Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   		5  
 5'  3'   		6  
 5'  3'   		7  
 5'  3'   		8  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TATGCGCAGAAGATATCCGTGGTCAGTTGGAAAAACTGGGCAACACATCTGAATTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctttctcttttttgccttcttactttttgtagcaatatataattatcctttggtgtgcatttagagcatgtctttgtggttttagttggcact...

Basic information

species Vitis vinifera
transcript Vv13s0047g00170.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0047g00170.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os02g55200.1 (Oryza sativa), 5'ss of exon 4
TATGCGCAGAAGATATCCGTGGTCAGTTGGAAAAACTGGGCAACACATCTGAATTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctttctcttttttgccttcttactttttgtagcaatatataattatcctttggtgtgcatttagagcatgtctttgtggttt-tagttggcact
| || |||||||| ||| | |   ||||| ||      |   |||     ||| ||||||| ||||| ||||| ||  |||| |||||||||||||||||||| | |  || ||| ||  |   |      | |   | |    |||   || | |||  ||   | |     | |||||   |  ||   |  |   |||
TGTGTGCAGAAGACATCAGGGAAGAGTTGAAATCTAAAGAAGACAACCAAGAACTGTGTTCTCAACTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtacggcaattttctcttggggacttgaggatatgtgaacctgctattgata-cgtttattgcctactccctccgtgtctaaataattgacacgtttgact

upper sequence: Vv13s0047g00170.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os01g01420.2 (Oryza sativa), 5'ss of exon 3
TATGCGCAGAAGATATCCGTGGTCAGTTGGAAAAACTGGGCAACACATCT--GAATTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctttctcttttttgccttcttactttttgtagcaatatataatta--tcctttggtgtgcatttagagcatgtctttgtggttttagttggcact
| || ||| |||| ||| | |   | |||  ||| ||   ||| ||| |   ||| ||||||| ||||| ||||| ||  |||| |||||||||||||||||||| | |  || ||| ||  |   |   |   | | |   ||  |   |||    | |||   |   | |   |     ||  |||     || ||  ||  
TGTGTGCACAAGACATCAGGGAAGAATTG--AAATCTAAACAAGACAACCAAGAACTGTGTTCTCAACTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtacgacaattttctcttggggactgg-aggatatatgtgaacctgctattgatacgtttatagcctactcctactccctccgtgtctaaataatttacat-

upper sequence: Vv13s0047g00170.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G049672_T01 (Zea mays), 5'ss of exon 4
TATGCGCAGAAGATATCCGTGGTCAGTTGGAAAAACTGGGCAACACATCTGAATTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctttctcttttttgccttcttactttttgtagcaatatataattatcctttggtgtgcatttagagcatgtctttgtggttttagttggcact--
| || ||||| || ||| | |   ||||  ||      |   | |  |  ||  | |||||||| || ||||| ||  |||| ||||||||||||||||||||||||  ||  || ||    ||  || | |    |     |||  | ||   |       |      | |  |||  |    || |  |  |||      
TGTGTGCAGACGACATCAGGGAGGAGTTAAAATCTTCAGAAGATAACTTAGACCTATGTTCACAGCTTGGAGCTGTGTTAGGAATGCTTGGGGACTGCTGgtatgtctgttggctctt--aactatttccctcaaatgtttttattcacttcatcagcaaactaagaaaatactatgattactagggtgcaaatggttggat

upper sequence: Vv13s0047g00170.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA04G15130.1 (Glycine max), 5'ss of exon 4
TATGCGCAGAAGATATCCGTGGTCAGTTGGAAAAACTGGGCAACACATCTGAATTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctttctcttttttgccttcttactttttgtagc--aatatataattatcctttggtgtgcatttagagcatgtctttgtg-gttttagttggcact
| || |||||||| || |||| |||||| |||||| | || ||||| || || || |||||||| |||||||||||  | ||||||||||| ||||||||||||||  | |  || | ||     |   ||   || ||   | |   |||| |  || | |     ||||    | ||| | ||    | | | |      |
TCTGTGCAGAAGACATTCGTGATCAGTTAGAAAAAGTTGGTAACACTTCAGAGTTATGTTCACAGCTAGGAGCAGTCTTGGGTATGCTTGGTGACTGCTGgtatgttttcttgctctcttctaccccccctccctgcagtcaactggttaatcagtctgttgctcttatttt---cctgtttgtgcatatatcaatctttcat

