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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...taaactggagtaaaattctggtttccaaatgggagtttctagttgttttcctatttcttcttgttgacttggtagttttcatttgattttcaatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAACTATCTCTATGCCAAAGTTGCAAAATTTGTTGAGAACAAGTTGGAGTTG

Basic information

species Vitis vinifera
transcript Vv17s0000g01720.t01
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: LOC_Os07g46720.2 (Oryza sativa), 3'ss of exon 3
--taaactggagtaaaattctggtttccaaatgggagtttctagttgttttcctatttcttcttgttgacttggtagttttcatttgattttcaatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAACTATCTCTATGCCAAAGTTGCAAAATTTGTTGAGAACAAGTTGGAGTTG
   |||||    |  |    |  | |  |      |  ||  |  |  | |      | ||  | | ||  |  ||  ||     | |    ||||  ||||||||||||| ||||||||||| |||||| |||| || || |||||||| |||||  | ||| | ||  ||||||| ||||| | |||||| |  || || 
aacaaacttatttttaccaattctgttgacgcaatacgtttaaaatactctgtgcgatattggtatcgatgtaataaattggtgcttaaccacaat--gcagGGAATGGTATTCTTGGCATTTTCCTGAGCTGGTCAAAATCGTGAATGATAACTACGTTTATTCTAAGATTGCAAAGTTTGTGGTGAACAAATCTGATTTA

