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

...atttttttagcttttaaattttttctgttgggcttctgtcaatttagttcctcaaaactctgtcatcttagttgtgagttttttatatatgacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG

Basic information

species Vitis vinifera
transcript Vv17s0000g08170.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os06g34690.1 (Oryza sativa), 3'ss of exon 4
----------------atttttttagcttttaaattttttctgttgggctt------ctgtcaatttagttcctcaaaact--ctgtcatcttagttgtgagttttttatata---------tgact---tgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG
                || ||||     | |  | |  | ||| ||   ||      |||     |||  |   ||| | |  |||  |   ||    | |||  || || ||         | |||   || ||||| ||||||||  ||||||| ||||| |||||||||||||||||||| || || || ||||||||| | |
gtatgtggaacgttagatgttttctctctgttgagtactactgatgaaattattagtctgatgtgttaaattgccaatattttctgctaatgtatgaattagtacttaatctaactttcttgtcactctttggcagTCTATGATTGAGCTAAGCCGTACACAGGATGAAGAAGTTGGTGATGGCACAACATCTGTCATTGTTTTAG

upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: LOC_Os02g14929.1 (Oryza sativa), 3'ss of exon 4
atttttttagcttttaaattttttctgttgggcttctgtca-atttagttcctcaaaactctgtcatcttagttgtgagttttttatatatgacttg-acagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG
| |      ||   ||  |  |     ||| |||  | ||  |      | ||| |  ||| ||| | |   ||   | |  |||||   |        ||||| ||||||||  ||||||||||||| ||||||||||| || ||||| || || || || ||||||||||
aatgaaactgcacgtagctcctaaaccttgagctcttttcttagccctattctcgatgctcagtcctgt--attcctaatactttatgagttgtccatgcagTCTATGATTGAGCTAAGCCGCACACAGGATGAAGAAGTAGGAGATGGCACGACATCTGTTATTGTTCTTG

upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G175510_T02 (Zea mays), 3'ss of exon 4
----atttttttagcttttaaattttttctgttgggcttctgtcaatt-tagttcctcaaaactctgtcatcttagttgtgagttttttatatatgacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG
     | | | || | |   |  ||| | || |    | | ||| ||  |   |  |   |   |  |   |||| |||||      || | | | | |   ||||| ||||||||| |||| || |||||||||||||||||||||||||| ||||| || ||||||||||| |
acccgtatatataccctaccatatttgtgtgctaatgtgcagtctatggttcatgttgtgagtcccatgtacttaattgtgg-----ttgtgtttaaatgtgcagTCTATGATTGAACTAAGTCGTACACAAGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG

upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G069765_T02 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------------------atttttttagcttttaaattttttctgttgggcttc---tgtcaatttagttcctcaaaactctgtcatcttagttgtgagttttttatatatgact-----tg---------acagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG
                                                                              ||| | |    |  |||| |  ||   | |  |   | |  |  || ||        |  | | || |  ||||  |||    | ||  | | |     ||          ||||| ||||| ||| |||| || ||||| |||||||||||||||||||| ||||| || ||||||||||| |
gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagaccccatatatatacctaattgtatgtg-cagtctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAG

upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G069765_T04 (Zea mays), 3'ss of exon 4
---------------------------------------------------------------------------atttttttagcttttaaattttttctgttgggcttc---tgtcaatttagttcctcaaaactctgtcatcttagttgtgagttttttatatatgact----------tga----cagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG------------------------------
                                                                              ||| | |    |  |||| |  ||   | |  |   | |  |  || ||        |  | | || |  ||||  |||    | ||  | | |          | |    ||||| ||||| ||| |||| || ||||| |||||||||||||||||||| ||||| || ||||||||||| |                              
gtatgccaaattatcttggttgcttagctgtggaagtctgttgatgaaattatcagtcaaccatcacatattttttcctttatggtggatggatttgtgttgcgagaccccatatatatacctaattgtatgtg-cagtctgatttatgttgcaagtcccatgtacctaattgtggttgtgttaatgtgcagTCTATGATCGAACTAAGTCGTACACAGGATGAAGAAGTTGGTGATGGCACTACATCTGTCATTGTTCTAGGTATGGGTATTTTTTTGTGAAATTTCTTTT

upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA16G33380.1 (Glycine max), 3'ss of exon 5
---------------------------------------------------------------------atttttttagcttttaaattttttctgttggg-------cttctgtcaat-------ttagttcctcaaaactctgtcatct--tagttgtgagttttttatatatgacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG
                                                                     | |    |    |  |   | | |||  ||         ||||||| |||       |||||| |||   | | ||  |  |  ||  | ||  | | |||| |     |  |||||| |||||||||||||| ||||| ||||| ||||||||||| |||||||| || || |||||  ||||||
gtatttgtatcttttgcttcgctttattgatattgctttgtcacacatacattatacatactgctatatactgcactgcactccaggctatgtcttgtgaaagcatcacttctgttaatctaaggcttagtttctctttattgtgaaacttaataactctgtttctcttatttgaatgtatacagTCTATGATTGAATTAAGTCGCACCCAAGACGAAGAAGTTGGAGATGGAACAACATCTGTCATCATTCTTG

upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA20G35760.1 (Glycine max), 3'ss of exon 2
atttttttagcttttaaattttttctgt---tgggcttctgtcaatttagttcctcaaaactctgtcatcttagttgtgagttttttatatatgacttga--cagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG
     |  | |  |    || ||||| |   | | ||| |     |||| || ||      | ||  || ||  |  |     | |  ||| ||  | ||  ||||| ||||||||||| || ||||| ||||||||||||||||| |||||||| || || |||||  ||||||
----gtgaaaccatggctttctttctatgcattgactttttaaggtttaattgctgtttggtgtgcaattttc-taatactgctatattatttggatggatgcagTCTATGATTGAATTGAGTCGCACCCAAGATGAAGAAGTTGGAGATGGAACAACGTCTGTCATCATTCTTG

upper sequence: Vv17s0000g08170.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA09G28650.3 (Glycine max), 3'ss of exon 5
-------------------------------------------------------------------atttttttagcttttaaattttttctgttggg-------cttctgtcaat-------ttagttcctcaaaactctgtcatct-tagttgtgagttttttatatatgacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG
                                                                   | |    |    |  | | | | |||  ||         ||||||| |||       |||||| |||   | | ||  |  |             | ||||       |  |||||| |||||||| ||||| ||||| |||||||||||||| || |||||||| || || |||||  ||||||
gtatttgtatcttttgcttcactttattgatattgctgtcacacatacgttatacatactgctatatactgcactgcactccagactatgtcttgtgaaaacatcacttctgtgaatctaaggcttagtttctctttattgtgaaacttaccaacactgtcctcttattggaatgtatacagTCTATGATTGAGTTAAGTCGCACCCAAGATGAAGAAGTCGGAGATGGAACGACATCTGTCATCATTCTTG

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|352773628|gb|FQ472410.1|FQ472410
EST:     ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG                         TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
genomic: ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAGgtatggtgtg ... gacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
EST: gi|352764588|gb|FQ472945.1|FQ472945
EST:     ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG                         TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
genomic: ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAGgtatggtgtg ... gacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
EST: gi|37189192|gb|CF608541.1|CF608541
EST:     ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG                         TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
genomic: ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAGgtatggtgtg ... gacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
EST: gi|352769725|gb|FQ468653.1|FQ468653
EST:     ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG                         TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
genomic: ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAGgtatggtgtg ... gacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
EST: gi|71857425|gb|DT006480.1|DT006480
EST:     ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG                         TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
genomic: ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAGgtatggtgtg ... gacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
EST: gi|71857213|gb|DT006268.1|DT006268
EST:     ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG                         TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
genomic: ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAGgtatggtgtg ... gacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
EST: gi|71857633|gb|DT006688.1|DT006688
EST:     ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG                         TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
genomic: ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAGgtatggtgtg ... gacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
EST: gi|71857432|gb|DT006487.1|DT006487
EST:     ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG                         TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
genomic: ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAGgtatggtgtg ... gacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
EST: gi|71859366|gb|DT008421.1|DT008421
EST:     ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG                         TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
genomic: ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAGgtatggtgtg ... gacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
EST: gi|71857184|gb|DT006239.1|DT006239
EST:     ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG                         TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
genomic: ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAGgtatggtgtg ... gacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
EST: gi|71856945|gb|DT006000.1|DT006000
EST:     ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG                         TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
genomic: ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAGgtatggtgtg ... gacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
EST: gi|71857006|gb|DT006061.1|DT006061
EST:     ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG                         TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
genomic: ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAGgtatggtgtg ... gacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
EST: gi|71858194|gb|DT007249.1|DT007249
EST:     ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG                         TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
genomic: ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAGgtatggtgtg ... gacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
EST: gi|71855063|gb|DT004118.1|DT004118
EST:     ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAG                         TCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT
genomic: ATGGAAATTCTATTCTTCGGGAGTTAGATCTTGCTCATCCAGCTGCTAAGgtatggtgtg ... gacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agttcctcaaaactctgtcatcttagttgtgagttttttatatatgacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG
                                 ttttttatatatgact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atttttttagcttttaaattttttctgttgggcttctgtcaatttagttcctcaaaactctgtcatcttagttgtgagttttttatatatgacttgacagTCCATGATTGAATTAAGCCGCACACAAGATGAAGAAGTTGGTGATGGAACTACTTCAGTCATTGTTCTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - -tgttggg
- - - - - - - - - - - - - - - - - -ctgtcaa
- - - - - - - - - - - - - - - - - - - - - - - - -cctcaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ctgtcat