upper sequence: Vv13s0047g00170.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GLYMA06G47010.1 (Glycine max), 5'ss of exon 4
TATGCGCAGAAGATATCCGTGGTCAGTTGGAAAAACTGGGCAACACATCTGAATTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctttctcttttttgc-cttcttactttttgtagc--aatatataattatcctttggtgtgcatttagagcatgtctttgtggttttagttggcact--
| || ||||| || || |||| |||||| |||||| | || ||||| || || || |||||||| |||||||||||  | ||||||||||| ||||||||||||||  | |  || | ||   || |  ||     |      | |   |||| |  || |       ||||        | || |||  | ||  |  |  |  
TCTGTGCAGAGGACATTCGTGATCAGTTAGAAAAAGTTGGTAACACTTCAGAGTTATGTTCACAGCTAGGAGCAGTCTTGGGTATGCTTGGTGACTGCTGgtatgttttcttgctctcttctactccccaccacccgcgatctactgactaatcagtctgttactcttatttt-----cctgttagtgcatatatctatctttca

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|351047067|gb|FQ454677.1|FQ454677
EST:     GAACTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTG                         TCGAGCAACAGGAGATGCTGATTCAGCAGTCACATATTTTGAAGAGAGTGT
genomic: GAATTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctt ... tgtgttgcagTCGAGCAACAGGAGATGCTGATTCAGCAGTCACATATTTTGAAGAGAGTGT
EST: gi|28964625|gb|CB343658.1|CB343658
EST:     AGGAGCAGTTTTAGGTATGCTTGGGGACTGCTG                         TCGAGCAACAGGAGATGCTGATTCAGCAGTCACATATTTTGAAGAGAGTGT
genomic: AGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctt ... tgtgttgcagTCGAGCAACAGGAGATGCTGATTCAGCAGTCACATATTTTGAAGAGAGTGT
EST: gi|351038304|gb|FQ460996.1|FQ460996
EST:     GAACTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTG                         TCGAGCAACAGGAGATGCTGATTCAGCAGTCACATATTTTGAAGAGAGTGT
genomic: GAATTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctt ... tgtgttgcagTCGAGCAACAGGAGATGCTGATTCAGCAGTCACATATTTTGAAGAGAGTGT
EST: gi|110362765|gb|EC926319.1|EC926319
EST:     GAATTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTG                         TCGAGCAACAGGAGATGCTGATTCAGCAGTCACATATTTTGAAGAGAGTGT
genomic: GAATTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctt ... tgtgttgcagTCGAGCAACAGGAGATGCTGATTCAGCAGTCACATATTTTGAAGAGAGTGT
EST: gi|110386747|gb|EC951369.1|EC951369
EST:     ACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTG                         TCGAGCAACAGGAGATGCTGATTCAGCAGTCCACATATTTTGAAGAGAGTG
genomic: ACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctt ... tgtgttgcagTCGAGCAACAGGAGATGCTGATTCAGCAGT-CACATATTTTGAAGAGAGTG
EST: gi|351055326|gb|FQ441924.1|FQ441924
EST:     GAACTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTG                         TCGAGCAACAGGAGATGCTGATTCAGCAGTCACATATTTTGAAGAGAGTGT
genomic: GAATTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctt ... tgtgttgcagTCGAGCAACAGGAGATGCTGATTCAGCAGTCACATATTTTGAAGAGAGTGT
EST: gi|110363678|gb|EC927285.1|EC927285
EST:     GTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTG                         TCGAGCAACAGGAGATGCTGATTCAGCAGTCACATATTTTGAAGAGAGTGT
genomic: GTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctt ... tgtgttgcagTCGAGCAACAGGAGATGCTGATTCAGCAGTCACATATTTTGAAGAGAGTGT
EST: gi|351038515|gb|FQ464381.1|FQ464381
EST:     GAACTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTG                         TCGAGCAACAGGAGATGCTGATTCAGCAGTCACATATTTTGAAGAGAGTGT
genomic: GAATTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctt ... tgtgttgcagTCGAGCAACAGGAGATGCTGATTCAGCAGTCACATATTTTGAAGAGAGTGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TATGCGCAGAAGATATCCGTGGTCAGTTGGAAAAACTGGGCAACACATCTGAATTGTGTTCACAACTAGGAGCAGTTCTAGGTATGCTTGGGGACTGCTGgtatgtcctttctcttttttgccttcttactttttgtagcaatatataattatcctttggtgtgcatttagagcatgtctttgtggttttagttggcact

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCAG