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

gtccaacttctctttcccattcctaataatcacggaaagcatagctacctctgctaataggatgaatcatgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC

Basic information

species Vitis vinifera
transcript Vv00s0301g00030.t01
intron # 12
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os07g37740.1 (Oryza sativa), 3'ss of exon 12
-------------------------------------------------------------------------------------gtcca---acttctctttcccattcctaataatcacggaaagcatagctacctctgctaataggatgaatcatgcagctcttgttcactgtttctgttgtttcacctg-gtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC
                                                                                      || |   |  | | | |   |   || |||||     |  |   |  ||  | |  | ||   || |||  |  ||   | ||  |      | ||| |  ||  || |  |||||||||| || |||||||||||||| ||||| ||||| ||||||||||||||||| ||  | || || || ||| |||| || || |||   |   |     
gtcagtcctgcgaataacaaatactccctccgtttcatattataagactttctagcattgcccatattcatatagatgttaataaatctagacatatgtgtctagaaagtcttataatataaaacggagaaagtatgttt--ttatgaaataaattctcaag---tagtctatctgagccgttttgacatttgtgaatgcagCAAGTGTACATGTACTTCCGAGGAAGTGGAAAAGCTGCTGAGATGAAGCGTGATGCAACTAGGGGTGCTATGCGGGCAGCTTTTTAATTATCAGAAAAGA

upper sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os05g42330.1 (Oryza sativa), 3'ss of exon 11
--gtccaacttctctttcccattcctaataatcacggaaagcatagctacctctgctaataggatgaatcatgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC
  || |||| |  | |   ||||| ||       |  | |    |      |||  || |   ||      |  || || ||  || || ||        ||||      ||||||||||||| ||||||||||| || ||||| ||||| || |||||||| ||||| || ||| | || ||  ||||  | ||||| | | |   ||   |  
aggttcaacatagcatggacattctta-------catacatttcaatcgtttct--tagtcaaattttcattttagatcatgaccattgattgc------tcactcaacatgcagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCCGCAGAGATGAAACGTGAGGCGGCACGTGGTGCTCTGAGCTCCGCATTCTGATGAAACATGCCTT

upper sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: LOC_Os01g57220.1 (Oryza sativa), 3'ss of exon 11
gtccaacttctctttcccattcctaataatcacggaaagcatagctacctctgctaataggatgaatcatgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC
  | ||  | |  |||   || | |  ||         |||  |||  ||    |       |    |  | || | |  |||     ||  |  ||||     |   ||||||||||||| ||||| ||||| || ||||| || || ||||||||||| ||||| || ||  | || || |||||  | || || | |    ||   | | 
ccctaagattttgttcttgttgcaataaaatttccgctgcaatgctgtcttcatt-------ttctcctgggagatgtcattctgaacttg-gccgttt-----gaaatgcagCAAGTATACATGTATTTCCGTGGAAGTGGGAAGGCTGCTGAGATGAAACGTGAGGCAGCTCGTGGTGCTATGAGATCGGCCTTTTGATAGAGCTGCTTCG

upper sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G169773_T01 (Zea mays), 3'ss of exon 10
----------------------------------------------gtccaacttctctttcccattcctaataatcacgg--aaagcatagctacctctgctaataggatgaatcatgc-----agctcttgttcactgtttctgttgtt-tcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC
                                              ||     |  || ||  ||  | |  |  |   |    | ||||    | ||||  | | ||  | ||| || |           ||||    | |  | ||||| | | || |||| ||||||||||| ||||||||||| || ||||| ||||| || ||||||||||| || || ||  | || || ||||||  ||| || | |    || |     
gtgggtatcatgtttttaccttttgctgtccctagaattctgatgtgtagggatattcattagcaa-catggtgtttctgtctcatgcatcataatctctcttta-agtttcaattattctagaagagagctgttttgagatattattgttctgaacttgttt-cagCAAGTATACATGTACTTCCGTGGAAGTGGAAAAGCTGCAGAGATGAAGCGAGAGGCGGCCCGTGGTGCTATGAGGAATGCCTTTTGATAGAGCGACCTAG

upper sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GRMZM2G041181_T01 (Zea mays), 3'ss of exon 12
gtccaacttctctttcccattcctaataatcacggaaagcatagctacctctgctaataggatgaatcatgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC
                |  ||    || ||||     | | |  |||  | | || |    |  ||   | ||| | |     |||    |  || ||  |||  |  |||||||||| || ||||||||||| || ||||| || || || |||||||||||||| ||  | || || || ||||| || ||||| ||||  ||   |    
--------------gtcagttttctattatca-----accgtt-ctaattttcctga----accaac--ttcag-tgtgacatacttgagccctttttggacc--gcgtgcagCAAGTGTACATGTACTTCCGTGGAAGTGGAAAGGCTGCAGAGATGAAGCGTGATGCGACGAGGGGTGCAATGAGAGCCGCATTTTAAGTGTGGTGTGGTA

upper sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA15G07480.2 (Glycine max), 3'ss of exon 11
gtccaacttctctttcccattcctaataatcacggaaagcatagctacctctgctaataggatgaatcatgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC
|| | | |   | |    ||   |    |    |||||   ||  || | ||   | |      || ||   || |  |||||||| ||| | | ||| ||       | ||||||||||||||||||||||| |||||||| || || |||||||||||||  || || ||||||||||| ||||||| |||| | | |      | ||   
gttcgaatatacatctgaatatttttggaaagtggaaa---tacttagcactttgactgaacataaccaa--agttaatgttcactttttgtttggttgca-------tacagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCAATGAGGGATGCAATATGATAAATTACTTTGT

upper sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA13G31830.1 (Glycine max), 3'ss of exon 13
gtccaacttctctttcccattcctaataatcacggaaagcatagctacctctgctaataggatgaatcatgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC
||   | |   | |  | |||  |    |    |||||   |    || |   || |    || |   | | |   | |||||||| ||| ||||  ||  | |      ||||||||||||||||||||||| |||||||| || || |||||||||||||  || || |||||||||||  |||||||||||   | |             
gtttgaatatacatctcaatttttttggaaagtggaaacacttagcactttgactga--acataaccaaagta---catgttcactttttttgtttgtttgcata-----cagCAAGTATATATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAGCAGGAGGCTGCAAGAGGAGCATTGAGGGCTGCAAGATGA-------------

upper sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA07G31090.3 (Glycine max), 3'ss of exon 11
gtccaacttctctttcccattcctaataatcacggaaagcatagctacctctgct---aataggatgaat--catgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC
||   | | | |||    |    ||  |||||    ||||| | | ||| |   |   |||   |||| |  | | |  |     |  |||   | | || |||    || | | ||||||||||| ||||||||||| |||||||| || || ||||||||||| || |||||||| || ||||| |||||||||||| | | | ||  ||||    
gtttgattacacttcttgaacttta-caatcatcttaagcacatccaccaccattttgaatgacatgatttccttacgacatacctctactcactgt-ttctttggtttgctatacagCAAGTATACATGTACTTCCGTGGCAGTGGTAAGGCTGCTGAGATGAAACGGGAAGCCGCCAGGGGAGCAATGAGGGCTGCAATATGATGCATCAATCATG

upper sequence: Vv00s0301g00030.t01 (Vitis vinifera), 3'ss of exon 12
lower sequence: GLYMA13G25460.1 (Glycine max), 3'ss of exon 11
gtccaacttctctttccca--ttcctaataatcacggaaagcatagctacctctgctaataggatga-------atcatgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC
||   ||| | |||    |  || | ||| |||      |      | | |  |   |||   ||||       || |   | | | |    |||   | | || |||    || | | ||||||||||| ||||||||||| |||||||| || || ||||||||||| || || |||||||| |||||  ||||||||||| | | |  |  || |    
gtttgactacacttcttgaactttccaatcatcttaagcacatgcaccagcattttgaatgccatgatttccttatgaattaccacataccaactcactat-ttctttggtttgctatacagCAAGTATACATGTACTTCCGCGGCAGTGGGAAGGCCGCTGAGATGAAACGGGAGGCCGCAAGGGGAGCACTGAGGGCTGCAATATGATTCATCAGTCTTG

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|110694691|gb|EE072020.1|EE072020
EST:     GGTTTGGAATGTTCTGTGTTGAATCAGTGCTCAGCATCTGGGTTATTCAG                         CAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGT
genomic: GGTTTGGAATGTTCTGTGTTGAATCAGTGCTCAGCATCTGGGTTATTCAGgtccaacttc ... tggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGT






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aggatgaatcatgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC
                                      tttcacct  CT-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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtccaacttctctttcccattcctaataatcacggaaagcatagctacctctgctaataggatgaatcatgcagctcttgttcactgtttctgttgtttcacctggtttgcagCAAGTATATATGTACTTCCGAGGCAGTGGCAAAGCAGCTGAGATGAAGCGTGAAGCCGCAAGAGGAGCCATGAGGGCTGCATTGTAAGGCTGCAATTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG