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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCAGAATTGGATATCAATAAAAGGTGATAAATTTGTATTTCCAGGAGGTGGAACACAATTTATTCATGGAGCAGATCAATACTTGGATCAGATTTCACAGgttgaccatttctacaattctgacttggtattgtttgtatttacattgtattagtccccatcttttgacttgaatatgcag

Basic information

species Vitis vinifera
transcript Vv18s0001g01600.t01
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g01600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: LOC_Os01g62800.1 (Oryza sativa), 5'ss of exon 2
CCAGAATTGGATATCAATAAAAGGTGATAAATTTGTATTTCCAGGAGGTGGAACACAATTTATTCATGGAGCAGATCAATACTTGGATCAGATTTCACAGgttgaccatttctacaattctgacttggtattgtttgtat-ttacattgtattagt--ccccatcttttgacttgaatatgcag
 |||||||||||    | |      |||||||||  |||||| ||||| ||||| |||||||| ||||||||| |||||||| ||||||||||||| || ||   |   || |||  || |    ||  | | ||   || || |    | | |||  | ||| || |     ||   || |||
GCAGAATTGGATTAGTAAAGCTAAGGATAAATTTAGATTTCCTGGAGGAGGAACTCAATTTATCCATGGAGCAAATCAATACCTGGATCAGATTTCTCAAgtatgctgattgtacttttatctgatgaaaattttatcatgttgctgactctcagtagcaccacctgtctctctgttcatccag

upper sequence: Vv18s0001g01600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G092120_T02 (Zea mays), 5'ss of exon 2
CCAGAATTGGATATCAATAAAAGGTGATAAATTTGTATTTCCAGGAGGTGGAACACAATTTATTCATGGAGCAGATCAATACTTGGATCAGATTTCACAGgttgaccat------ttctacaattctgacttggtattgtttgtatttacattgtattagtccccatcttttgacttgaatatgcag
 |||||||||||  | |        ||||||||   |||||| ||||| ||||| ||||| |||||||||||| |||||||| | || ||||| || ||||||     |      |||| |||  ||| ||||| |||  |  |  ||||  || | |||  |      ||     ||    | |||
ACAGAATTGGATCACCAAGGTCAAAGATAAATTCAGATTTCCTGGAGGCGGAACTCAATTCATTCATGGAGCAAATCAATACCTAGACCAGATCTCCCAGgttcgatgtcaaatattcttcaaaactg-cttggaatt--taatccttactctg-actagagcaacctgttccctctgttcgtccag

upper sequence: Vv18s0001g01600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GRMZM2G042295_T01 (Zea mays), 5'ss of exon 2
CCAGAATTGGATATCAATAAAAGGTGATAAATTTGTATTTCCAGGAGGTGGAACACAATTTATTCATGGAGCAGATCAATACTTGGATCAGATTTCACAGgtt-gaccatttctacaattctgacttggtattgtttg-tatttacattgtattagtccccatcttttgacttgaatatgcag
 |||||||||||  | |        ||||||||   |||||| ||||| ||||| ||||| |||||||||||| ||| |||| | || |||||||| |||||| ||        |   |||  |||   |    |||  |    ||  ||  |    || | | |||     ||   || |||
ACAGAATTGGATCACCAAGGTCAAAGATAAATTCAGATTTCCTGGAGGCGGAACTCAATTCATTCATGGAGCAAATCGATACCTAGACCAGATTTCCCAGgtttgatgtcaaacattcttcaaactgcttgaaatttaatcacgactctgactagagccacctgtttccctctgctcatccag

upper sequence: Vv18s0001g01600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA14G24900.1 (Glycine max), 5'ss of exon 2
CCAGAATTGGATATCAATAAAAGGTGATAAATTTGTATTTCCAGGAGGTGGAACACAATTTATTCATGGAGCAGATCAATACTTGGATCAGATTTCACAGgttgaccatttctacaattctgacttggtattgtttgtatttacattgtattagtccccatcttttgacttgaatatgcag
 || |||||||||||||||||    ||||||||||| ||||| || |||||||| |||||||| ||||| |||||| ||||| |||||||||||||  |||||   |  || |  || |  |   || ||||  |||       |   || |     | || |||  | |||||| |||||
TCAAAATTGGATATCAATAAAGAAGGATAAATTTGTTTTTCCTGGTGGTGGAACTCAATTTATACATGGTGCAGATAAATACCTGGATCAGATTTCTGAGgttagtctcttatttaaattcgttctgatatttgttgc-----taacatactgagagctat-tttgaaattgaatgtgcag

upper sequence: Vv18s0001g01600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: GLYMA13G09520.1 (Glycine max), 5'ss of exon 2
CCAGAATTGGATATCAATAAAAGGTGATAAATTTGTATTTCCAGGAGGTGGAACACAATTTATTCATGGAGCAGATCAATACTTGGATCAGATTTCACAGgttgaccatttctacaattctgacttggtattgtttgtatttacattgtattagtccccatcttttgacttgaatatgcag
 || |||||||||| ||||||  | ||||||||||| ||||| || |||||||| || ||||| ||||| |||||| ||||| |||||||||||||  |||||   |   ||| ||| |      || ||||  |||  |  | ||  |   ||        |||  | |||||| | |||
TCAAAATTGGATATTAATAAAGAGGGATAAATTTGTTTTTCCTGGTGGTGGAACTCAGTTTATACATGGTGCAGATAAATACCTGGATCAGATTTCTGAGgttagtc---tcttcaaattcattctgatatttgttgc-taaatatactgcgagctaa----tttgaaattgaatgtacag

upper sequence: Vv18s0001g01600.t01 (Vitis vinifera), 5'ss of exon 2
lower sequence: AT1G77260.1 (Arabidopsis thaliana), 5'ss of exon 2
CCAGAATTGGATATCAATAAAAGGTGATAAATTTGTATTTCCAGGAGGTGGAACACAATTTATTCATGGAGCAGATCAATACTTGGATCAGATTTCACAGgt--------tgaccatttctacaattctgacttg-gtattg-----tttgtatttacattgtattagtccc-catctttt--gacttgaatatgcag
 || ||||||||   || | |    ||||| ||||| || || ||||||||||| ||||| || |||||||| ||||| ||||| || ||||| || |||||        |||   || ||||   | |   | | ||||||     | ||| |||   |||| ||  ||    ||  | |  || |  ||| |||||
TCAAAATTGGATTAGAAGAGAGAAAGATAAGTTTGTTTTCCCTGGAGGTGGAACTCAATTCATCCATGGAGCTGATCAGTACTTAGACCAGATCTCCCAGgtttgttttttgattcttcctacctgtttttttggtgtattggctaatctgttttttt-ttgtgttgatcttatattctcttagattgaaatttgcag

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|37187347|gb|CF606700.1|CF606700
EST:     GAACACAATTTATTCATGGAGCAGATCAATACTTGGATCAGATTTCACAG                         ATGGTTCCTGACATTGCATTTGGTAACCACACCCGAGTTGTCTTGGACATT
genomic: GAACACAATTTATTCATGGAGCAGATCAATACTTGGATCAGATTTCACAGgttgaccatt ... gaatatgcagATGGTTCCTGACATTGCATTTGGTAACCACACCCGAGTTGTCTTGGACATT




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCAGAATTGGATATCAATAAAAGGTGATAAATTTGTATTTCCAGGAGGTGGAACACAATTTATTCATGGAGCAGATCAATACTTGGATCAGATTTCACAGgttgaccatttctacaattctgacttggtattgtttgtatttacattgtattagtccccatcttttgacttgaatatgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGCA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGCAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGATCA