACGGAAAgtaagtacctttggaatttgttgatagtcttctttaatatc--atctaagctca--tagcccagtaactgccaaaattttggggcatcaggcttatcgtcagtg---

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|110711036|gb|EE087773.1|EE087773
EST:     AGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAA                         GTATCCGTTGAAAGCTGTTAAAGTAATGCATACTGTGGCATTGAGGACTGA
genomic: AGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaagtcgcc ... atttctcaagGTATCCGTTGAAAGCTGTTAAAGTAATGCATACTGTGGCATTGAGGACTGA
EST: gi|27586266|gb|CB008961.1|CB008961
EST:     AGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAA                         GTATCCGTTGAAAGCTGTTAAAGTAATGCATACTGTGGCATTGAGGACTGA
genomic: AGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaagtcgcc ... atttctcaagGTATCCGTTGAAAGCTGTTAAAGTAATGCATACTGTGGCATTGAGGACTGA
EST: gi|110388166|gb|EC952886.1|EC952886
EST:     AGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAA                         GTATCCGTTGAAAGCTGTTAAAGTAATGCATACTGTGGCATTGAGGACTGA
genomic: AGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaagtcgcc ... atttctcaagGTATCCGTTGAAAGCTGTTAAAGTAATGCATACTGTGGCATTGAGGACTGA
EST: gi|351030123|gb|FQ430865.1|FQ430865
EST:     AGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAAGTGCCCATGGAAA                         GTATCCGTTTGAA-GCTGTTAAAGT
genomic: AGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaagtcgcc ... atttctcaagGTATCCGTT-GAAAGCTGTTAAAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATCATCCTACACCAACAAGGGCCGAAGTTTCTGATATTGCAATTGCTGTAAGAGAAGGTGCTGATGCAGTTATGCTTTCTGGAGAAACTGCCCATGGAAAgtaagtcgccctggctagcatttagtcgcatcaataccaaatttgaatttgtttatgctagcagtactaacttttttctttagtttcttagttaaaacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ataccaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - taaaaca