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G110233_T01 (Zea mays), 3'ss of exon 3
-----------------------------------------------------------taaactggagtaaaattctggtttc-caaatgggagtttctagttgttttcctatttcttcttgttgacttggtagttttcatttgattttcaat------ttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAACTATCTCTATGCCAAAGTTGCAAAATTTGTTGAGAACAAGTTGGAGTTG
                                                           ||  | | | | | |  | |  | | |  || | |   |||  |  | |   |||       |      ||   | | || |||   || |||||      |||||||||||||| ||| ||||| ||||||||| | || ||||| ||||||||||| || || ||||||||  |||| || ||| ||| |||||| |  || |||
gtactgtccttgttcatgttctcatataattgtttatggttaacttcttataagcgtaataggccgtatttatagacagtctgctctgatagaaaactctgataatatgaatatgcaaatattccttattatgattatttattgctttctcaataaaacattgcagGGAATGGTTCTCATGGCACTTCCCTGAGCTTGTCAAGATTGTGAATGACAATTACCTTTATGCCAAGCTTGCTAAGTTTATTGTGAACAAATCTGATTTG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GRMZM2G144995_T01 (Zea mays), 3'ss of exon 3
-------------------------------------taaactggagtaaaattctggtttccaaatgggagtttctagttgttttcctatttcttcttgttgacttggtagttttcatttgattttcaatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAACTATCTCTATGCCAAAGTTGCAAAATTTGTTGAGAACAAGTTGGAGTTG
                                     |   ||       |     ||     |  |  |||  | |   |||     |||  | |     ||| |   || | ||   |  ||     | | |||||||||||| ||| ||||| ||||||||| | || ||||| ||||| ||||| || || ||||||||  |||| || ||| | | |||||| |  || |||
gtctgttgcttgttctcctataactgtttattgtcaattttctaagaggcatcataggcagggagctttgaggatatgaatgtgccaatatgcccttggtatgattatttactgttttctcaataaaacact-gcagGGAATGGTTCTCATGGCACTTCCCTGAGCTTGTCAAGATTGTGAACGACAATTACCTATATGCCAAGCTTGCTAAGTTTATCGTGAACAAATCTGATTTG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA05G03150.1 (Glycine max), 3'ss of exon 3
------taaactggagtaaaattctggtttccaaatgggagtttct-----------agttgttttcctatttcttcttgttgacttggtag-------ttttcatttgattt-tcaatt---tgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAACTATCTCTATGCCAAAGTTGCAAAATTTGTTGAGAACAAGTTGGAGTTG
      |       | |  ||| ||   ||    || | | |||||           | |||||||| |        ||||  ||| |           | |  ||||| ||| ||||||   ||||| || ||||| ||||||||||| |||||| ||||||| || || ||||| || ||||| ||||||||||||||||||||| ||||| | |||    |||||
gtagtatgtctcaaatttgaatgctcaattaattatagaattttcttattcaatataatttgttttctttgagaacattgtgaactggaagaattcatttctctatttgctttgtcaattatgtgcagAGAGTGGTATTCTTGGCATTTTCCTGAGCTGGTGAAAATTGTAAATGATAATTATCTGTATGCCAAAGTTGCAAAATTTATTGAGGATAAGGCAAAGTTG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA07G11560.1 (Glycine max), 3'ss of exon 3
--------------------taaactggagtaaaattctggtttccaaat----gggagtttctagttgttttcctatttcttcttgttgacttggt--agttttcatttgattttcaatt---tgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAACTATCTCTATGCCAAAGTTGCAAAATTTGTTGAGAACAAGTTGGAGTTG
                     | |||  | |||   | |  ||| || |        |||||       ||     | || ||    | ||    ||  | || ||   |  |  ||||||   ||||| |||||||| ||||||||||| || ||  ||||||||||  | ||||| || ||||| |||||||||||||| |||||| ||||| | || |   || ||
gtagtttgtgttcaacagtgaatactctaataagtctataattttcatactctaaatagttttcttcctttaaggaaattattaaactcgaaagagttcaattctctgctattcatcaattgtatgcagAGAATGGTATTCTTGGCATTTTCCAGAACTGGTGAAGATTATAAATGATAATTATCTGTATGCCAAAGTTGCTAAATTTATTGAGGATAAATCAAAGCTG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: GLYMA17G13770.1 (Glycine max), 3'ss of exon 3
-------------------taaactggagtaaaattctggtttccaaatgggagtttctagttgttttcctatttcttcttgttgacttggtagttttcatttgattt--------tcaatt---tgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAACTATCTCTATGCCAAAGTTGCAAAATTTGTTGAGAACAAGTTGGAGTTG
                    |  ||  | |||  ||    ||| ||  |||        | |||||  | |        ||  | |  ||| ||  ||||| | | ||        ||||||   ||||| || ||||| || ||||| || |||||| ||||||| || || ||||| || ||||| ||||||||||||||||||||| ||||| | |||    |||||
gtagtatgtttcaacattggatgctcaattaattttaaaattttca--tggtcaaaataatttgttccctttgagaaaatttgtaaactggaaggattcatgtaacttttggcttgtcaattatgtgcagAGAGTGGTATTCATGGCACTTTCCTGAGCTGGTGAAAATTGTAAATGATAATTATCTGTATGCCAAAGTTGCAAAATTTATTGAGGATAAGGCAAAGTTG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT3G12860.1 (Arabidopsis thaliana), 3'ss of exon 3
-taaactggagtaaaattctggtttccaaatgggagtttctagttgttttcctatttcttcttgttgacttggtagttttcatttgattttcaatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAACTATCTCTATGCCAAAGTTGCAAAATTTGTTGAGAACAAGTTGGAGTTG
 |    |    ||   || ||  || || ||      || |   ||||  | ||        || |  ||  | || |   |||   ||||     ||||| ||||||||||| ||||| ||||||||| | || |||||||| ||||||||||| ||||| ||||||||| ||||  || | |   ||||||   |||||
gtttgttttcttattgttttgcctttcagattatgtcttgt--ctgttaccgtaagagaaaatggtttctgagcagctcatattatgtttt-----tgcagAGAATGGTACTCATGGCACTTCCCTGAGCTTGTCAAGATAGTTAATGACAACTACCTCTACGCCAAAGTTTCAAAGATTATCGTCGACAAGTCAAAGTTG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: AT1G56110.1 (Arabidopsis thaliana), 3'ss of exon 3
taaactggagtaaaattctggtttccaaatgggagtttctagttgttttcctatttcttcttgttgacttggtagtttt-catttgattttcaatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAACTATCTCTATGCCAAAGTTGCAAAATTTGTTGAGAACAAGTTGGAGTTG
                | || |||     |     ||||   |||| |     |||          | ||||||| |   |  || ||  |    || |||||||||||| || ||||| ||||| ||  | ||||||||||| |||||||||||||| || |||   ||| ||||  |  ||||  ||||||   |||||
---------------gtttgttttgtgcttttccctttcagattgtgt----gttttcctcgagaaaattggtagctgaactgtttataatgttattacagGGAATGGTATTCGTGGCACTTCCCCGAACTAGTGAAGATAGTCAATGACAACTATCTTTACGCCCGTGTTTCAAAGATGATTGATGACAAGTCAAAGTTG

upper sequence: Vv17s0000g01720.t01 (Vitis vinifera), 3'ss of exon 3
lower sequence: PP1S88_119V6.1 (Physcomitrella patens), 3'ss of exon 3
----------------------------------------taaactggagtaaaattctggtttccaaatgggagtttctag---ttgttttcctatttcttcttgttgact------tggtagttttcatttgattttcaatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAACTATCTCTATGCCAAAGTTGCAAAATTTGTTGAGAACAAGTTGGAGTTG
                                        | |       | | || |  |          |   ||| ||    | || |   |  | | | |    || |      || ||  ||   ||||      |   |||||||| |||||||||||||||||||| ||| |||||||||| ||||||||||||||    ||||||||  | |  || |||||  || |||| | |    | 
gtgagtttcgtttacccccccttcttacttcgcttttgtgtgattatatttgatatcccagcagaggctgagagatttgtaagcatggtctgtgtgatacgtatctcggattgtagtgtgctaaattatgtttgcaacatatcgtgcagGGAGTGGTACTCTTGGCATTTCCCCGAGCTGGTGAAGATTGTGAATGACAACTACACATATGCCAAGCTAGTTAAGTTTGTGAAGGACAAATCGAGCCTC

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|110712950|gb|EE088442.1|EE088442
EST:     CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAA                         GGAATGGTACTCTTAGCATTTCCCTGAAGT-GGTGAAGATAGTGAATGACA
genomic: CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAGgtttgttatt ... caatttgcagGGAATGGTACTCTTGGCATTTCCCTGA-GTTGGTGAAGATAGTGAATGACA
EST: gi|110686032|gb|EE063274.1|EE063274
EST:     CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAG                         GGAATGGTACTCTTGGCATTTCCCCGAGTTGGTGAAGATAGTGAATGACAA
genomic: CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAGgtttgttatt ... caatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAA
EST: gi|110690304|gb|EE067284.1|EE067284
EST:     CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAG                         GGAATGGTACTCTTGGCATTTCCCCGAGTTGGTGAAGATAGTGAATGACAA
genomic: CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAGgtttgttatt ... caatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAA
EST: gi|110718517|gb|EE095438.1|EE095438
EST:     CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAG                         GGAATGGTACTCTTGGCATTTCCCCGAGTTGGTGAAGATAGTCAATGACAA
genomic: CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAGgtttgttatt ... caatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAA
EST: gi|33405708|gb|CF211335.1|CF211335
EST:     CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAG                         GGAATGGTACTCTTGGCATTTCCCCGAGTTGGTGAAGATAGTCAATGACAA
genomic: CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAGgtttgttatt ... caatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAA
EST: gi|161719328|gb|FC068961.1|FC068961
EST:     CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAG                         GGAATGGTACTCTTGGCATTTCCCCGAGTTGGTGAAGATAGTGAATGACAA
genomic: CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAGgtttgttatt ... caatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAA
EST: gi|33404147|gb|CF209774.1|CF209774
EST:     CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAG                         GGAATGGTACTCTTGGCATTTCCCCGAGTTGGTGAAGATAGTGAATGACAA
genomic: CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAGgtttgttatt ... caatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAA
EST: gi|110701410|gb|EE078950.1|EE078950
EST:     CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAG                         GGAATGGTACTCTTGGCATTTCCCCGAGTTGGTGAAGATAGTCAATGACAA
genomic: CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAGgtttgttatt ... caatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAA
EST: gi|161720525|gb|FC070912.1|FC070912
EST:     CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAG                         GGAATGGTACTCTTGGCATTTCCCCGAGTTGGTGAAGATAGTCAATGACAA
genomic: CTTCTCGATACTCTTGATAAAGATATCAATTCCTTCTCCATGAGAGTCAGgtttgttatt ... caatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttcctatttcttcttgttgacttggtagttttcatttgattttcaatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAACTATCTCTATGCCAAAGTTGCAAAATTTGTTGAGAACAAGTTGGAGTTG
                                         ttttc  CT-rich tract
                              ttttcatttgattttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
taaactggagtaaaattctggtttccaaatgggagtttctagttgttttcctatttcttcttgttgacttggtagttttcatttgattttcaatttgcagGGAATGGTACTCTTGGCATTTCCCTGAGTTGGTGAAGATAGTGAATGACAACTATCTCTATGCCAAAGTTGCAAAATTTGTTGAGAACAAGTTGGAGTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGGAG
- - - - agtaaaa
- - - - - - - - - - - - ccaaatg