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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gatttaagtgtttccatcatagtgttattgatgctgatgttggattctgaaatctatgcttttataattccattgaataagttttatgggtatctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATATATGCAGATGGATGGGGAGCCATGGAAACAGCCAATAAACAATGAGTTTT

Basic information

species Vitis vinifera
transcript Vv11s0052g01840.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: LOC_Os08g15090.1 (Oryza sativa), 3'ss of exon 13
--gatttaagtgtttccatcatagtgtta-ttgatgctgatgttggattctgaaatctatgcttttataattccattgaataagttttatgggtatctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATATATGCAGATGGATGGGGAGCCATGGAAACAGCCAATAAACAATGAGTTTT
    ||||  |    |    |   ||  | ||    ||   | |||  |  || |   ||    | | ||||  ||| ||       ||        |||||||| |||||||| |||||||| |||| ||||||  | |||| | | ||||| ||||| |||||||||||||||||||| || ||| |  || | ||||  |
tcagtttagataaa-cagctactttgcaaattacaactccagatggcattcgacactgatatcctcaaaatt--atttaagcgacgctacctactgttttcagGCAGCAGCAATACGATTGGAGATCAAAGGTGGGCAATGGAGGGATGCATACATGCAAATGGATGGGGAGCCATGGAAGCAACCATTGGACCACGAGTACT

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA17G07480.1 (Glycine max), 3'ss of exon 11
gatttaagtgtttccatcatagtgttattgatgctgatgtt-ggattctgaaa-tctatgctttt--ataattccattgaataagttttatgggtatctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATATATGCAGATGGATGGGGAGCCATGGAAACAGCCAATAAACAATGAGTTTT
|  ||    || |||||  |    ||||   |||   | ||   ||| ||||| | | |  || |  || |        | |   || |||   ||||||||||||  |||| || ||||||||| ||||||||||| |||||||  | ||||||||||| |||||||| || || |||||||| ||| | | ||| || || |
gtcttg---gtctccattgtttctttat-attgccattatttacattgtgaaaatttgtctttctcaatgaccagccccactggtttctatttatatctttcagGCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAATGCATATATGCAAATGGATGGAGAACCTTGGAAACAACCATTGAGCAAGGACTTCT

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA13G01360.2 (Glycine max), 3'ss of exon 11
gatttaagtgtttccatcata-gtgttattgatgctgatgttggattctgaaatctatgcttttataattccattgaa---taagttttatgggta--tctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATATATGCAGATGGATGGGGAGCCATGGAAACAGCCAATAAACAATGAGTTTT
    |   | || |||| ||  |  |  |  |   |  | ||   |    |   | |  |        |||  ||||    | |||| | |   ||  ||||||||||  |||| || ||||||||| ||||||||||| |||||||  | || |||||||| |||||||| || || |||||||||||| | | ||| || || |
---ctttatattgccataatttgcatcgtcaaaatttgtctt---tctcaatgaccagtcccactggtttctcttgactcttgagttctgtttataaatctttcagGCATCAGCTATTCGATTGGAAGTCAGAGGTGGACAGTGGAAAAACGCCTATATGCAAATGGATGGAGAACCCTGGAAACAGCCATTGAGCAAGGACTTCT

upper sequence: Vv11s0052g01840.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: AT5G57690.1 (Arabidopsis thaliana), 3'ss of exon 9
--gatttaagtgtttccatcatagtgttattgatgctgatgttggattctgaaatctatgcttttataattccattgaataagttttatgggtatctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATATATGCAGATGGATGGGGAGCCATGGAAACAGCCAATAAACAATGAGTTTT
   || |||   || | || | | |   ||  ||   |||| |  ||        | |     |  ||  |    || | ||  ||      || |   ||||| ||||| ||  |  |||| || ||||| ||||| |||||  | || | |||||| |||||||| ||||||||||||||||| || | ||  || |  |
catatctaacatttacaattacactac-ataaatatggatgatatatgtctttggcaa-atcgtggtagctaatgtgcaaaaacttgggttttaacgaacagGCGGCAGCGATAAGGCTGGAGATAAGAGGAGGAGACTGGAAAGATGCGTTTATGCAAATGGATGGAGAGCCATGGAAACAGCCTATGACCAGAGACTACT

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|110400722|gb|EC967297.1|EC967297
EST:     ATGCTTCATTTGTAATGGTGGAACTCATCTCTGCCAAGCACATTGCACAG                         GCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATAT
genomic: ATGCTTCATTTGTAATGGTGGAACTCATCTCTGCCAAGCACATTGCACAGgtattgcagt ... tatctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATAT
EST: gi|30303616|gb|CB980410.1|CB980410
EST:     ATGCTTCATTTGTAATGGTGGAACTCATCTCTGCCAAGCACATTGCACAG                         GCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATAT
genomic: ATGCTTCATTTGTAATGGTGGAACTCATCTCTGCCAAGCACATTGCACAGgtattgcagt ... tatctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATAT
EST: gi|30304336|gb|CB981130.1|CB981130
EST:     ATGCTTCATTTGTAATGGTGGAACTCATTTCTGCCAAGCACATTGCACAG                         GCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATAT
genomic: ATGCTTCATTTGTAATGGTGGAACTCATCTCTGCCAAGCACATTGCACAGgtattgcagt ... tatctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATAT
EST: gi|26266030|gb|CA817093.1|CA817093
EST:     ATGCTTCATTTGTAATGGTGGAACTCATCTCTGCCAAGCACATTGCACAG                         GCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATAT
genomic: ATGCTTCATTTGTAATGGTGGAACTCATCTCTGCCAAGCACATTGCACAGgtattgcagt ... tatctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATAT
EST: gi|83276057|gb|DV940065.1|DV940065
EST:     ATGCTTCATTTGTAATGGTGGAACTCATCTCTGCCAAGCACATTGCACAG                         GCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATAT
genomic: ATGCTTCATTTGTAATGGTGGAACTCATCTCTGCCAAGCACATTGCACAGgtattgcagt ... tatctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tctgaaatctatgcttttataattccattgaataagttttatgggtatctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATATATGCAGATGGATGGGGAGCCATGGAAACAGCCAATAAACAATGAGTTTT
                                             tatctttc  CT-rich tract
              ttttataattccattg  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gatttaagtgtttccatcatagtgttattgatgctgatgttggattctgaaatctatgcttttataattccattgaataagttttatgggtatctttcagGCTGCAGCAATCCGATTGGAAATCAGAGGTGGAGAGTGGAAGCAAGCATATATGCAGATGGATGGGGAGCCATGGAAACAGCCAATAAACAATGAGTTTT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - -ccatcat
- - - - - - - - - - - - - - -gatgctg
- - - - - - - - - - - - - - - - - - -tgttgga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccatt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaataag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttatggg