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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGCTGCAGACTGTTGGGATGCTGAGATTGAGTGCTCTTATGGATGGATTGAGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgagtgatgaattaaaattgttggagaaatatttggagttagatggcacttaacgttgaaaaaatcatatgtttcttctattatggtgttcagaagctt...

Basic information

species Vitis vinifera
transcript Vv17s0000g00160.t01
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os08g42560.1 (Oryza sativa), 5'ss of exon 5
TGCTGCAGACTGTTGGGATGCTGAGATTGAGTGCTCTTATGGATGGATTGAGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgagtgatgaa-------ttaaaattgttggagaaat-atttggagttagatgg-cacttaacgttgaaaaaatcatatgtttcttctattatggtgttcagaagctt
|||||| |||||||||||||| ||||||||||||||||| |||||||| || || || || |||||||| |||||||| ||||||||||| || ||  | || ||     ||       | || ||| ||| | | || || || || |   |||  |     |  |   |   | |  |   || |   ||||| ||           
TGCTGCTGACTGTTGGGATGCAGAGATTGAGTGCTCTTACGGATGGATAGAATGTGTGGGCATTGCTGACAGATCTGCGTATGATTTGCGAGCTCATTCTgtaagcctacaacatctcttgaatatttttgcacatattatgtgtagctctttggatatgctgcacttggattttga-gttcctcattggttatgttgcat--------

upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: LOC_Os04g32650.1 (Oryza sativa), 5'ss of exon 5
TGCTGCAGACTGTTGGGATGCTGAGATTGAGTGCTCTTATGGATGGATTGAGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgagtgatgaat----taaaattgttggagaaatatttggagttagatggcacttaacgttgaaaaaatcatatgtttcttctattatggtgttcagaagctt
|||||| || || |||||||| |||||||| ||||||| ||| ||||||||||| ||||| ||||||||||| |||||||||||| ||||||| ||| ||||  |   |   |    | ||||  ||      |  |  ||   | | ||| | ||  | |    | ||||| || | | | |  |          | | |  |
TGCTGCTGATTGCTGGGATGCAGAGATTGAATGCTCTTTTGGGTGGATTGAGTGTGTTGGGATTGCTGATAGGTCTGCATATGATCTGCGTGCTCACTCGgtatgcattacctatcattaaatgcttacgctcacttgggggacttgctgggagtttgc-tcattataatcaaatatatgtcccttccaaac---taaatgtct

upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM5G821551_T03 (Zea mays), 5'ss of exon 5
TGCTGCAGACTGTTGGGATGCTGAGATTGAGTGCTCTTATGGATGGATTGAGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgag--tgatgaattaaaattgttggagaaatatttggagttagatggca----cttaacgttgaaaaaatcat--atgtttcttctattatggtgttcagaagctt--------------------------------------------------------------------------------------
|||||| |||||||||||||||||||| |||||||| ||||| ||||| ||||| || ||||||||||||||||||||||||||||||   || ||||| || ||  |  || ||     |   |  ||| |  ||   || || ||        | | |  |||  | |    |  |   | ||  | | ||| |||       |||                                                                                      
TGCTGCTGACTGTTGGGATGCTGAGATAGAGTGCTCGTATGGGTGGATAGAGTGTGTGGGTATTGCTGATAGATCTGCATATGATTTGAAAGCTCACACTgtaagcttattgcatctttttcactctagataatttatcagatacatatttttgtccttatattgctacagcagttgaaactgctcatctcatgttgtaactgcacttggtaaatgaattttgtatgttgtcctctgtttggtgtgcaaatatgctactaatattgccgtgattctctgcttactatctcacag

upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G041797_T01 (Zea mays), 5'ss of exon 5
TGCTGCAGACTGTTGGGATGCTGAGATTGAGTGCTCTTATGGATGGATTGAGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgagtg------atgaattaaaattgttggagaaatatttggagttagatggcactta-------acgttgaaaaaatcat-atgtttcttctattatggtgttcagaagctt------------------------------------------------------------------------------
|||||| || ||||||||||||||||| |||||||||||||| ||||| ||||| || ||||||||||||||||||||||||||||||   || ||||  || ||        ||   ||  |     |||| || |     |||  | ||    ||         | ||||| |     ||   ||| ||  | | ||| |||       ||                                                                               
TGCTGCTGATTGTTGGGATGCTGAGATAGAGTGCTCTTATGGGTGGATAGAGTGTGTGGGTATTGCTGATAGATCTGCATATGATTTGAAAGCTCACAGTgtaagctcactgcatctttttcacacactggataatttaccagagacatatttttctcctttggatatgttgatacgtcaattgagttgctcatctcatgttgtagctgcactccctaaatgaaatttgtatcgttgttctctttttgctgtgctactaatattctcatgattgtctacttttatctcacag

upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: GRMZM2G171688_T01 (Zea mays), 5'ss of exon 5
TGCTGCAGACTGTTGGGATGCTGAGATTGAGTGCTCTTATGGATGGATTGAGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgagtgatgaattaaaattgttggagaaatatttggagttagatggcacttaacgttgaaaaaatc-atatgtttcttctattatggtgttcagaagctt---
|||||| || ||||||||||| |||||||| ||||| ||||| ||||||||||| ||||| ||||||||||| ||||| ||||| || ||||| ||| ||||  ||    | |    |   |    ||| |    |  | |   |  || |  ||      |   |  |  || | | | ||   |  | || || ||      
TGCTGCTGATTGTTGGGATGCAGAGATTGAATGCTCCTATGGTTGGATTGAGTGTGTTGGAATTGCTGATAGGTCTGCCTATGACTTACGTGCCCACTCGgtatgtat--agtccgtacactctaggaattgccggttgctttgtt-cattatacaccagtacttttgacttgatacctatacc-taatattaaggaggcaaaa

upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: PP1S310_3V6.1 (Physcomitrella patens), 5'ss of exon 4
TGCTGCAGACTGTTGGGATGCTGAGATTGAGTGCTCTTATGGATGGATTGAGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgagtgat--gaattaaaattgttggagaaatatttggagttagatggcacttaacgttgaaaaaatcatatgtttcttctattatggtgttcagaagctt--------------------------------
 ||   |||||| ||||| ||||||||||| ||||||||||| ||| | ||||| ||||||  ||| ||  ||||||| || ||| |    || || || ||  |||     | ||  |||| |||   || |  |   | ||   |||   | |  || |    | | ||  | || ||    | |  | |   |   |                                  
CGCCCAAGACTGCTGGGACGCTGAGATTGAATGCTCTTATGGTTGGTTCGAGTGTGTTGGTTGTGCAGACCGATCTGCGTACGATCTCAAAGCTCATACAgtatgtgcctcaagttttaatttttgctcaatttgtcatacttttttggggatgatggtcgcccta-ttattagcttgttgggctttactctctgggttccctcattcaatctgctcattctggttgggcccag

upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ09403 (Selaginella moellendorffii), 5'ss of exon 4
TGCTGCAGACTGTTGGGATGCTGAGATTGAGTGCTCTTATGGATGGATTGAGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgagtgatgaattaaaattgttggagaaatatttggagttagatggcacttaacgttgaaaaaatcatatgtttcttctattatggtgttcagaagctt
||| || || || ||||| |||||||||||||||||||| |||||||| || || |||||| |||| ||||||||||| || || |||   || ||| |||| ||   |         |  |      | |  | |   ||  ||  |  |  | ||    | |                                    
TGCCGCGGATTGCTGGGACGCTGAGATTGAGTGCTCTTACGGATGGATAGAATGTGTTGGTCTTGCGGATAGATCTGCTTACGACTTGAAAGCGCACTCGgtaagctgttctcccttttattcctcttagttgtcgtcttt--atttctttctatgtctgtacag-----------------------------------

upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ34615 (Selaginella moellendorffii), 5'ss of exon 4
TGCTGCAGACTGTTGGGATGCTGAGATTGAGTGCTCTTATGGATGGATTGAGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgagtgatgaattaaaattgttggagaaatatttggagttagatggcacttaacgttgaaaaaatcatatgtttcttctattatggtgttcagaagctt
||| || || || ||||| |||||||||||||||||||| |||||||| || || || ||| |||| ||||||||||| || || |||   || ||| |||| ||   |         |  |      | |  | |   ||  ||  |  |    ||      |                                    
TGCCGCGGATTGCTGGGACGCTGAGATTGAGTGCTCTTACGGATGGATAGAATGTGTCGGTCTTGCGGATAGATCTGCTTACGACTTGAAAGCGCACTCGgtaagctgttctcccttttattcctcttagttgtcgtcttt--atttctttctgtgtctgtgcag-----------------------------------

upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ16329 (Selaginella moellendorffii), 5'ss of exon 4
TGCTGCAGACTGTTGGGATGCTGAGATTGAGTGCTCTTATGGATGGATTGAGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgagtgatga-attaaaattgttggagaaatatttggagttagatggcacttaacgttgaaaaaatcatatgtttcttctattatggtgttcagaagctt
||||||||| || |||||||||||||| |||||||| || |||||||| || || |||||  | |||||| | ||||| || || |||   |||||| |||| ||  |      |   ||  ||   ||  | |||    ||   | || | |   |                                            
TGCTGCAGATTGCTGGGATGCTGAGATCGAGTGCTCATACGGATGGATAGAATGTGTTGGCCTCGCTGATCGCTCTGCGTACGACTTGGAGGCACACTCGgtaagctagatcgcttgcatcctttctgagttctttcct-ttcctttgctcgtgcag--------------------------------------------

upper sequence: Vv17s0000g00160.t01 (Vitis vinifera), 5'ss of exon 5
lower sequence: EFJ17803 (Selaginella moellendorffii), 5'ss of exon 4
TGCTGCAGACTGTTGGGATGCTGAGATTGAGTGCTCTTATGGATGGATTGAGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgagtgatgaattaaaattgttggagaaatatttggagttagatggcacttaacgttgaaaaaatcatatgtttcttctattatggtgttcagaagctt
||||||||| || |||||||||||||| |||||||| || |||||||| || || |||||  | |||||| | ||||| || || |||   |||||| |||| ||  |         |||| | |     | |||| ||||   |          | |     |                                    
TGCTGCAGATTGCTGGGATGCTGAGATCGAGTGCTCATACGGATGGATAGAATGTGTTGGCCTCGCTGATCGCTCTGCGTACGACTTGGAGGCACACTCGgtaagcta--------gattgcttgcatcctctttg-agttctttcctttcctttgctcgtgcag-----------------------------------

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|18458200|gb|BM436478.1|BM436478
EST:     GCATATGATTTGCGTGCACACACG                         GATAAAAGCGGTGTTCCCCTTGTGGCACATGAAAAATTTGCAGAACCTAGA
genomic: GCATATGATTTGCGTGCACACACGgtgagtgatg ... ctttgtgtagGATAAAAGCGGTGTTCCCCTTGTGGCACATGAAAAATTTGCAGAACCTAGA
EST: gi|29783904|gb|CB343962.2|CB343962
EST:     AGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACG                         GATAAAAGCGGTGTTCCCCTTGTGGCACATGAAAAATTTGCAGAACCTAGA
genomic: AGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgagtgatg ... ctttgtgtagGATAAAAGCGGTGTTCCCCTTGTGGCACATGAAAAATTTGCAGAACCTAGA
EST: gi|46917791|gb|CN547120.1|CN547120
EST:     ATGATTTGCGTGCACACACG                         GATAAAAGCGGTGTTCCCCTTGTGGCACATGAAAAATTTGCAGAACCTAGA
genomic: ATGATTTGCGTGCACACACGgtgagtgatg ... ctttgtgtagGATAAAAGCGGTGTTCCCCTTGTGGCACATGAAAAATTTGCAGAACCTAGA
EST: gi|29783991|gb|CB344183.2|CB344183
EST:     AGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACG                         GATAAAAGCGGTGTTCCCCTTGTGGCACATGAAAAATTTGCAGAACCTAGA
genomic: AGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgagtgatg ... ctttgtgtagGATAAAAGCGGTGTTCCCCTTGTGGCACATGAAAAATTTGCAGAACCTAGA
EST: gi|28965206|gb|CB344239.1|CB344239
EST:     AGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACG                         GATAAAAGCGGTGTTCCCCTTGTGGCACATGAAAAATTTGCAGAACCTAGA
genomic: AGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgagtgatg ... ctttgtgtagGATAAAAGCGGTGTTCCCCTTGTGGCACATGAAAAATTTGCAGAACCTAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGCTGCAGACTGTTGGGATGCTGAGATTGAGTGCTCTTATGGATGGATTGAGTGCGTTGGTATTGCTGATAGATCTGCATATGATTTGCGTGCACACACGgtgagtgatgaattaaaattgttggagaaatatttggagttagatggcacttaacgttgaaaaaatcatatgtttcttctattatggtgttcagaagctt

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aattaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ggagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaaaaat