Skip to another splice site:
1  
 5'  3'   		2  
 5'  3'   		3  
 5'  3'   		4  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aagctctgttactgcaacaagaaccaaccgcttagccccctgtttgagtggtaataggtttcttttaattctatcttctgaagagccttataatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAAAGCAGAAGTGATGGCCAAAACTCAGAAGTCTCAGAGCAAGGGTAATGCA

Basic information

species Vitis vinifera
transcript Vv13s0074g00140.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os01g59990.1 (Oryza sativa), 3'ss of exon 5
-aagctctgttactgcaacaagaacc--aaccgcttagccccctgt--ttgagtggtaataggtttcttttaattctatcttctgaagagccttataatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAAAGCAGAAGTGATGGCCAAAACTCAGAAGTCTCAGAGCAAGGGTAATGCA---
 |   || | | || |     |  ||   |    || |  || ||   ||   || |   || ||     ||||     ||| |||   |  ||||||    |||||| || |||||| |  |||||||||||||||||||||| || |||||||| ||||| |||   || ||| |||||||| | |||   ||||||  |||    
tagcttcgggtgcttccttttgccccctgaatattttgggccatgcaattttttgctctcagattcaaactaatgtgtgcttttgatatgt-ttataa----cagTGAGATCAAGGAGCGCATCAAGAAAACCAAGGATGAGAAAAAGGCAAAGAAGGCAGAGGTG---GCAAAATCTCAGAAGACACAGTCGAAGGGTGGTGCTACC

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G142640_T03 (Zea mays), 3'ss of exon 4
-aagctctgttactgcaacaagaaccaaccgcttagccccctgtttgagtggtaataggtttcttttaattctatcttctgaagagccttataatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAAAGCAGAAGTGATGGCCAAAACTCAGAAGTCTCAGAGCAAGGGTAATGCA---
  |  ||||  | | | | |  | |  | |   |||   ||  |         ||||  | ||   | |||        ||||  | | |  |   |||||||| || |||||| |  ||||||| |||||||||||||||||||| ||||| || || ||||    |||  | |||||| | ||||  ||||||   |     
gtatgtctgccagttctatattaccataacaaatagataccgatgct-----caatacctctccgctcatt--------tgaactgtcgtg-accatgcagTGAGATCAAGGAGCGCATCAAGAAGACCAAGGATGAGAAGAAAGCGAAGAAGGCGGAGGTGAG---CAAGTCCCAGAAGACGCAGACAAAGGGTGCGGTCCAG

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA03G34700.1 (Glycine max), 3'ss of exon 4
aagctctgttactgcaacaagaaccaaccgcttagccccctgtttgagtggtaata---ggtttcttttaattctatcttctgaagagccttataatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAAAGCAGAAGTGATGGCCAAAACTCAGAAGTCTCAGAGCAAGGGTAATGCA
    | | |||||  ||  |     ||    |||   |  | |  |||   || |      | |   |||  | | | |     ||   || ||   |||||||||||||||||||||| |||||||||| |||||||||||||| || |||||||||||||| |  |||||  | || ||  |     | || || | | | 
-gtattttttactttaatcatgtaaaata--ttatttctgtttcagagccttactttttaatgtggattacatatgtttatctgagtctctgatgtggtgcagTGAAATTAAGGAGAGGATCAAGAAAACAAAGGATGAGAAGAAGGCTAAGAAAGCAGAAGTTACAGCCAAGTCACAAAAAGCAGGAGGGAAAGGCATTTCT

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA19G37370.1 (Glycine max), 3'ss of exon 4
--aagctctgttactgcaacaagaaccaaccgcttagccccctgtttgagtggtaataggtttcttttaattctatcttctgaagagccttataatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAAAGCAGAAGTGATGGCCAAAACTCAGAAGTCTCAGAGCAAGGGTAATGCA
   |  | | ||||       | ||        ||    |   | || | |  ||| || | |  ||      ||| |   | |     | ||   |||||||||||||||||||||| |||||||||| |||||||||||||| || ||||||||||||||     ||||  | || ||  |     | || || ||||  
cgtatatattttaccttgtgtaaaatt--ttatttgtttcagcgctttatttttaacagctctacttattacatatttatcggaatctatgatgtggtgcagTGAAATTAAGGAGAGGATCAAGAAAACAAAGGATGAGAAGAAGGCTAAGAAAGCAGAAGTTGCTTCCAAGTCGCAAAAAGCAGGAGGGAAAGGCAATGTT

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA13G21520.1 (Glycine max), 3'ss of exon 4
-------aagctctgttactgcaacaagaaccaaccgcttagccccctgtttgagtggtaataggtttcttttaattctatcttctgaagagccttataatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAAAGCAGAAGTGATGGCCAAAACTCAGAAGTCTCAGAGCAAGGGTAATGCA
       || |  | ||  ||   |     |  |    | |     || ||||  ||  |||| |        |||  | | |     ||    | ||    ||||||||||||||||||||| |||||||||| |||||||| |||||||| ||||||||||||||    || ||  | || || || ||  | || || | |   
tcatccaaaaccttatttatgtttctgagtcttatttttaacagttctttttgcttgcaaatatgg-------aatattgtgtatctgagtctatgatgtgatgcagTGAAATTAAGGAGAGGATCAAGAAAACTAAGGATGACAAGAAAGCTAAGAAAGCAGAAGTTGCAGCTAAGTCCCAAAAATCACAAGGGAAAGGAAGTATT

upper sequence: Vv13s0074g00140.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA10G07680.1 (Glycine max), 3'ss of exon 4
----aagctctgttactgcaacaagaaccaaccgcttagccccctgtttgagtggtaataggtttcttttaattctatcttctgaagagccttataatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAAAGCAGAAGTGATGGCCAAAACTCAGAAGTCTCAGAGCAAGGGTAATGCA---
     || | | |   | | | ||  | ||  ||   |||| |   ||| | || |  |   || |||| || | ||| |     |       ||    |||||||||||||||||||||  ||||||||| |||||||||||||| || |||||||||||   | | |||||  | || || || ||  | || || ||||     
tgtatagatatatatttactataatcatcattcgg--agcctcaattttaactgctcttt--ttgctttcaaatatatgtatctgaatctacgatgtgatgcagTGAAATTAAGGAGAGGAACAAGAAAACAAAGGATGAGAAGAAGGCTAAGAAAGCAGA---GTTTGCCAAGTCCCAAAAATCACAAGGGAAAGGAAATGTTTCG

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|37188150|gb|CF607501.1|CF607501
EST:     AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCG                         TGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
genomic: AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCGgtatgatttc ... taatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
EST: gi|22011818|gb|BQ796852.1|BQ796852
EST:     AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCG                         TGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
genomic: AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCGgtatgatttc ... taatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
EST: gi|71868597|gb|DT017652.1|DT017652
EST:     AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCG                         TGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
genomic: AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCGgtatgatttc ... taatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
EST: gi|77581842|gb|DV219879.1|DV219879
EST:     AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCG                         TGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
genomic: AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCGgtatgatttc ... taatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
EST: gi|71873024|gb|DT022079.1|DT022079
EST:     AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCG                         TGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
genomic: AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCGgtatgatttc ... taatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
EST: gi|110384865|gb|EC949331.1|EC949331
EST:     AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCG                         TGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
genomic: AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCGgtatgatttc ... taatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
EST: gi|110413307|gb|EC979086.1|EC979086
EST:     AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCG                         TGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
genomic: AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCGgtatgatttc ... taatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
EST: gi|71866495|gb|DT015550.1|DT015550
EST:     AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCG                         TGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
genomic: AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCGgtatgatttc ... taatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
EST: gi|30136747|gb|CB922085.1|CB922085
EST:     AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCG                         TGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
genomic: AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCGgtatgatttc ... taatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
EST: gi|110359284|gb|EC920528.1|EC920528
EST:     AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCG                         TGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
genomic: AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCGgtatgatttc ... taatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
EST: gi|110363994|gb|EC927631.1|EC927631
EST:     AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCG                         TGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA
genomic: AGAACTGAAAAACCAGAAGTTCGAGATGCTGCTAGGGAGGCTGCTCTTCGgtatgatttc ... taatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gagtggtaataggtttcttttaattctatcttctgaagagccttataatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAAAGCAGAAGTGATGGCCAAAACTCAGAAGTCTCAGAGCAAGGGTAATGCA
                 ttttaat  putative branch site (score: 3)
             tttcttttaattctat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aagctctgttactgcaacaagaaccaaccgcttagccccctgtttgagtggtaataggtttcttttaattctatcttctgaagagccttataatgtgcagTGAAATTAAGGAGAGGGTCAAGAAAACCAAGGATGAGAAGAAAGCAAAGAAAGCAGAAGTGATGGCCAAAACTCAGAAGTCTCAGAGCAAGGGTAATGCA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCAAG
- - -ctgttac
- - - - - - -gcaacaa
- - - - - - - - - - - accaacc
- - - - - - - - - - - - - - - - - -ccccctg
- - - - - - - - - - - - - - - - - - - - - - tgagtgg