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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcgatacccattgtattttgatctaagttttattgcaacttgtttgttgttcattgccttagattttctatgtgaaattttacag

Basic information

species Vitis vinifera
transcript Vv01s0010g02460.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os04g40950.1 (Oryza sativa), 5'ss of exon 6
CATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcgatacccattgtattttgatctaagttttattgcaacttgtttgttgttc------attgccttagattttctatgtgaaattttacag----------------------
|||||||||| | ||||||||||||||||| |||||||| || ||||||||||| ||||||||||||||||| |||||||| |||||||| || || |||||   |||   || |||| |   ||| ||||     | |||||| |||| || || |       | |   | |    | | || ||||   ||                          
CATGTTTGTTGTTGGTGTCAATGAGAAGGAGTACAAGCCTGACATCGACATTGTGTCCAATGCTAGCTGCACCACCAACTGCCTTGCTCCACTTGCCAAGgtgtgttcctcactcattttcacttg-tcta----ctgttgcaaattgtgtggtgatgttaagaaattggtcactactaccatatgaagccttgtccttatcaaattgtctgcctgcag

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os08g03290.3 (Oryza sativa), 5'ss of exon 5
CATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcgatacccattgtattttgatctaagttttattgcaacttgtttgttgttcattgccttagattttctatgtgaaattttacag
 ||||||||    |||||||| ||| |  | ||||   | ||||| || ||||| || |||||||||||||| || ||||| ||||||||||| || |||||   ||   | || | || |   |  ||||  ||   |||  |||| |   ||| |  ||   |  || |   |||     ||   | ||
GATGTTTGTCTGCGGTGTCAACGAGGACAAGTACACTTCAGATATTGATATTGTCTCAAATGCTAGCTGCACCACAAACTGCCTTGCTCCTCTTGCCAAGgtatttttctttccgagtg-acaattttctactttcagttg-gacttttggtttggttcttaatt--gactcgttatc----atccaatag

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G176307_T01 (Zea mays), 5'ss of exon 6
CATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcgatacccattgtattttgatctaagttttattgcaacttgtttgttgttcattgccttagattttctatgtgaaatt-ttacag
|||||||||  | |||||||| |||||||| |||||| | || ||  ||||||| ||||||||||||||||| |||||||| ||||||||||| |||||||| ||||  || |  |||   |  ||   |||     |||||  |||     |  |  ||  ||| | |||   ||  |    ||  | |||
CATGTTTGTCGTTGGTGTCAACGAGAAGGAGTACAAGTCTGACATTAACATTGTCTCCAATGCTAGCTGCACAACCAACTGCCTTGCTCCTCTTGCTAAGgt-gctt--atgctgatttactgctgccataa-----attgct-cttagggatcctatatcacctaaaattggttacttatttttgctgcag

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G071630_T02 (Zea mays), 5'ss of exon 5
CATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcgatacccattgtattttgatctaagttttattgcaacttgtttgttgttcattgccttagattttctatgtgaaattttacag---
|||||| ||| | |||||||| |||||||| |||||| | || ||| ||||||| || |||||||||||||| |||||||| |||||||| || |||||||| ||||  ||     ||   |  |||  |||     |||||  |||     || |  |||  || | | |   ||  |    |||| | |   
CATGTTCGTTGTTGGTGTCAACGAGAAGGAGTACAAGTCTGACATCAACATTGTCTCTAATGCTAGCTGCACAACCAACTGCCTTGCTCCGCTTGCTAAGgt-gctt--atgttgctttactgctgacataa-----attgct-cttaggcattctatattatctaaaactggttacttttttttttgctgcag

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G046804_T02 (Zea mays), 5'ss of exon 6
CATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcgatacccattgtattttgatctaagttttattgcaacttgtttgttgt-tcattgccttagattttctatgtgaaattttacag
|||||||||| | |||||||||||| |  | ||||   | ||| |  ||||||||||||||||||||||||| || ||||| |||||||| || |||||||| ||   |     |  |  |   |  | ||  | ||  |||   |    ||| |  |||||   | |   | |||| |||  ||    |||
CATGTTTGTTGTTGGTGTCAATGAGGACAAGTACACCTCGGATGTTAACATTGTTTCCAATGCTAGCTGCACCACAAACTGCCTTGCTCCCCTTGCTAAGgt-gcactgtccttctcttaagcattctgtagctgtttctgctcttccaatgtaggatcatttgttaacgatgtcta-gtgtcataaaccag

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G180625_T02 (Zea mays), 5'ss of exon 6
CATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcgatacccattgtattttgatctaagttttattgcaacttgtttgttgt-tcattgcctta-gattttctatgtgaaattttacag
|||||||||| | |||||||||||| |  | ||||   ||||| |  ||||||||||||||||||||||||| || ||||| |||||||| || ||||||||   | |  | |   ||  ||  |  | ||  | ||  |||   |   | || |  |||||   | | ||| |   |||| | |    |   
CATGTTTGTTGTTGGTGTCAATGAGGACAAGTACACCTCCGATGTTAACATTGTTTCCAATGCTAGCTGCACCACAAACTGCCTTGCTCCCCTTGCTAAGgtg--tgctgtccttcttaaatcattttttatctgttcctgcccttccgtcgtagaatcatttattaatgatatctaatgtcataaaccag--

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: EFJ22884 (Selaginella moellendorffii), 5'ss of exon 6
CATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgt-tgcttcga-tacccattgtattttgatctaagttttattgcaacttgtttgttgttcattgccttagattttctatgtgaaattttacag
 ||||| ||  ||||||| || ||||  ||||||||   |||||| ||||| |||||||| || || ||||||||||| |||||||| ||||| || ||||| || | |||    ||||||| |||   ||  |||||     |    |||| | ||||  |    | |  || || |               
AATGTTCGTCGTGGGTGTGAACGAGAGCGAATACAAAGACGATATGGACATCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCACCTCTTGCGAAGgtgtgttgcgagcttccattgtctttccgtcacagtttctcgac----tgttcgatgtttctga--taatcttctccag--------------

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: EFJ30760 (Selaginella moellendorffii), 5'ss of exon 6
CATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgt-tgcttcga-tacccattgtattttgatctaagttttattgcaacttgtttgttgttcattgccttagattttctatgtgaaattttacag
 ||||| ||  ||||||| || ||||  |||||||||  |||||| ||||| |||||||| || || ||||||||||| |||||||| ||||| || ||||| || | |||    ||||||| |||   || ||||||     |    |||| | ||||  |    | |  || || |               
AATGTTCGTCGTGGGTGTGAACGAGAGCGAATACAAGGACGATATGGACATCGTTTCCAACGCGAGTTGCACTACCAATTGTCTTGCGCCTCTTGCGAAGgtgtgttgcgagcttccattgtctttccgtcaaagtttctcgac----tgttcgatgtttctga--taatcttctccag--------------

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|33406621|gb|CF212248.1|CF212248
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGATAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|161720959|gb|FC070345.1|FC070345
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|110703819|gb|EE080998.1|EE080998
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|30134772|gb|CB920110.1|CB920110
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|110701389|gb|EE078905.1|EE078905
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAA                         GTTATTAATGACAGATTTGGCATTGTTGAAGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|110384047|gb|EC948461.1|EC948461
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|110697161|gb|EE073909.1|EE073909
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|161721814|gb|FC070505.1|FC070505
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|161716699|gb|FC065571.1|FC065571
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGATAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|110363529|gb|EC927123.1|EC927123
EST:     CTTGCTCCTCTGGCTAAG                         GTTATTAATGATAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: CTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|30134770|gb|CB920108.1|CB920108
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|110687944|gb|EE065928.1|EE065928
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|110373445|gb|EC937683.1|EC937683
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|161713863|gb|FC062559.1|FC062559
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|110707375|gb|EE083731.1|EE083731
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|161718038|gb|FC067580.1|FC067580
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|71857565|gb|DT006620.1|DT006620
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|161712390|gb|FC061695.1|FC061695
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTTCA
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTT-CA
EST: gi|71856620|gb|DT005675.1|DT005675
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|161715330|gb|FC065818.1|FC065818
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTTTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|110688396|gb|EE066900.1|EE066900
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|110371235|gb|EC935092.1|EC935092
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|161719339|gb|FC068279.1|FC068279
EST:     TTGTTTCCCATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
EST: gi|161720005|gb|FC067735.1|FC067735
EST:     TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAG                         GTTATTAATGATAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC
genomic: TTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcga ... aattttacagGTTATTAATGACAGATTTGGCATTGTTGAGGGTCTTATGACCACTGTTCAC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CATGTTTGTTATGGGTGTCAATGAGAAGGAATACAAGCCCGATATCGACATTGTTTCCAATGCTAGCTGCACTACCAACTGTCTTGCTCCTCTGGCTAAGgttgcttcgatacccattgtattttgatctaagttttattgcaacttgtttgttgttcattgccttagattttctatgtgaaattttacag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC