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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TGTTAATTCTCACCCCGTTCGCAATTGCTGTCGAGGGACCACAGATGTGGGCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacatgacaactactgtgtttttcttgtactgtttgtttgtgttttattatctctgtatctatatgttttttttgtgatagaaaaaaccagaggc...

Basic information

species Vitis vinifera
transcript Vv19s0177g00300.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G12080.1 (Glycine max), 5'ss of exon 4
-TGTTAATTCTCACCCCGTTCGCAATTGCTGTCGAGGGACCACAGATGTGGGCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacatgacaactactgtgtttttcttgtactgtttgtt-tgtgttttattatctctgtatctatatgttttt-tttgtgatagaaaaaaccagaggc
 |   ||||||||| || |||||||||||||| || |||||||||||||||||||||||||||||||  ||  | ||||||||||||||||| ||| |||||||||  ||  |  ||||||   | | |  |||  | | |  | ||| | |||| ||  ||  |   || | | | | | |||      |    |||    |
CTTGCAATTCTCACACCCTTCGCAATTGCTGTGGAAGGACCACAGATGTGGGCTGCTGGATGGCAAACAGCTATGTCTCAAATTGGACCCCAATTCATATggtaatttcaataagactact---tatataatgttatctctactatgtttgttatcatggctacactcatctctatctgtatgtatctctattttccatgctc

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G25290.1 (Glycine max), 5'ss of exon 4
-TGTTAATTCTCACCCCGTTCGCAATTGCTGTCGAGGGACCACAGATGTGGGCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacatgacaactactgtgtttttcttgtactgtttgtttgtgttttattatctctgtatctatatgttttttttgtgat---agaaaaaaccagaggc
 || || ||||||| || |||||||||||||| || ||||| || ||||||||||||||||||||||  ||| | ||||||||||||||||| ||| |||||||||  || ||  | |||| |  | |  || ||   |  | ||    |    | | |||||||  || | | ||||   || |   ||   | | |||    
TTGCTA-TTCTCACACCCTTCGCAATTGCTGTGGAAGGACCGCAAATGTGGGCTGCTGGATGGCAAACAGCCATGTCTCAAATTGGACCCCAATTCATATGgtaatttcaagaagattact-tactgtaattttatcat--ggttacactcatctctatctgtatgcatctctattttccatgctttaaggtgatatcaggaaa

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA02G45840.1 (Glycine max), 5'ss of exon 4
TGTTAATTCTCACCCCGTTCGCAATTGCTGTCGAGGGACCACAGATGTGGGCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacatgacaactactgtgtttttcttgtactgtttgtttgtgttttattatctctgtatctatatgttttttttgtgatagaaaaaaccagaggc--
|  |||||||||| || || || |||||||| |||||||||||||||||||| |||||||||||||  ||  | |||||||||||||||||  |  ||||||||| |||  |   |||  || | | |  |||  ||  || |    ||  || |    | |||||  |  || |  |      | || |  |      |  
TTGTAATTCTCACACCATTTGCGATTGCTGTGGAGGGACCACAGATGTGGGCAGCTGGATGGCAAACAGCACTCTCTCAAATTGGACCCCAAGTTATATGgtaattacaaaatgtcta--gtctatctgatgttatgcatgctatgtttccataaaggttatatcttgaaattgtcataaattcacaatattctttttccga

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA14G02930.1 (Glycine max), 5'ss of exon 4
TGTTAATTCTCACCCCGTTCGCAATTGCTGTCGAGGGACCACAGATGTGGGCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacatgacaactact-------gtgtttttcttgtactgtttgttt----gtgttttattatctctgt--atctata-tgttttttttgtgatagaaaaaaccagaggc
|  |||||||||| || || || |||||||| |||||||||||||||||||| |||||||||||||  ||  | |||||||||||||||||  |  ||||||||| |||      |||||        |||| | | ||   ||||| | |    |||   |   ||     |  ||  ||| | ||||||||  || |               
TTGTAATTCTCACACCATTTGCGATTGCTGTGGAGGGACCACAGATGTGGGCAGCTGGATGGCAAACAGCACTCTCTCAAATTGGACCCCAAATTATATGgtaattacaaattgtctactctatctgatgttatccatgctatgtttctgtaaaggtgacatgaaattgtgataaattcataatattttttttccgacaa--------------

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA07G38830.1 (Glycine max), 5'ss of exon 3
TGTTAATTCTCACCCCGTTCGCAATTGCTGTCGAGGGACCACAGATGTGGGCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacatgacaactactgtgtttttcttgtactgtttgtttgtgttttattatctctgtatc-tatatgttttt-tttgtgatagaaaaaaccagaggc
| || |||||||| || || || |||||||| ||||| ||| ||||||||||||| || |||||||  ||| | ||| ||||||| ||| |||| || ||||||  | |  | | ||||    ||   | |||| ||| ||| ||  |  |   || | ||||    |||  |   | |||  || |  | | || ||  ||
TATTGATTCTCACGCCTTTTGCCATTGCTGTGGAGGGCCCAAAGATGTGGGCTGCAGGCTGGCAAACAGCCTTGTCTGAAATTGGTCCCAATTTTGTTTGgtaagtatagta-atctacaaatttcagcatgta-tgtatgtatgcatagttggatttatgtagaacataaataaatatttaagaaaacacacactaggcgc

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA17G01890.1 (Glycine max), 5'ss of exon 3
TGTTAATTCTCACCCCGTTCGCAATTGCTGTCGAGGGACCACAGATGTGGGCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacatgacaactactgtgtttttcttgtactgtttgtttgtgttttattatctctgtatctatatgttttttttgtgatagaaaaaaccagaggc---
| || |||||||| || || || |||||||| ||||| ||| ||||||||||||| || |||||||  ||| | ||| ||||||| ||| |||| || ||||||  | |  |   ||||     | | | |||  |  || ||| | || |||| ||| |   | |     |    || |||  |    ||            
TATTGATTCTCACGCCTTTTGCCATTGCTGTGGAGGGCCCAAAGATGTGGGCTGCAGGCTGGCAAACAGCCTTGTCTGAAATTGGTCCCAATTTTGTTTGgtaagtatagta-gtctacaaatctctgcatgt--taattttttttcttctattttctatcctttttctcttcaaattggtggaactgcaattttagattttt

upper sequence: Vv19s0177g00300.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA13G27680.1 (Glycine max), 5'ss of exon 3
TGTTAATTCTCACCCCGTTCGCAATTGCTGTCGAGGGACCACAGATGTGGGCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacatga---caactact--gtgttt-ttcttgtactgtttgtttgtgttttattatctctgta---tctatatgttttttttgtgatagaaaaaaccagaggc----------------------------------------------
|||||||||| || || || || |||||||| ||||| ||  || | |||||||| || |||||||  || || ||||||||||| ||| |||| ||||||||| |||||      || |  |   ||||  || ||| | || ||      | ||| ||||   |||    | ||| |  | || ||| |  | |  ||   || ||                                               
TGTTAATTCTGACACCTTTTGCCATTGCTGTTGAGGGCCCCAAGGTTTGGGCTGCAGGCTGGCAAACAGCTGTATCTCAAATTGGTCCCAATTTTGTATGgtaagcacatttttttaattttttactgttagtttttgaattggttcaacaagatttcttattgttgtgctttttatttcatgttgttgggccaaattaacttagtggattctgtttatcaaatgttgttaactaatggattttgatgtttgtag

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|71880947|gb|DT030002.1|DT030002
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|110714546|gb|EE091579.1|EE091579
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|30300650|gb|CB977444.1|CB977444
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|71879653|gb|DT028708.1|DT028708
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|110417550|gb|EC983615.1|EC983615
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|33405610|gb|CF211237.1|CF211237
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|110357684|gb|EC921351.1|EC921351
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|71877621|gb|DT026676.1|DT026676
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|33405689|gb|CF211316.1|CF211316
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|110398825|gb|EC965301.1|EC965301
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|71879150|gb|DT028205.1|DT028205
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|71877606|gb|DT026661.1|DT026661
EST:     GTTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|45771430|gb|CN007282.1|CN007282
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|110382211|gb|EC938786.1|EC938786
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|110380178|gb|EC945423.1|EC945423
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|110389184|gb|EC954003.1|EC954003
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA
EST: gi|71880372|gb|DT029427.1|DT029427
EST:     GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATG                         GTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCGTA
genomic: GCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacat ... tacatggtagGTGGGTGGCGGCCCAGAGTGTATTCTATCACCTCTACAATCAGGTGTCATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TGTTAATTCTCACCCCGTTCGCAATTGCTGTCGAGGGACCACAGATGTGGGCTGCTGGATGGCAAAATGCCGTTTCTCAAATTGGACCCCATTTCGTATGgtaatcacatgacaactactgtgtttttcttgtactgtttgtttgtgttttattatctctgtatctatatgttttttttgtgatagaaaaaaccagaggc

- - - - - - - - - - - - - - - - - - - - - - - - - GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaaaa