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

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aggaagcaacatcttgtatgatacatggctttgtcttttatattaggtcctttgggttgaatgaatcaactcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT

Basic information

species Vitis vinifera
transcript Vv01s0150g00180.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os01g70200.1 (Oryza sativa), 3'ss of exon 3
aggaagcaacatcttgtatgatacatggctttgtcttttatattaggtcctttg--ggttgaat-gaatcaactcctatctaactcttttaattgattga-cagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
               |||   |    |  | | ||   || ||    || | ||    |||  | | | ||  |    ||| |   || |   ||    | |||||||||  | ||  | ||||||||||| || ||| |||||||||| ||||||||||| || || |||||| | || || || ||||| |||||  |  ||
---------------gtaaattttccgcttatctccaatacatcctatcatctgctcattggctcgtagcatgtggagtctgatgtttctgtatgtcctatcagAGGTGCCCGCGCGTCGGTTTGGGAGAATTTCAAGAACAACCCGCTGTTTGACATCTCAACCGATCACCCACCCACGTACTACGAAGATATGCAGAGATCT

upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G301552_T01 (Zea mays), 3'ss of exon 10
aggaagcaacatcttgt------atgatacatggctttgtcttttatattaggtcctttg------ggttgaatgaatcaactcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
   || || |    |||       |||| ||         |  || |     ||| ||           ||  |   |   ||  | ||| |   || |   || |  ||||||||||  | ||| |||| ||||||||||| ||| ||||||||||||| |||||||| ||||| |||||| |||| || || ||||||||||| | | | 
gtaaatcatctatctgtctgcaagtgatgcagcttccctccactttttcccagtcattcatcacaacactgcgtccttggtctgatctctgatcattctgcatgttctacagAGGTGCTCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCGACTTACTACGAAGACATGCAGCATTCA

upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G000581_T01 (Zea mays), 3'ss of exon 3
-----------------------aggaagcaacatcttgtatgatacatggctttgtcttttatattaggtcctttgggttgaatgaatcaactcctatct--aactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
                         || ||| | ||        | |    |||  | ||    | |   || |           |       ||  ||||   |   || |   || |  ||||||||||  | ||| |||| ||||||||||| ||| ||||||||||||| |||||||| ||||| |||||| |||| || || ||||||||||| ||| | 
gtaaatcatctatctgtctgcaagtgatgcagcttccctctatgtccgcatcttctttttccccagtcattcatcacaacactgcgtcctgggtctgatctcttatcattctgcatgttctacagAGGTGCTCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCGACTTACTACGAAGACATGCAGCGTTCA

upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G152029_T01 (Zea mays), 3'ss of exon 3
----aggaagcaacatcttgtatgatacatggctttgtc---ttttatattaggtccttt------gggttgaatgaatcaactcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
    |  |   | |    || | |  |    ||||        ||| |     ||| ||           ||  |   |   ||  | ||| |   || |   || |  ||||||||||  | ||| |||| ||||||||||| ||| ||||||||||||| |||||||| ||||| |||||| |||| || || ||||||||| | ||| | 
gtaaatcatctatctgtctgcaagtgatgcagcttccctccactttttccccagtcattcatcacaacactgcgtccttggtctgatctctgatcattctgcatgttctacagAGGTGCTCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCATCGACTTACTACGAAGACATGGAGCGTTCA

upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G141094_T02 (Zea mays), 3'ss of exon 2
----aggaagcaacatcttgtatgatacatggctttgtc---ttttatattaggtccttt------gggttgaatgaatcaactcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
    |  |   | |   ||| | |  |    ||||        ||| |     ||| ||          |||  |   |   ||  | ||| |   || |   || |  | ||||||||  | ||| |||| ||||||||||| ||| ||||||||||||| |||||||| ||||| |||||| | || || || ||||||||||| ||| | 
gtaaatcatatatctatttgcaagtgatgcagcttccctccactttttccccagtcattcatcacaacattgtgtccttggtctgatctctgatcattctgcatgttctatagAGGTGCTTGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACTGATCACCCACCAACTTACTACGAAGACATGCAGCGTTCA

upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G059825_T01 (Zea mays), 3'ss of exon 3
-----------aggaagcaacatcttgtatgatacatggctttgtcttttatattaggtcctttgggt--tgaatgaatcaactcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
           |     | |||     |   ||      ||   || ||| |  |    ||  ||  |  ||  |  ||   ||  |  || |     ||   || |  ||||||||||  | ||| | || ||||||||||| ||| |||||||||| ||||||||||| || || |||||| | ||||| || ||||||||||| ||  | 
gtaattcatctatctgtctacaagcaatgcaattggcacctcgctcatttttggtcctcccactgcttcctgggtctattctctgatgactgatggcattgcctgttctacagAGGTGCTCGTGCATCGGTCTGGGAGAACTTCAAGAACAACCCGCTGTTTGACATCTCGACCGATCACCCACCAACATACTACGAAGACATGCAGCGCTCG

upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G448834_T02 (Zea mays), 3'ss of exon 2
aggaagcaacatcttgtatgatacatggc-tttgtcttttatattag-gtcctttgggttgaatgaatcaactcctatc-taactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
 | |||  |  ||   |  | | |||  | |         ||   |   |  |    ||| | | |   |  | | ||  |   |   | |         ||| || ||  | ||  | || ||||||||||| |||||||||||||| || |||||||| || ||||||||  |||| || || || |||||||| || || 
-gcaagtcaagtcggctccggtccattccatccaatgccaatgccaatatagtacatgtttatttatatatatgccatggttggtggatgatcatgcatgcagGGGCGCTCGCGCGTCGGTGTGGGAGAACTTCAAGGACAACCCGCTGTTCGACATCTCGACGGAGCACCCGTCGACGTACTACGAGGACATGCAGCGCGCC

upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G056702_T01 (Zea mays), 3'ss of exon 3
aggaagcaacatcttgtatgatacatggctttgtcttttatattaggtcctttgggttgaatgaatc--aactcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
 | | |   |  | |  ||   || |     |  |     |    |  || |||  |  ||     |  |  | ||| |||   | | || ||      ||| || ||  | ||| |||| ||||||||||| ||| ||||||||||||| |||||||| || || |||||| | || || || || |||||||| ||||| 
-gtacgtcgctaccttcattgcacgtcctaataacaagccttgatgagccattgaatcaaagagtcctgatgtgctaccta--ccgtatacttacaatgcagGGGCGCCCGTGCATCAGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCAACGGACCACCCACCCACGTACTACGAGGACATGCAGCGTGCC

upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM5G898668_T01 (Zea mays), 3'ss of exon 3
aggaagcaacatcttgtatgatacatggctttgtcttttatattaggtcctttgggttgaatgaatcaactcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
 | ||  || |  |    || |   |   | ||||| |     || |       | |     |   |  || |  || |||     | | |      ||| || ||| | ||  | || ||||||||||| ||| ||||||||||||| |||||||| || || |||||  |||| || || || |||||||| ||  | 
-gtaattaataaatcaactg-tctgtctgtctgtctgtctgtctacgagtgagtgatccggcgg--cggcttccctcaaacgtcacttacttccgcgcagGGGCGCACGCGCGTCGGTCTGGGAGAACTTCAAGAACAACCCGCTCTTCGACATCTCGACGGACCACCCGGCGACGTACTACGAGGACATGCAGCGCTCG

upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA04G37920.1 (Glycine max), 3'ss of exon 3
aggaagca-acatcttgtatgatac-atggctttgtcttttatattaggtcctttgggttgaatgaatcaactcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
   |||||  |||   || || | | ||| |||  | |   | |  |  |         |||       | |||  |   |      ||   |   | | |||||||| || |||||||| |||||||||||||||||||| || || |||||||| ||||||||||| ||||| |||||||| || || |||||||| || 
--taagcatgcatgaagtttggttccatgtcttgatataccaaaacaaatgacaaaaaatgatcctgaaagctcaaactgactgtactttggtatcttatagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACTGAGCATCCAACAACATATTACGAGGATATGCAACGAGCA

upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G33420.1 (Glycine max), 3'ss of exon 3
aggaagcaacatcttgtatgatacatggctttgt-cttttatattaggtc-ctttgggttgaatgaatcaactcctat-------ctaactct-tttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
          ||   || || | ||||   |  | |||| |||  |   | |  | || | ||  ||| | |     |       || ||  | |||       |  |||||| ||||| |||||||| |||||||||||||||||||| | ||| |||||||||||||||||||| ||||| || || || || ||||||||| | || 
----------atgaagtttggtgcatgcaatgatgctttcataacaaaacacacttggatcaacaaataatcctggttgatgaaactgaccgtgttttgcaatcttgcagAGGCGCAAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCTGCTGTTTGACATCTCCACTGAGCATCCAACCACTTACTACGAGGACATGCAAAGAGCC

upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA06G17140.1 (Glycine max), 3'ss of exon 3
aggaagcaacatcttgtatgatac-atggctttgt-cttttatattaggtcctttgg-gttgaatgaatc---aactcctatctaactct-tttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
         |||   || || | | ||| |||  | |||| |||  |   |   |     | |||||  |   ||   | | || ||| |  ||   |   | |||||||||| || |||||||| |||||||||||||||||||| || || |||||||| ||||| ||||| ||||| ||||| || || ||||||||||| |||
-------tgcatgaagtttggttccatgtcttgatgctttcataccaaaacgaataacaataaatgatcctgaaagctcaaactgactgtacttttgtatcttacagAGGTGCCAGAGCAGCAGTGTGGGAGAACTTTAAGGACAATCCACTGTTTGACATTTCCACAGAGCATCCAACAACATACTACGAGGACATGCAACGAGCT

upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT5G61840.1 (Arabidopsis thaliana), 3'ss of exon 3
------------------------------------------------------------------------------------------------aggaagcaacatcttgtatgatacatggctttgtctt-ttatattaggtcctttgggttgaatgaatcaactcctatctaactcttttaattgattg--acagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
                                                                                                 |||   || |      |  | |      ||| ||    | | ||  |  |  ||| |||     || | |    ||     |  |||     | ||  |||| |||||||| ||||| || ||||| ||||| || ||||| ||||| ||||||||||| || ||||||||||| ||||||||||| ||||||||  | || 
gtaatttttttcttatgaaagttcttagctattgttcataataaatttcataaatctcctaaaacagttcataattgctttatcggtttggaattttggacataaaactc---aaaaaaggaaaatttatcagactgtttttagagccatggattgttcttataatcagtgatgatgtttgtttgtcaaactggcacagGGGTGCAAGAGCAGCTGTATGGGAAAACTTCAAAGACAATCCGCTGTTTGACATCTCAACAGAGCACCCAACAACATATTATGAGGACATGCAGAGAGCA

upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ05285 (Selaginella moellendorffii), 3'ss of exon 3
aggaagcaacatcttgtatgatacatggctttgtcttttatattaggtcctttgggttgaatgaatca-actcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
                        |  | | | ||  | | ||        || | |||||   |||  | |||  ||| ||  |||    | ||   ||| |||||  | || || ||||||||||| || ||||| || || |||||||||||||| || |||||||| |  || || ||||| |||||||| || |||
----------------------gtaaagttctctcaat-acatagaaaagctttgtttgaaaagatcttattccgttctgacattttctgctcat--gcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTATGAGGACATGCAGCGAGCT

upper sequence: Vv01s0150g00180.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: EFJ25836 (Selaginella moellendorffii), 3'ss of exon 3
aggaagcaacatcttgtatgatacatggctttgtcttttatattaggtcctttgggttgaatgaatca-actcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
                        |  | | | ||  | | ||        || | |||||   |||  | ||   ||| ||  ||     | ||   ||| |||||  | || || ||||||||||| || ||||| || || |||||||||||||| || |||||||| |  || || || || |||||||| || |||
----------------------gtaaagttctctcaat-acatagaaaagctttgtttgaaaagatcttattcggttctgacatttgctgctcat--gcagGGGTGCTCGTGCTGCTGTTTGGGAGAATTTCAAGGATAATCCTCTCTTTGACATCTCTACCGAGCACCCGATTACGTACTACGAGGACATGCAGCGAGCT

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|161710032|gb|FC058089.1|FC058089
EST:     GGTTTGTTTTATGATGTGAATAATGACCCTGAAGGTGGTTACTATGCAAG                         AGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGA
genomic: GGTTTGTTTTATGATGTGAATAATGACCCTGAAGGTGGTTACTATGCAAGgtatgtgggt ... tgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGA






















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ggtcctttgggttgaatgaatcaactcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT
                                taactcttttaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aggaagcaacatcttgtatgatacatggctttgtcttttatattaggtcctttgggttgaatgaatcaactcctatctaactcttttaattgattgacagAGGTGCAAGGGCAGCAGTTTGGGAGAACTTTAAGGACAACCCGCTCTTTGACATCTCCACTGAGCACCCAACGACATATTATGAAGACATGCAACGTGCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- gaagcaa
- - - - - - - - - - - acatggc
- - - - - - - - - - - - - - - - - - - - - - - - - - -gggttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gaatcaa