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'   

Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctagagtgttgtaaaaaacccttttgcacatacaaatccctgttctttggtatctataatctcttaaaaagtttgtttttcattgcactactaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACAACCCGCCAGTCAGCTCGTGCGCTCCTTGCTATACATGACTACTTCTCCC

Basic information

species Vitis vinifera
transcript Vv13s0084g00660.t01
intron # 11
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G056099_T01 (Zea mays), 3'ss of exon 9
--------------------------------------------------------ctagagtgttgtaaaaaaccc------ttttgcac-atacaaat-ccctgttctttgg-----tatctata-atctcttaaaa-----agttt----gtttttcattgcactactaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACAACCCGCCAGTCAGCTCGTGCGCTCCTTGCTATACATGACTACTTCTCCC
                                                         | || |||  ||   |   |      |||    | |||||  | | ||  | ||  |     ||| |||  | |||||         || |     |  |||   ||  ||| ||     ||||||||||||||||||| || ||  |||| |||||||| || || ||||||| ||| ||  | ||||||||||| ||||| || ||||||||||| || |
gtaaacttttcagatacctccaaccctggcaaacatttagttttgttgtttctgttgttgactgtcatagggagatcatgtcatttgattcgatacattttctctacttttaagaaatatatgtatgtagctcttggtgttcctagctctgaagacttttggtgttctattatcgttagGCTGACAATCTACGACAGCAGACCTTACATCAGATGCAACGTATCCTGACAATCCGACAAGCTGCTCGTGCGCTTCTTGCAATCCATGACTACTTTTCAC

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GRMZM2G174284_T01 (Zea mays), 3'ss of exon 9
-----------------------------------------------------------ctagagtgttgtaaaaaacccttttgcac-atacaaatccctgttctttggtatctataatctcttaaaaagtttgtttttcattgcactactaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACAACCCGCCAGTCAGCTCGTGCGCTCCTTGCTATACATGACTACTTCTCCC
                                                              ||  |   ||  |   | |||    | |||||  | ||   | |||   |  |||  | | |      || ||  |     ||  ||| |     |||||||||||||||||||| || ||  | || |||||||| ||||| |||||||  || ||  | ||||| ||||| ||||| ||||| |||||||| || |
gtaaactttctgatacttctaaccctgtcaaacatttagttttgctgtttctgttattgactgatagggatatcatgtcatttgattcgatacattttccccatttttaagaaatatg-tatgtagctctgtctgaatacttctgttctatttgcctcagGCTGACAATCTACGACAGCAGACCTTGCATCAGATGCAACGCATCCTGACAATTCGACAAGCCGCTCGCGCGCTTCTTGCAATACACGACTACTTTTCAC

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA15G37220.1 (Glycine max), 3'ss of exon 7
ctagagtgttgtaaaaaacccttttgcacatacaaatccctgttctttggtat-ctataatctctta--aaaagtttgtttttcattgcactactaatt-ccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACAACCCGCCAGTCAGCTCGTGCGCTCCTTGCTATACATGACTACTTCTCCC
|| |  | |||| |  ||   |||   | |||  | |  |  |   | |   |  || ||| ||| |   |    |   |||   | |   |  | ||| | ||||||||||||| || |||||||| || ||||| |||||||| ||||||||||| ||||| ||||||||||| ||||||||||||||||||||||| || |
cttgc-tcttgttagcaaatattt---atatattatttacaataaatagccctattaaaatatctaattcatgactccatttctgtggtgtttatgattacaagGCTGACAATCTTCGCCAACAAACTCTTCAACAAATGCACCGTATACTGACAACTCGCCAATCAGCTCGTGCACTCCTTGCTATACATGACTACTTTTCGC

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA13G26280.1 (Glycine max), 3'ss of exon 11
ctagagtgttgtaaaaaacccttttgcacatacaaatccctgttctttggtatctata-atctcttaaaaagtttgtttttcattgcact-actaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACAACCCGCCAGTCAGCTCGTGCGCTCCTTGCTATACATGACTACTTCTCCC
  |   | |||| || ||   ||||| | ||      |  |         |||  | | ||||    ||    |   |||   | |   | || | |   ||||||||||||| || || ||||| || ||||| |||||||| ||||||||||| ||||| |||||||| || ||||||||||||||||||||| | || |
--aagctcttgttaacaaatattttgtatattatttacaataaataaccctattaaaatatctaactaatgactccatttctgtggtgtttacgattataagGCTGACAATCTTCGCCAGCAAACTCTTCAACAAATGCACCGTATACTGACAACTCGCCAATCAGCTCGCGCACTCCTTGCTATACATGACTACATTTCGC

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA10G44270.1 (Glycine max), 3'ss of exon 9
----------------------------------------ctagagtgttgtaaaaaacccttttgcacatacaaatccctg----ttctttggtatctataat--ctcttaaaa-agtttg---tttttcattgcactactaattcca--gGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACAACCCGCCAGTCAGCTCGTGCGCTCCTTGCTATACATGACTACTTCTCCC
                                        |     | |   | ||||  || || || | |  | | | ||     |  ||| || | |  ||  || |||||| |  |||    | || |||    |  | |||  |  |||||||||  | || || || ||| | || || || ||||||||| ||||||| || ||||| |||||||| || ||||| |||||||||||||| ||  
gtatgcttttcttactcacatgtgtgcgatcagtttggtacatatttctcaaagaaaatgctctttcatacagcatttcatggcagattattgataacaaacatcactattaaaataacttggctctgtttatttttgtggtcatttgaaagGCTGACAACTTGCGCCAGCAGACGTTGCATCAAATTCACCGCATATTGACAACTCGGCAGTCGGCTCGTGCACTACTTGCAATACATGACTACTTTTCTA

upper sequence: Vv13s0084g00660.t01 (Vitis vinifera), 3'ss of exon 11
lower sequence: GLYMA20G39050.1 (Glycine max), 3'ss of exon 11
----------------------------------------ctagagtgttgtaaaaaacccttttgcacatacaaatccctgt----tctttggtatctataatctc--ttaaaaag-------tttgtttttcattgcactactaattcc--agGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACAACCCGCCAGTCAGCTCGTGCGCTCCTTGCTATACATGACTACTTCTCCC
                                        |     | |   | ||||  || || || | |  | | | ||     |  ||| |||| |  ||| |  ||||||         | ||||  |  |||   |  | |||    ||||||||||| | || || || ||  | ||||| || ||||||||| ||||||| || || || |||||||| || ||||| |||||||||||||| ||  
gtaaacttttcttactcacatgtacgcgatcagtttggttcatttttctcaaagaaaatgctctttcatacagcatttcatggcagattattgatatcaaacatcactattaaaataacttagctctgttcatttttgtggtggtcatttgaaagGCTGACAATTTGCGCCAGCAGACTTTGCAACAAATTCACCGCATATTGACAACTCGGCAATCGGCTCGTGCACTACTTGCAATACATGACTACTTTTCTA

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|156737550|gb|EV241663.1|EV241663
EST:     TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAG                         GCTGACAATCTACGAACAACAA-CGCTACAACAGATGCACCGCATACTGAC
genomic: TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttc ... ctaattccagGCTGACAATCTACGA-CAACAAACGCTACAACAGATGCACCGCATACTGAC
EST: gi|45771026|gb|CN006878.1|CN006878
EST:     TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAG                         GCTGACAATCTACGACAACAAACGCTACAACAAATGCACCGCATACTGACA
genomic: TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttc ... ctaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
EST: gi|110358202|gb|EC922250.1|EC922250
EST:     TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAG                         GCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
genomic: TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttc ... ctaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
EST: gi|110393937|gb|EC959530.1|EC959530
EST:     TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAG                         GCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
genomic: TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttc ... ctaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
EST: gi|110697733|gb|EE074978.1|EE074978
EST:     TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAG                         GCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
genomic: TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttc ... ctaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
EST: gi|110360089|gb|EC922696.1|EC922696
EST:     TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAG                         GCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
genomic: TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttc ... ctaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
EST: gi|110685242|gb|EE063437.1|EE063437
EST:     TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAG                         GCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
genomic: TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttc ... ctaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
EST: gi|110382490|gb|EC946786.1|EC946786
EST:     TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAG                         GCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
genomic: TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttc ... ctaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
EST: gi|30321084|gb|CD004346.1|CD004346
EST:     TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAG                         GCTGACAATTTTCGACAACAAACGCTACAACAGATGCACCGCATACTGACA
genomic: TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttc ... ctaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
EST: gi|110383071|gb|EC947420.1|EC947420
EST:     TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAG                         GCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
genomic: TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttc ... ctaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
EST: gi|30320498|gb|CD003760.1|CD003760
EST:     TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAG                         GCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
genomic: TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttc ... ctaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
EST: gi|18458746|gb|BM437024.1|BM437024
EST:     TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAG                         GCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
genomic: TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttc ... ctaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
EST: gi|110428204|gb|EC994669.1|EC994669
EST:     TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAG                         GCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
genomic: TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttc ... ctaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
EST: gi|45771257|gb|CN007109.1|CN007109
EST:     TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAG                         GCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA
genomic: TGGCCATGGCCATGGGAAAGCTGGGGACTCTTGAGGGGTTTATTCGTCAGgtattccttc ... ctaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttggtatctataatctcttaaaaagtttgtttttcattgcactactaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACAACCCGCCAGTCAGCTCGTGCGCTCCTTGCTATACATGACTACTTCTCCC
                                           tactaat  putative branch site (score: 1)
                  ttaaaaagtttgtttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctagagtgttgtaaaaaacccttttgcacatacaaatccctgttctttggtatctataatctcttaaaaagtttgtttttcattgcactactaattccagGCTGACAATCTACGACAACAAACGCTACAACAGATGCACCGCATACTGACAACCCGCCAGTCAGCTCGTGCGCTCCTTGCTATACATGACTACTTCTCCC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAGCTC
- - - - - -taaaaaa
- - - - - - - - - ccctttt
- - - - - - - - - - - - - cacatac
- - - - - - - - - - - - - - - - - - tccctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttaaaaa