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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAACTGTTGATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatgtccctcatgactatcaacccacacgctttaatcaatttatcagcctttatattactcatacgatagttctaaatgcattgtgtcttatgcatttc...

Basic information

species Vitis vinifera
transcript Vv07s0031g01860.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os05g12490.1 (Oryza sativa), 5'ss of exon 2
GCAACTGTTGATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatg-----tccctcatg----actatcaacccacacgctttaatcaatt-----tatcagcctttatattactcatacgatagttctaaatgcattgtgtcttatgcatttc-------------
||| |  | |||||||  || |||||||||||  |||| || || ||||| ||||| ||||||||||| ||||||||||||||| |||| || |||||||||| |     |   | |||    | |||  || || | | | | |||| ||      || |  || ||    |||||     |      |      |  |    |  |  |                
GCAGCATTAGATGCTGGAGCTTGGATGTTCAACATTGTGACATCTGTTGGTATCATCATGGTCAACAAGGCCTTAATGGCTACACATGGTTTTAGTTTTGgtacgataaattgataatgctttattatttactcatatg-tgtgatcacttggaaagatgaatctgtaacaaactcagctactgaacacatgcttgtactaatatgggggtgctattgcttgtacag

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os02g40090.4 (Oryza sativa), 5'ss of exon 2
GCAACTGTTGATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatgtccctc-atgactatcaacccacacgctttaatcaatttatcagcctttatattac-tcatacg-atagtt---ctaaatgcattgtgtcttatgcatttc---------------------------------------------------
|||    | |||||||  |||||||||||||| ||||| || || ||||| ||||| ||||||||||| || |||||||| ||| |||| || |||||||||| | |   | || | |    || |    | || |||          |||||      || || || | ||||||   |||||   |       || ||||                                                       
GCAGTGCTGGATGCTGGAGCATGGATGTTCAACGTTGTGACATCAGTTGGTATCATCATGGTCAACAAGGCATTAATGGCCACACATGGTTTTAGTTTTGgtaagacatgctataattcctcactcgt--ggttgaattgtcaagaatgccttgtccgcacgtcttatggatagttggactaaaccgaactatcgttgtgcagcaaaccagtcagattttttgtgctaatgatgtgttccattgtgtgtttgtgcag

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os12g05780.3 (Oryza sativa), 5'ss of exon 2
GCAACTGTT-GATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatgtccctcatgactatcaacccacacgctttaatcaatttatcagcctttatattactcatacgatagttctaaatgcattgtgtcttatgcatttc--
  |  || | |||  ||| |||||||  |||||  |   ||| || ||||||||||| ||||||||||| ||  | ||||||||| ||||||||||||| |||||||   |    ||  | ||   | |   |||  | |  || |   ||    || | |   | |     |   |||      || |  | |   |||   
-AAGGTGCTAGATTTTGCGGCATGGAGTTTCAACATCACCACATCCGTTGGAATCATCATGGTCAACAAGGCTCTGATGGCTACACATGGATTCAGTTTCGgtatgttttttgctacc-ttaagatatatattttg-tgatgttttattccaggctactccgtgttctgggatgacaaacttgcagtattatgttgttttagt

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os12g05830.1 (Oryza sativa), 5'ss of exon 2
GCAACTGTTG-ATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatgtccctca-tgactatcaacccacacgctttaatcaatttatcagcctttatattactcatacgatagttctaaatgcattgtgtcttatgcatttc--------
  |  || || ||  ||| |||||||  |||||  |   ||| || ||||||||||| ||||||||||| ||  | ||||||||  ||||||||||||| ||| |||   | | |  ||| |    || |    ||  |   |||||     ||| |  |  | ||    || |||||     | |  || || || ||  |        
-AAGGTGCTGGATTTTGCGGCATGGAGTTTCAACATCACCACGTCTGTTGGAATCATCATGGTCAACAAGGCTCTGATGGCTACGCATGGATTCAGTTTCGgtgtgtgtgttacttgctacc--ttcagatatcttggttc-tttat-----tttgtgatgatgatgtttta-ttctaggcttactccgtgttctgaatgacaaactagc

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM5G823629_T03 (Zea mays), 5'ss of exon 1
GCAACTGTTGATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatg----tccctcatgactat--caacccacacgctttaatcaatttat---cagcctttatattactcatacgatagttctaaatgcattg-----tgtcttatgcatttc------------------------------------
||| |  | ||||||| |||||||||||||||||| ||||| || ||||| ||||| ||||||||||||| ||||||||| ||  |||| || |||||||||| |    | ||  ||    ||  | | |  || ||  |     ||| |    |  | | | |  ||   | | |  |  |   | ||    |     |    | ||| | ||                                    
GCAGCACTAGATGCTGGCGCATGGATGTTCAATGTCGTCACATCTGTTGGTATCATCATGGTCAACAAAGGCTTAATGGCGACTCATGGCTTTAGTTTTGgtaagagcatgcccaatcttcattcctaactgcatgcgatgcctgattcacgcgcgccttcttttctatctaaaagtaaactactattgtgcagaaaaattcagtctgcttgtcttgtgctaatttgttcactaccttttgctcctacag

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G089630_T03 (Zea mays), 5'ss of exon 2
GCAACTGTTGATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatgtcc-----------ctcatgactatcaacccacacgctt----taatcaatttatcagcctttatattact---------catacgatagttctaaatgcattgtgtcttatgcatttc-----------------------------------------------------------------
||| |  | || |||| |||||||||||||||||| ||||| || ||||| ||||| ||||||||||||||||||||||| ||  |||| || ||||| |||| | ||            || |  |||| | | |  |||  |    |    |||| | | || | | | || ||          | || |   || |      |    |||| ||  |  |                                                                  
GCAGCACTAGACGCTGGCGCATGGATGTTCAATGTCGTCACATCCGTTGGTATCATCATGGTCAACAAAGCCTTAATGGCGACGCATGGTTTTAGTTTCGgtaagaccgtgcccaacctttcgttcctataaccgcgtacgagtacgatgcctaattcacccgcgtctttgtttctgtctaaaactaaactacgattttgctgagaaccagtctaattaaactatggctgtgcatagaaccagtctgatcgtcttatactaatttgttcgctgctatttgcttcgacag

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G147446_T01 (Zea mays), 5'ss of exon 2
GCAACTGTTGATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatgtccctcatgactatcaacccacacgctttaatcaatttatcagcctttatattactcatacgatagttctaaatgcattgtgtcttatgcatttc---
||  |  | ||    || |||||||  ||||||||   ||| ||||||||| |||| ||||||||||| ||||| |||||||| ||||| |||||||| |||||| |  |  |  ||      |||   | |||| | |   || |  |   | |     ||   |  || ||||        ||  |  |  ||  |     
GCTGCCCTCGACTTCGCAGCATGGAGTTTCAATGTCACCACATCGGTTGGACTCATCATGGTCAACAAGGCCTTGATGGCTACGTATGGGTTCAGTTTCGgtatgcctgtgct--ctgctcgtccagg-gatttatttaccatacctccgactttcaccttcggtctctacttcttgcgcttctgactgcttagcgctattat

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G071378_T03 (Zea mays), 5'ss of exon 2
GCAACTGTTGATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatgtccctcatgactatcaacccacacgctt-taatcaat--ttatcagcctttatattactcatacgatagttctaaatgcattgtgtcttatgcatttc
||  |  | ||    || |||||||  ||||||||   ||| ||||| ||| |||| ||||||||||| || || |||||||| ||||||||||||||||||| | |  |  |  ||    |||       || ||||  ||  | ||       |||||||   ||  ||   |      ||   | |  ||  ||   || 
GCCGCCCTCGACTTCGCGGCATGGAGCTTCAATGTCACCACGTCGGTCGGACTCATCATGGTCAACAAGGCGTTGATGGCTACGTATGGATTCAGTTTTGgtacgcctgtgct--ctgctcacctggtgatttgtaatttatcgtcatacatgaatatattatatatctgactctcacctctggcctcttgctcttgtgctt-

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA06G15280.2 (Glycine max), 5'ss of exon 2
GCAACTGTTGATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatgtccc--tcatgactatcaacccacacgctttaatcaatttatcagcctttatattactcatacgatagttctaaatgcattgtgtct-tatgcatttc
||  |  ||||||| ||  ||||| |||||||||| ||||| || || ||||| ||| | ||||| || ||||| |||||||||||||| || |||||||||||| ||   |||||||| |   ||||    || |  | ||| | | | |  | ||     | ||   | || | | | ||| |  | ||| | ||   || 
GCTTCCATTGATGCAGCATCATGGCTGTTCAATGTGGTCACGTCTGTGGGAATTATTCTTGTCAATAAGGCCTTGATGGCTACATATGGTTTTAGTTTTGgtatgacctcatcatgactttt--cccatttcctctcttgaatctttgatctgtcatgcctatgattttaaagatgtca-tgcttcttttctatttgttgttt

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA08G15250.1 (Glycine max), 5'ss of exon 1
GCAACTGTTGATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtat-gtccctcatgactatcaacccacacgctttaatcaatttatcagcctttatattactcatacgatagttctaaatgcattgtgtctta-tgcatttc
 |  |  ||||||  ||  |||||||||||||| | ||||| || || ||||| ||  | || || |||||| | |||||||||||||| ||||| |||||||| |    || ||||  |   | ||  |    ||||  | |   |   | || ||||    ||  |  | |  | | ||| ||| ||   | ||||||  
ACTGCACTTGATGTGGCATCATGGATGTTCAATATAGTCACATCTGTCGGAATAATCCTTGTGAATAAAGCCCTCATGGCTACATATGGTTTCAGCTTTGgtatagagtttcttgacccttt-ctcatccttgataatttactccactttcattttattttcaatgtg-caatgttcactgctttgagttgcaatgcattcg

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA05G31940.1 (Glycine max), 5'ss of exon 3
GCAACTGTTGATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatgtc-cctcatgactatcaacccacacgctttaatcaatttatcagcctttatattactcatacgatagttctaaatgcattgtgtcttatgcatttc-
 |  |  ||||||  ||  |||||||||||||| | ||||| || || ||||| ||  | || || |||||| | |||||||||||||| ||||| ||||||||      || ||||  |   ||||  |    ||||  | |   |   | || ||||    ||  |  | | || | ||| |||      || | ||   
ACTGCACTTGATGTGGCATCATGGATGTTCAATATAGTCACATCTGTGGGAATAATCCTTGTGAATAAAGCCCTCATGGCTACATATGGTTTCAGCTTTGgtatacagtttcttgacccttt-cccatccctgataatttactccactttcattttattttcaatgtgcaaatgctcactgc-ttgcaatgcattcgttgag

upper sequence: Vv07s0031g01860.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT4G39390.2 (Arabidopsis thaliana), 5'ss of exon 2
GCAACTGTTGATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatgtccctcatgactatcaacccacacgctttaatcaatttatcagcctttata--ttactcatacga---tagttctaaatgcattgtgtcttatgcatttc------------
||  |  | ||   |||  ||||| | |||||||| || ||||| |||||||||||  | || |||||||| ||||||||||| ||||| || ||||| |||  ||   || |  || | | | || || |||   |  |  ||| || |        | |||  |   |    | | |||||     | |    | ||  | |             
GCGGCATTAGACATTGCATCATGGCTATTCAATGTGGTTACTTCCGTTGGAATCATCCTCGTTAACAAAGCTTTAATGGCTACTTATGGCTTTAGTTTCGgtgagtttttctt--cttttatcacaaactcttcccttgaaatattagtcaacggggttgacttgtttcaactcactactaaaactgatttaagatctgtttcttaatgtgatacag

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|34544353|gb|CF512585.1|CF512585
EST:     AATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTG                         CGACTACGTTAACTGGTCTGCATTTTGCCACAACAACCTTGATGACTACTG
genomic: AATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatgtccct ... tatcctacagCGACTACGTTAACTGGTCTGCATTTTGCCACAACAACCTTGATGACTACTG
EST: gi|110721721|gb|EE099039.1|EE099039
EST:     AATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTG                         CGACTACGTTAACTGGTCTGCATTTTGCCACAACAACCTTGATGACTACTG
genomic: AATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatgtccct ... tatcctacagCGACTACGTTAACTGGTCTGCATTTTGCCACAACAACCTTGATGACTACTG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAACTGTTGATGCTGCCGCATGGATGTTCAATGTTGTCACTTCGGTTGGAATCATTATGGTCAACAAAGCCTTAATGGCTACATATGGATTCAGTTTTGgtatgtccctcatgactatcaacccacacgctttaatcaatttatcagcctttatattactcatacgatagttctaaatgcattgtgtcttatgcatttc

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cccacac