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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCTCTTTTTCAAGCAGGAAATGGAGCTTTCTTTGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCAgtaagtaaataatcatgtatgtcattctctaatggtcctttcccatttatttggggctaatgctgacacattggaaactgtattgttttag

Basic information

species Vitis vinifera
transcript Vv00s0601g00030.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0601g00030.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os03g10370.1 (Oryza sativa), 5'ss of exon 2
CCTCTTTTTCAAGCAGGAAATGGAGCTTTCTTTGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCAgtaagtaaataatcatgtatgtcattctctaatggtcctttcccatttatttggggctaatgctgacacattggaaactgtattgttt-tag
 || ||||||||||| || ||||||||||| |||||||| ||||| ||||||||||||||||| ||||| |||||  |||| |||||||     |||         ||   ||||  |   |||  | ||  |      ||||| |  | ||| |   ||  | |  | |  ||
TCTTTTTTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTTCAAAATGCTGGGAAAACATCGCTTGTGAATGTCATTGCTgtaagta-----tca--------gtttcttaattatttattc--acttgctgaattataatgatttctcatggatcaccatgtaatctgcag

upper sequence: Vv00s0601g00030.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G007188_T01 (Zea mays), 5'ss of exon 2
CCTCTTTTTCAAGCAGGAAATGGAGCTTTCTTTGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCAgtaagtaaataatcatgtatgtcattctctaatggtcctttcccatttatttggggctaatgctgacacattggaaactgtattgttttag---
|||||| |||||||| || ||||||||||| ||| |||| || || ||||||||||||||||||||||| ||     |||| |||||||  |||||||     || ||   ||     | | | |    | | |   |  |    ||   ||||   ||   | |  |||| |   
CCTCTTCTTCAAGCAAGAGATGGAGCTTTCATTGGTAGGGCTCCAAAATGCTGGGAAAACATCACTTGTGAACTCCATTGCTgtaagtat-taatcat-----tcttttcttaccacccatatactggatgtataatgaaatatatgtatcattcataaacatgtattttttgcag

upper sequence: Vv00s0601g00030.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G081622_T01 (Zea mays), 5'ss of exon 2
CCTCTTTTTCAAGCAGGAAATGGAGCTTTCTTTGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCAgtaagtaaataatcatgtatgtcattctctaatggtcctttcccatttatttggggcta-atgctgacacattggaaac-tgtattgttttag
|||||| |||||||| || ||||||||||| |||||||| || || |||||||||||||| |||||||| ||   | |||| |||||||     | | | || || ||   ||    || | | |    | ||||  |  | ||  | |  | | | |||| |||||| ||  ||
CCTCTTCTTCAAGCAAGAGATGGAGCTTTCCTTGATAGGGCTCCAAAATGCTGGGAAAACGTCACTTGTGAACTCTATTGCTgtaagta-----ttaggcat-tcttttggtaccactcatatactggatgtttgatgaaatatatttatccttggtaaacatgtatttttgcag

upper sequence: Vv00s0601g00030.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: PP1S6_409V6.2 (Physcomitrella patens), 5'ss of exon 3
CCTCTTTTTCAAGCAGGAAATGGAGCTTTCTTTGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCAgtaagta-----aataatcatgtatgtcattctctaatggtcctttcccatttatttggggctaatgctgacacattggaaactgt----attgttttag
||| || |||||||| || |||||||| ||  ||||||| || ||||| |||||||||||||| ||||| |||||| |||| ||| |||     |||  ||   |  |  |       ||||  | | || ||  |    |  | | |  ||   | |  |   | ||    ||| |||   
CCTGTTCTTCAAGCAAGAGATGGAGCTGTCGCTGATAGGTCTGCAGAACGCTGGGAAAACATCGCTTGTCAATGTTATTGCGgtatgtatctgtaattttctcctccgcaagcaagctatggcgcatgcctataaacgctgtacaagttgtggaccgtcagggtcagttcggattatttaca

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|30256144|gb|CB971987.1|CB971987
EST:     TGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCA                         ACTGGTGGATATAGTGAAGACATGATTCCTACG
genomic: TGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCAgtaagtaaat ... attgttttagACTGGTGGATATAGTGAAGACATGATTCCTACG
EST: gi|110703370|gb|EE080157.1|EE080157
EST:     GAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCA                         ACTGGTGGATATAGTGAAGACATGATTCCTACG
genomic: GAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCAgtaagtaaat ... attgttttagACTGGTGGATATAGTGAAGACATGATTCCTACG
EST: gi|110379513|gb|EC944712.1|EC944712
EST:     TGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCA                         ACTGGTGGATATAGTGAAGACATGATTCCTACG
genomic: TGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCAgtaagtaaat ... attgttttagACTGGTGGATATAGTGAAGACATGATTCCTACG
EST: gi|30256212|gb|CB972055.1|CB972055
EST:     TGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCA                         ACTGGTGGATATAGTGAAGACATGATTCCTACG
genomic: TGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCAgtaagtaaat ... attgttttagACTGGTGGATATAGTGAAGACATGATTCCTACG
EST: gi|33407863|gb|CF213490.1|CF213490
EST:     TGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCA                         ACTGGTGGATATAGTGAAGACATGATTCCTACG
genomic: TGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCAgtaagtaaat ... attgttttagACTGGTGGATATAGTGAAGACATGATTCCTACG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCTCTTTTTCAAGCAGGAAATGGAGCTTTCTTTGATAGGACTTCAGAATGCTGGGAAAACATCACTTGTTAATGTTGTTGCAgtaagtaaataatcatgtatgtcattctctaatggtcctttcccatttatttggggctaatgctgacacattggaaactgtattgttttag

- - - - - - - - - - - - - - - - - - - - - - -  ATGCTG