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'   		14  
 5'  3'   		15  
 5'  3'   		16  
 5'  3'   		17  
 5'  3'   		18  
 5'  3'   		19  
 5'  3'   		20  
 5'  3'   
21  
 5'  3'   		22  
 5'  3'   		23  
 5'  3'   		24  
 5'  3'   		25  
 5'  3'   		26  
 5'  3'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaaagttgcagatgtctctataaattcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttggaatttttatgccaaaatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA

Basic information

species Vitis vinifera
transcript Vv07s0005g00200.t01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: LOC_Os11g43970.1 (Oryza sativa), 3'ss of exon 20
gtaaagttgcagatgtctctataaattcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttggaatttttatgccaaaatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA
                     | | |      |||       |  ||| |   |  || | | |  |||| |   |  | |         |   |  ||||  | |  |     || | ||||||| || || ||||| ||||||||||| |  |||||  |||||||||| ||||||| ||| |||||||| || ||||||||||||||||| || ||||
--------------------gttactctccatctcatcatattgcaaacatattatcatactcacacagt-tggaatctcacagtgctttactcttaaattactttttc----cttcttagGATGTTGTCACAGAGAACGAATTTGAGAAAAGGCTTCTGGCAGATGTTATACCACCTAATGACATTGGAGTCACCTTTGATGATATTGGAGCCTTGGAAA

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GRMZM2G052403_T01 (Zea mays), 3'ss of exon 11
gtaaagttgcagatgtctctataaattcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttggaatttttatgccaaaatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA
                               |  | || | ||| | |   ||   |   ||  |    |   |  ||||||||| | | |   |  | ||   |  ||    ||| ||||||||| || || ||||||||||||||||| |  ||| |    |||||||| ||||||| ||| |||||||| || ||||||||||||||||| || || |
-------------------------------gtacaatcccctacatattgccgtgctttttggt--gattcctcgagttatttactga-acactctacttacaagtcctt--tttctcagGATGTTGTCACAGAGAATGAATTTGAGAAAAGGCTTTTGGTGGATGTTATACCACCTAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GRMZM2G126453_T02 (Zea mays), 3'ss of exon 5
gtaaagttgcagatgtctctataaattcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttggaatttttatgccaaaatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA
                                   ||  ||||   || |   |||  | ||       |   | |||||| ||  | | ||  |  |  | | |  ||    ||| ||||||||| || || |||||||| |||||||| |  ||| |  |||||||||| || || | ||| |||||||| || ||||||||||||||||| || || |
----------------------------------gtacactctcccaatattgtcatgagttctggtgattcctcaagttagttgctga-atactctatgtataaatcctt--tttctcagGATGTTGTCACAGAGAATGAGTTTGAGAAAAGGCTTTTGGCAGATGTTATACCTCCAAATGACATTGGAGTTACCTTTGATGATATTGGAGCCTTGGAGA

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA10G02400.1 (Glycine max), 3'ss of exon 19
--------------------gtaaagttgcagatgtctctataaa--ttcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttgga-----atttttatgccaaaa-----tttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA
                      ||| ||  |  | | || || |   ||  |||   |||| |  |  |  |     |   ||  |     | ||    || ||||  | |  ||| |||     |  | ||| |    |     |||| |||||||||||||||||||||||||||||||| ||||||||| | |||||||||||||| | ||||||||| || || |||||||||||||||||||||||||
gtaatttaatataagatgttacaaacttaaacctttttccatcatattttgtggagatattttgcattactactggtattcatctagtttctttaccttgtcattttttgaattgtgggattgtcacctgtattcttggaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCACCAACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA10G02410.1 (Glycine max), 3'ss of exon 16
gtaaagttgcagatgtctctataaattcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttggaatttttatgccaaaatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA
   ||| |  |||| | |   || |||| |  | | | | | ||  |        ||   ||  || ||| |||    |||     | |   ||| |||||    ||      |||  |||||||||||||||||||||||||||||||| ||||| ||| | |||||||||||||| | ||||||||| || || |||||||||||||||||||||||||
---aagattaagatattttcgtatattc-taacacaagtatttagca-------tactggtttctctagtttat----ttacactgtaatg-gtttgaattgaattgt-----tttcccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATTCCACCGACTGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA02G17410.1 (Glycine max), 3'ss of exon 15
------------------gtaaagttgcagatgtctctata----aattcatggctctattctctaaaaaaa-----acctcacaaattaatccagtctatgaagttatttaatcacatgttggaatttttatgccaaaa-----tttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA
                   || | ||  | |  | |||  |    | ||  |||   |||| |  |  |  |     | |   | | ||  |  |   | | | | | |  | |      |||  |  | ||| |    |     |||| |||||||||||||||||||||||||||||||| ||||||||| | ||||||||||| || |  |||||||| || || |||||||||||||||||||||||||
gtaatttaatattagatgttacaattataaacctttctccatcatattttgtggagatattttgcattactactggtatccatctagtttctttaccttgtcatgatttgaattgtggaattgtcacctgtattctttgaattgtttttccagGATGTGGTTACTGAGAATGAATTTGAGAAAAAACTTCTTGCTGATGTTATTCCGCCAACCGATATTGGGGTCACATTTGATGATATTGGAGCTTTAGAAA

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA02G17400.1 (Glycine max), 3'ss of exon 16
gtaaagttgcagatgtctctataaattcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttggaatttttatgccaaaatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA
   ||| |  |||| | | | || |||| |  | | | | |  |  |         |   ||  ||  || |||  |   | |  |      ||| |||||    ||      ||   ||||| |||||||||||||||||||||||||| ||||| ||| | |||||||||||||| | ||||||||| || || ||||| |||||||||||||||||||
---aagattaagatatttttgtatattc-taacacaagtattcagca-------tgctggtttctctggtttattta--cactggaatg---gtttgaattgaattgt-----ttgcccagGACGTGGTTACTGAGAATGAATTTGAGAAAAAACTACTTACTGATGTTATTCCACCGACTGATATTGGGGTCACATTTGACGATATTGGAGCTTTAGAAA

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: AT4G02480.1 (Arabidopsis thaliana), 3'ss of exon 19
gtaaagttgcagatgtctctataaattcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttggaatttttatgccaaaatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA
                               |   |||| | | |   ||             |  | | |||  |||||     || |   |||||      | | | | | | ||||||||||| ||||||||||| ||||||||||| |||||  | || ||||| ||||||||||| ||||| || ||  | |||||||||||||||||| | ||||
-------------------------------gtaatattatgttacttaatttctttcttcccaagctgcctagtaagtt-ccggattaagagttgg------tttactatactgtttcagGATGTTGTTACTGAGAACGAATTTGAGAAAAAACTGTTGTCGGATGTCATTCCACCTAGCGATATAGGTGTTTCCTTTGATGATATTGGAGCTCTGGAAA

upper sequence: Vv07s0005g00200.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: AT1G02890.1 (Arabidopsis thaliana), 3'ss of exon 19
gtaaagttgcagatgtctctataaattcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttgg-aatttttatgccaaaatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA
                                     |  |   | | ||| || |       ||   | ||   || | | ||      || ||   |||| |||||| | | | ||||||||||| ||||| ||||||||||| ||||| ||||| || ||||| || ||||| || |||||||| || ||  ||||   ||||||||| ||||| ||||
------------------------------------gtaattatatagaaatcttatg---ctattttgactccaaattaactt--ctggattttaacaattattatgctatattatttcagGATGTTGTTACAGAGAATGAATTCGAGAAAAAACTACTATCAGACGTCATTCCTCCAAGTGATATCGGTGTTTCTTTCAGTGATATTGGGGCTTTGGAAA

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|110727315|gb|EE103938.1|EE103938
EST:     TTCTACAAGGTATTCAAAGTGAAAGCAAGAGTTTGAAGAAATCCCTCAAG                         GATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATT
genomic: TTCTACAAGGTATTCAAAGTGAAAGCAAGAGTTTGAAGAAATCCCTCAAGgtaaagttgc ... aatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATT
EST: gi|161711192|gb|FC058662.1|FC058662
EST:     TTCTACAAGGTATTCAAAGTGAAAGCAAGAGTTTGAAGAAATCCCTCAAG                         GATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATT
genomic: TTCTACAAGGTATTCAAAGTGAAAGCAAGAGTTTGAAGAAATCCCTCAAGgtaaagttgc ... aatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cagtctatgaagttatttaatcacatgttggaatttttatgccaaaatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA
              atttaat  putative branch site (score: 4)
                                               tttttc  putative PPT
                               aatttttatgccaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaaagttgcagatgtctctataaattcatggctctattctctaaaaaaaacctcacaaattaatccagtctatgaagttatttaatcacatgttggaatttttatgccaaaatttttcagGATGTGGTTACTGAGAATGAATTTGAGAAGAAACTTCTTTCAGATGTTATTCCACCTAGTGATATTGGAGTAACTTTTGATGATATTGGAGCTTTAGAAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GAGCTT