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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCTCTGTGCTTCAACCATGGCGACCGTGATGCAGAAAATCAAAGATATCGAAGATGAGgtattattcttctcgacaatctcaaaccctagctccatttcgcactcttggctcgtttctgagagaataagagagcgtaaaatccatatttttcgtgaat...

Basic information

species Vitis vinifera
transcript Vv07s0031g01620.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01620.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA04G39690.1 (Glycine max), 5'ss of exon 1
------------------------------------------TCTCTGTGCTTCAACCATGGCGACCGTGATGCAGAAAATCAAAGATATCGAAGATGAGgtattattcttctcgacaatctcaaaccctagctccatttcgcactcttggctcgtttctgagagaataagagagcgtaaaatccatatttttcgtgaat---
                                          |     | |||| |  |||||||| ||||||||||| |||||||||||||||||||||||| |    ||||        |   ||    |    |||  | ||   ||  |  ||   |    |     |     |   | |  | ||  |   | |    
CAGGGTTTAATCTGAATATCTTTCGCGTTGCCACTGAGGTTGTTATCTTTCTTCCAAAATGGCGACGGTGATGCAGAAGATCAAAGATATCGAAGATGAGgtacttgggttctgagtggaat---acaggggaatgattgtggacatgtgatttattcaagcagaacactaaccttttttcagcagtgttcatttagcacttc

upper sequence: Vv07s0031g01620.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA06G15180.2 (Glycine max), 5'ss of exon 1
------------------------------------------TCTCTGTGCTTCAACCATGGCGACCGTGATGCAGAAAATCAAAGATATCGAAGATGAGgta-ttattcttctcgacaatctcaaaccctagctccatttcgcactcttggctcgtttctgagagaataagagagcgtaaaatccatatttttcgtgaat---
                                          |   | | |||| |  |||||||| |||||||| ||||||||||| ||||||||||||||| || ||||    |  |  |    |    ||    |||     |  | || |  ||   | | |||  | ||    |     |  | ||  |   | |    
GGTTTAATCTGAATTTCTTTTGTGTTGCCACTGAGGTTATTATTATTTTTCTTCCAAAATGGCGACGGTGATGCAAAAAATCAAAGACATCGAAGATGAGgtacttgttctgagtggaatacagggaaatgagtg--attgtatgcattcggtttattcaagcg-gaacgatagccttttcgg-cagtgttcatttagcacttc

upper sequence: Vv07s0031g01620.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: PP1S26_115V6.1 (Physcomitrella patens), 5'ss of exon 1
----------------------------------------TCTCTGTGCTTCA--ACCATGGCGACCGTGATGCAGAAAATCAAAGATATCGAAGATGAGgtattattcttctcgacaatctcaaaccctagctccatttcgcactct-tggctcgtttctgagagaataagagagcgtaaaatccatatttttcgtgaat---
                                        | | ||||  | |  |||||| ||||||| |||||||||||||| ||||||||||||||||| |  ||   ||| ||    ||   ||  ||     || |   ||||   || | ||     ||    | ||     |   | | | |   | ||||  |   
AGGATCCAGAGAGGCTTGTTCGCTTCACATCCAGCTCTTCTTTTTGTGGGTAATCACCATGTCGACCGTCATGCAGAAAATCAAGGATATCGAAGATGAGgt-tagttgcactc-accgcgtctcgcctcagg--ggttgcattctctactgcccattatcaggaattgatgatgcttttcgaacaagaggatgcgtgggtttg

upper sequence: Vv07s0031g01620.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: EFJ09453 (Selaginella moellendorffii), 5'ss of exon 1
TCTCTGTGCTTCAACCATGGCGACCGTGATGCAGAAAATCAAAGATATCGAAGATGAGgtattattcttctcgacaatctcaaaccctagctccatttcgcactcttggctcgtttctgagagaataagagagcgtaaaatccatatttttcgtgaat
                |||||||||||||||||||| ||||| || ||||||||||||||       |||||| |    |    | |  | || ||       | || ||                                                
----------------ATGGCGACCGTGATGCAGAAGATCAAGGACATCGAAGATGAGgtgc--gctttctcggctgcattggtcgcccgatcgatggtttcttgtttgcgtag--------------------------------------------

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|28970187|gb|CB349220.1|CB349220
EST:     CTTCAACCATGGCGACCGTGATGCAGAAAATCAAAGATATCGAAGATGAG                         ATGGCAAGAACTCAGAAGAATAAAGCTACAGCTCATCATCTGGGCTTGTTA
genomic: CTTCAACCATGGCGACCGTGATGCAGAAAATCAAAGATATCGAAGATGAGgtattattct ... ttttttgcagATGGCAAGAACTCAGAAGAATAAAGCTACAGCTCATCATCTGGGCTTGTTA
EST: gi|71857454|gb|DT006509.1|DT006509
EST:     CTTCAACCATGGCGACCGTGATGCAGAAAATCAAAGATATCGAAGATGAG                         ATGGCAAGAACTCAGAAGAATAAAGCTACAGCTCATCATCTGGGCTTGTTG
genomic: CTTCAACCATGGCGACCGTGATGCAGAAAATCAAAGATATCGAAGATGAGgtattattct ... ttttttgcagATGGCAAGAACTCAGAAGAATAAAGCTACAGCTCATCATCTGGGCTTGTTA
EST: gi|294965456|gb|GW839027.1|GW839027
EST:     CTTCAACCATGGCGACCGTGATGCAGAAAATCAAAGATACCGAAGATGAG                         ATGGCAAGAACTCAGAAGAATAAAGCTACAGCTCATCATCTGGGCTTGTTA
genomic: CTTCAACCATGGCGACCGTGATGCAGAAAATCAAAGATATCGAAGATGAGgtattattct ... ttttttgcagATGGCAAGAACTCAGAAGAATAAAGCTACAGCTCATCATCTGGGCTTGTTA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCTCTGTGCTTCAACCATGGCGACCGTGATGCAGAAAATCAAAGATATCGAAGATGAGgtattattcttctcgacaatctcaaaccctagctccatttcgcactcttggctcgtttctgagagaataagagagcgtaaaatccatatttttcgtgaat

- - - - - - - - - - - - - - - - - - - - - - - - CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaatcca