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'   		13  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gttgaaatcttgcctgtgcttgtcctgttgatattcacggacttggtaaatttgagcaatgggacacgctcacctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG

Basic information

species Vitis vinifera
transcript Vv06s0009g00690.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: LOC_Os05g36960.1 (Oryza sativa), 3'ss of exon 8
-gttgaaatcttgcctgtgcttgtcctgttgatattcacggacttggtaaatttg--agcaatgggacacgctcacctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG
  | |  ||||    |   |   |     ||| |||     | | ||| || ||   |  | |     | |||||   | | |   | || |  | |    |||| |||||||| || |||||||||||||| || |||||  ||||||| |||||||| ||||| || || ||||||||||| |
tatagttatctcttttacacacatttatctga-atttgtaaaataggtgaagttattattatttttctatgctcaa--actgacagcataatgctttctttagGTTGTTGGAACACCGAATTACATGTGTCCAGAGCTTCTCACAGATATCCCTTATGGATTCAAGTCAGACATCTGGTCTCTTG

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA12G31330.1 (Glycine max), 3'ss of exon 8
gttgaaatcttgc-ctgtgcttgtcctgttgatatt-cacggacttggtaaatttg-agcaatgggacacgctcacctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG
  |  ||| |  |  ||      |  | ||   |||      | ||  ||||| || ||  |  ||    |   |  || |   |    |  | ||||  ||||| || ||||||||||| || ||||||||||||||||||||||||||||||||||| |||||||||||||| ||||| ||||
--tataatatgacattggtaccatattattagcattgtgtttatttcataaatgtgcagttactggttgtgga-agttaattgctgtaaatatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA13G38980.1 (Glycine max), 3'ss of exon 8
gttgaaatcttgc-ctgtgcttgtcctgttgatatt-cacggacttggtaaatttg-agcaatgggacacgctcacctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG
  |  ||| |  |  ||      |    ||   ||| ||   | ||  ||||| || ||  |  ||    |       ||| ||||   |  | ||||  ||||| || ||||||||||| || |||||||||||||| ||||| |||||||||||||| |||||||||||||| ||||| ||||
--tataatatgacattggtaccatatcattaccattgcatttatttcataaatgtgcagttactggttgtggaagttaattgatttaa-atatttgtgtgcagGTGGTAGGAACTCCCAACTATATGTGTCCTGAACTGCTTGCTGATATTCCTTATGGATTCAAATCTGATATTTGGTCACTAG

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA11G18340.1 (Glycine max), 3'ss of exon 8
--gttgaaatcttgcctgtgcttgtcctgt-tgatattcacggacttggtaaatttgagcaatgggacacgctcacctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG
   |  || | ||   |     ||    |  ||| |||||  |||     | ||     | ||         | |  || |   |    |  | | |   ||||| || |||||||| |||||||||||||||||||| ||||| |||||||| ||||| |||||||||||||| ||||| || |
gcttccaattttttaatccatctgattagcgtgacattcatagaca-aacacatagtcaccatatatgggattaa--taattgctgtaaatgtttctatgcagGTGGTAGGAACTCCTAATTACATGTGTCCTGAACTGCTTGCTGATATTCCGTATGGATTCAAATCTGATATTTGGTCACTCG

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA12G09910.1 (Glycine max), 3'ss of exon 8
--gttgaaatcttgcctgtgcttgtcctgt-tgatattcacggacttggtaaatttgagcaatgggacacgctcacctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG
   |  || | ||   |     ||    |  | | |||||  |||    || ||     | |          | |  || |   |    |  | | |    |||| || |||||||| ||||||||||| |||||||| ||||| |||||||| ||||| |||||||||||||| ||||| ||||
gcttccaattttttaatccatatgattagcgtaacattcatagaca-aatacatagtcaccacatatgggattaa--taattgctgtaaatgtttctatgtagGTGGTAGGAACTCCTAATTACATGTGCCCTGAACTGCTTGCTGATATTCCATATGGATTCAAATCTGATATTTGGTCACTAG

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: AT3G44200.1 (Arabidopsis thaliana), 3'ss of exon 8
gttgaaatcttgcctgtgctt-gtcctgttgatat-tcacggacttggtaaatttgagcaatgggacacgctcacctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG
     |||  |   | | ||| |   || |   |     | ||  |  ||  || | |  || | | | | |    |||   |     | || | |    |||| ||||||||||| || |||||||| || ||||| ||||| ||||| |||||||| || || || |||||||||||  |||
tccataatgattattattcttaggattgctctcaagcttctgaactaatac-ttagtgtgatagaaaatggt-gtttatgactcatggaattttatatttagGTTGTTGGAACTCCAAACTACATGTGCCCGGAACTGCTTGCTGATATCCCTTATGGTTTTAAGTCAGATATCTGGTCCTTAG

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: PP1S22_216V6.1 (Physcomitrella patens), 3'ss of exon 8
----------------------------------gttgaaatcttgcctgtgcttgtc-----ctgttgatat-tcacggacttg--gtaaatttgagcaatgg--gacacgctca---cctattcat-ttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG
                                   ||| |||  ||   |    |||       | ||   || || ||| | |   ||   ||||     |     |  | || |   ||    | |  | || |||       |||||||| || ||||| |||||||||||||| || || |||||||| || || ||||| |||||||| || || |||||  |||
gtaagtaatccgttgtgaacctcgtatcatttgcattggaatgatgatcgctgctgtgaatagtttttaccatctcgcggtcgtactgttcgtttggaagttaatcaatccactaatggccggaacgtgctgcttcttgctattgcagGTAGTAGGCACTCCAAATTACATGTGTCCAGAGCTACTTGCAGACATCCCATATGGATTCAAATCAGACATTTGGTCATTAG

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ32716 (Selaginella moellendorffii), 3'ss of exon 8
gttgaaatcttgcctgtgcttgtcctgttgatattcacggacttggtaaatttgagcaatgggacacgctcacctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG
                                             |||| ||     | |  |    |    |  |||        |   |      ||||| ||||| || || ||||| ||||| || ||||||||||| || || || |||||||||||||| ||||| |||||  |||
---------------------------------------------gtaagttc---tattctgttttggcagcgaatttgacaggaagaaaacattgcagGTGGTTGGGACCCCAAATTATATGTGCCCGGAACTTCTTGCCGACATCCCATATGGCTTCAAATCAGATATATGGTCGTTAG

upper sequence: Vv06s0009g00690.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: EFJ20709 (Selaginella moellendorffii), 3'ss of exon 8
gttgaaatcttgcctgtgcttgtcctgttgatattcacggacttggtaaatttgagcaatgggacacgctca-cctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG
                                             |||| ||    | ||        |||| || |||        |   |      ||||| ||||| || || ||||| ||||| || ||||||||||| || || || |||||||||||||| ||||| |||||  |||
---------------------------------------------gtaagtt----ctatactgttttctcagccaatttgacaggaagaaaacattgcagGTGGTTGGGACCCCAAATTATATGTGCCCGGAACTTCTTGCCGACATCCCATATGGCTTCAAATCAGATATATGGTCGTTAG

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|71862067|gb|DT011122.1|DT011122
EST:     GGGATTTTGGACTTGCCAAAACTTTGAAGGCTGATGACTTGGCTTCTTCA                         GTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCT
genomic: GGGATTTTGGACTTGCCAAAACTTTGAAGGCTGATGACTTGGCTTCTTCAgtaagtgcta ... atgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtaaatttgagcaatgggacacgctcacctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG
                     cgctcac  putative branch site (score: 3)
                             tattcattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttgaaatcttgcctgtgcttgtcctgttgatattcacggacttggtaaatttgagcaatgggacacgctcacctattcatttcctacttatgtgcacagGTAGTTGGAACTCCCAATTACATGTGTCCTGAACTTCTTGCAGATATTCCTTATGGCTTCAAATCTGATATCTGGTCTCTAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT
- - - - cttgcct
- - - - - - - -gtgcttg
- - - - - - - - - - - -cctgttg
- - - - - - - - - - - - - - - - - -cacggac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - caatggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cacgctc