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'   		9  
 5'  3'   		10  
 5'  3'   		11  
 5'  3'   		12  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gcatcccaacttaagatgctcttagtatcctgatgttgtatacaaatgctaacctcataaatctgtcatctctcgctgcctttgtctgtctatgttccagCACCATTCTAAGCTGCTGTGAGGATGGGACAATCTGGCGATGGGATGCTGTTGCAACACCCTGAGCTATTCGTAAGGGTCTCGTCACAGGGCTTCACCAG

Basic information

species Vitis vinifera
transcript Vv19s0014g05210.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA10G02690.3 (Glycine max), 3'ss of exon 11
gcatcccaacttaagatgctcttagtatcctgatgttg-tataca-aatgctaacctcataaatctgtcatctctcgctgcc-tttgtctgt---ctatgttccagCACCATTCTAAGCTGCTGTGAGGATGGGACAATCTGGCGATGGGATGCTGTTGCAA-CACCCTGAGCTA--TTCGTAAGGGTCTCGTCACAGGGCTTCACCAG
              |    ||||  |||  |||||||| |   || |||  |||    ||     | |  | | |  |||   || ||   |    ||||||  || || ||  | || |||||||||||||||||||| ||||| ||||||| |||| ||| | |||    |||  ||   |         |||    | |  ||   
--------------gtaattctttatatattgatgttgctgctcataattttaagacaatgttgtttttgtttataactgtagttcgttcttgtgttatgttgtagTACTATATTGAGTTGCTGTGAGGATGGGACAATATGGCGTTGGGATGATGTTACAAACTCCCCAGACTAACTTATCACATACTATATCAATCTGATGTAC---

upper sequence: Vv19s0014g05210.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA13G36310.1 (Glycine max), 3'ss of exon 12
gcatcccaacttaagatgctcttagtatcctgatgttgtatacaaatgctaacctcataaatctgtcatctctcgctgcctttgtctgt---ctatgttccagCACCATTCTAAGCTGCTGTGAGGATGGGACAATCTGGCGATGGGATGCTGTTGCAACACCCTGAGCTATTCGTAAGGGTCTCGTCACAGGGCTTCACCAG
              |    ||||  ||   ||||||   |||    || ||   |  |   |  ||  |        | | ||   |||   |||||||  || || ||  | || |||||||||||||||||||| ||||| ||||||| | |   ||| | |      |  |  ||  |   | | |              
--------------gtaattcttcatacattgatgtca-ataattttgatataatattgttttagtttttaactatagtcctttcttgtgtgctatgttgtagTACTATATTGAGTTGCTGTGAGGATGGGACAATATGGCGTTGGGATGTT-TCAAAACCCTCAACCTCAACCTCAACCGCAGCCTAA--------------
















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|110378718|gb|EC943862.1|EC943862
EST:     ATTCAATCAAAATCTCCAATCAGGCAGACTGCCATGTCCTTTGACGGAAG                         CACCATTCTAAGCTGCTGCGAGGATGGGACAATCTGGCGATGGGATGCTGT
genomic: ATTCAATCAAAATCTCCAATCAGGCAGACTGCCATGTCCTTTGACGGAAGgtgactctca ... tatgttccagCACCATTCTAAGCTGCTGTGAGGATGGGACAATCTGGCGATGGGATGCTGT
EST: gi|110374010|gb|EC938475.1|EC938475
EST:     ATTCAATCAAAATCTCCAATCAGGCAGACTGCCATGTCCTTTGACGGAAG                         CACCATTCTAAGCTGCTGCGAGGATGGGACAATCTGGCGATGGGATGCTGT
genomic: ATTCAATCAAAATCTCCAATCAGGCAGACTGCCATGTCCTTTGACGGAAGgtgactctca ... tatgttccagCACCATTCTAAGCTGCTGTGAGGATGGGACAATCTGGCGATGGGATGCTGT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgctaacctcataaatctgtcatctctcgctgcctttgtctgtctatgttccagCACCATTCTAAGCTGCTGTGAGGATGGGACAATCTGGCGATGGGATGCTGTTGCAACACCCTGAGCTATTCGTAAGGGTCTCGTCACAGGGCTTCACCAG
 tgctaac  putative branch site (score: 1)
                                       tctgtct  putative PPT
         tcataaat  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gcatcccaacttaagatgctcttagtatcctgatgttgtatacaaatgctaacctcataaatctgtcatctctcgctgcctttgtctgtctatgttccagCACCATTCTAAGCTGCTGTGAGGATGGGACAATCTGGCGATGGGATGCTGTTGCAACACCCTGAGCTATTCGTAAGGGTCTCGTCACAGGGCTTCACCAG

-catccca
- - - - - - - - - - - - - - cctgatg
- - - - - - - - - - - - - - - - - - - -atacaaa
- - - - - - - - - - - - - - - - - - - - - - - - - aacctca