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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CCACACAGAAGACCGTTGATGGGCCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagcttagttatcgagcagaggtctatgatttccattagatcttccttgtattgggtctcaatgattttgatggtttgcacatcaaatcatccaaagtccaatccattttttgtgatcatatag

Basic information

species Vitis vinifera
transcript Vv01s0010g02460.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os02g38920.1 (Oryza sativa), 5'ss of exon 8
CCACACAGAAGACCGTTGATGGGCCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagcttagttatcgagcagaggtctatgatttccattagatcttccttg--tattgggtctcaatgattttgatggtttgcacatcaaatcatccaaagtccaatccattttttgtgatcatatag
| || |||||||| ||||||||||| || |  |||||||||||||||||||| ||||||  |||||||||||| || ||||||||||| |||||||||||| | | |||   | ||     |   |  ||  ||   | |   || |  |     ||| |  |  ||| |||   ||| ||     |||   |  |                                 
CTACCCAGAAGACTGTTGATGGGCCCTCGATGAAGGACTGGAGAGGTGGAAGGGCTGCTAGCTTCAACATCATTCCTAGCAGCACTGGAGCTGCCAAGgta-taaacttgtatttctgtatgtattacattgttgataatgtttcgttatcagacatttgcacctaat-attgatatgtttcaaggatctcgtggtatcg-----------------------------

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os04g40950.1 (Oryza sativa), 5'ss of exon 8
CCACACAGAAGACCGTTGATGGGCCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagcttagttatcgagcagaggtctatgatttccattagatcttccttgtattgggtctcaatgattttgatggtttgcacatcaaatcatccaaagtccaatccattttttgtgatcatatag
| || ||||||||||||||||| || || |||||||||||||| |||||||| |||||    |||||||||||||| ||||||||||| ||||| |||||| | |                ||| | ||  |||   ||   || | |  ||   |  | ||| |||||  |    || || ||||  |||     | ||    ||   ||  |  |||| |     
CAACTCAGAAGACCGTTGATGGACCCTCGAGCAAGGACTGGAGGGGTGGAAGGGCTGCCAGTTTCAACATCATCCCTAGCAGCACTGGAGCTGCAAAGgtaatcat---------------gagatttaatatt---atcccatatgc--tgaggtcagcctccatgatgatttctgtctgtacatataat-----ataggtgcattagttagtaatgattag----

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os08g03290.3 (Oryza sativa), 5'ss of exon 7
CCACACAGAAGACCGTTGATGGGCCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagcttagttatcgagcagaggtctatgatttccattagatcttccttgtattgggtctcaatgattttgatggtttgcacatcaaatcatccaaagtccaatccattttttgtgatcatatag
|||| || |||||||||||||| || || |||||||||||||| ||||| || || ||    || |||||||| ||||||||||||||||||||||| |||| |     | ||            |  |  |   |  ||  |  | |  | |||   ||  |||| ||||||    ||  |   |   ||    |   ||                          
CCACCCAAAAGACCGTTGATGGACCGTCCAGCAAGGACTGGAGGGGTGGCAGGGCGGCCAGTTTTAACATCATTCCCAGCAGCACTGGTGCTGCCAAAgtacgtcatgaacttcaatgttgtgcatgcacaaccacagttcaaaatcctctttat--agttccaataattttgt--attctcctgtgttatggggctgcgta-------------------------

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G180625_T02 (Zea mays), 5'ss of exon 8
CCACACAGAAGACCGTTGATGGGCCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagcttagttatcgagcagaggtctatgatttccattagatcttccttgtattgggtctcaatgattttgatggtttgcacatcaaatcatccaaagtccaatccattttttgtgatcatatag
|||| |||||||| |||||||| || |||  |||||||||||||||||| || |||||   ||| |||||||| ||||||||||| |||||||||||||||  |         ||  |  | |   | |||  || |||   |||  |  |||| ||| |        |||  |     |     | |||||| |||   |  | ||  | ||||||| |||     
CCACCCAGAAGACTGTTGATGGACCCTCAGCCAAGGACTGGAGAGGTGGCAGGGCTGCCAGCTTTAACATCATTCCCAGCAGCACCGGTGCTGCCAAGgtatatg--------ataaaataca---caatg--ttgcatgcaatcaactctgtaatggtt-------gtttgcacaaacta---gttaaatcaacca---ttgattctctgttttgtgttcact---

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G176307_T01 (Zea mays), 5'ss of exon 8
CCACACAGAAGACCGTTGATGGGCCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagcttagttatcgagcagaggtctatgat-ttccattagatcttccttgtattgggtctcaatgattttgatggtttgcacatcaaatcatccaaagtccaatccattttttgtgatcatatag
| || |||||||| ||||||||||| |||   ||||||||||| |||||||| ||||||   ||||||||||| |||||||||||||| ||||| |||||    | ||      ||   |       | ||   ||  |  |     |  || |     | ||   || |||  ||||     |  | ||||  |  | ||                           
CTACCCAGAAGACTGTTGATGGGCCCTCATCTAAGGACTGGAGGGGTGGAAGGGCTGCTAGTTTCAACATCATTCCCAGCAGCACTGGAGCTGCTAAGgttagaaactggaccttc---cttttccttgtgcccttttaacaacatgtaattatgaattgccttcgtgctttgcatggaaaaaatgtgaaatagtgtatag---------------------------

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G071630_T02 (Zea mays), 5'ss of exon 7
CCACACAGAAGACCGTTGATGGGCCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagcttagttatcgagcagaggtctatgatttccattagatcttccttgtattgggtctcaatgattttgatggtttgcacatcaaatca-tccaaagtccaatccattttttgtgatcatatag------------
| || |||||||| ||||||||||| |||   ||||||||||| |||||||| ||||||   ||||||||||| |||||||||||||| ||||| |||||    | || |   |  | | |   || |||     | | |    ||||  || | ||   |  | | |  |  ||  ||||    ||||| || |    | |   ||   ||| |       |||               
CTACCCAGAAGACTGTTGATGGGCCCTCATCTAAGGACTGGAGGGGTGGAAGGGCTGCTAGTTTCAACATCATTCCCAGCAGCACTGGAGCTGCTAAGgttagaaactgaaacagtgtgaaatagtgtatagccacaact----cttctgtgaagtgaaaca-agtcacctccatt-tttgt---tcaaaccactttttatttgtattagtttgtaacagctatacttgatttcctgcag

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G046804_T02 (Zea mays), 5'ss of exon 8
CCACACAGAAGACCGTTGATGGGCCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagcttagttatcgagcagaggtctatgatttccat-tagatcttccttgtattgggtctcaatgattttgatggtttgcacatcaaatcatccaaagtccaatccattttttgtgatcatatag
|||| ||||| || ||||| || || |||  |||||||||||||||||| || |||||   ||| |||||||| || |||||||| |||||||||||||||    | || |  |     |  |  | |||| | || |  || |||||| ||||  ||  |||  |  ||    |     || |  |  ||  |   |  ||                          
CCACCCAGAAAACTGTTGACGGACCCTCAGCCAAGGACTGGAGAGGTGGCAGGGCTGCCAGCTTTAACATCATTCCTAGCAGCACCGGTGCTGCCAAGgtatagtgatt-gcaactacactcaaatttatgttctctacctacatcttctttgtgatgattctggagcatcacaaca---tgaattttcaactactgagggt--------------------------

upper sequence: Vv01s0010g02460.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: EFJ22884 (Selaginella moellendorffii), 5'ss of exon 8
CCACACAGAAGACCGTTGATGGGCCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagcttagt-tatcgagcagaggtctatgatttccattagatcttccttgtattgggtctcaatgattttgatggtttgcacatcaaatcatccaaagtccaatccattttttgtgatcatatag
| || || ||||| ||||||||||||||   |||||| ||| | |||||||| | ||||  ||||||||||||||| |||   || || |||||||||||| |   | |  | |||  ||     || |   ||  |  ||   | |  || |                                                                           
CAACCCAAAAGACTGTTGATGGGCCATCGTCCAAGGATTGGCGTGGTGGAAGGGGTGCTGGCTTCAACATCATCCCGAGCTCAACCGGAGCTGCCAAGgtaatcttcctgttctataaagttcccgt-tggaatgactgttttgtttctctag---------------------------------------------------------------------------

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|33406621|gb|CF212248.1|CF212248
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAG                         GCTGTTGGAAAGGTGCTGCCCGCACTGAATGGGAAGTTAACCGGCATGTCT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
EST: gi|161720959|gb|FC070345.1|FC070345
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAG                         GCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
EST: gi|110703819|gb|EE080998.1|EE080998
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAG                         GCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
EST: gi|30134772|gb|CB920110.1|CB920110
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAG                         GCTGTTGGAAAGGTGCTGCCCGCACTGAATGGGAAGTTAACCGGCATGTCT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
EST: gi|110701389|gb|EE078905.1|EE078905
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAA                         GCTGTTGGAAAAGTGCTGCCTGCACTGAATGGGAAGTTAAC-GGCATGTCT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
EST: gi|110384047|gb|EC948461.1|EC948461
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAG                         GCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
EST: gi|110697161|gb|EE073909.1|EE073909
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAA                         GCTGTTGGAAAAGTGCTGCCTGCACTGAATGGGGAGTTTACCCGGCATGTC
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACC-GGCATGTC
EST: gi|161716699|gb|FC065571.1|FC065571
EST:     GAAGAGCTGCTTCCTTCA-CATCATCCCCAGCAGCACTGGTGCTGCCA-G                         GCTGTTGGAA-GGTGCTGCC-GCACTG
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTG
EST: gi|110363529|gb|EC927123.1|EC927123
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAG                         GCTGTTGGAAAGGTGCTGCCCGCACTGAATGGGAAGTTAACCGGCATGTCT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
EST: gi|30134770|gb|CB920108.1|CB920108
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAG                         GCTGTTGGAAAGGTGCTGCCCGCACTGAATGGGAAGTTAACCGGCATGTCT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
EST: gi|110687944|gb|EE065928.1|EE065928
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGTCAAG                         GCTGTTGGAAAGGTGCTGCCCGCACTGAATGGGAAGTTAACCGGCATGTCT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
EST: gi|110373445|gb|EC937683.1|EC937683
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAG                         GCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
EST: gi|110707375|gb|EE083731.1|EE083731
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAG                         GCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGT-AACCGGCATGTCN
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
EST: gi|161718038|gb|FC067580.1|FC067580
EST:     GAAGAGCTGCTTCCTTCA-CATCATCCCCAGCAGCACTGGTGCTGCCA-G                         GCTGTTGGAA-GGTGCTGC-TGCACTGA
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGA
EST: gi|110707438|gb|EE083837.1|EE083837
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAG                         GCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
EST: gi|71856620|gb|DT005675.1|DT005675
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAG                         GCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
EST: gi|161715330|gb|FC065818.1|FC065818
EST:     GAAGAGCTGCTTCCTTCA-CATCATCCCCAGCAGCACTGGTGCTGCCAAG                         GCTGTTGGGAAGGTGCTGCCTGCACTGAATGGGAAGT-AACCGGCAT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCAT
EST: gi|110688396|gb|EE066900.1|EE066900
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAACACTGGTGCTGCCAAG                         GCTGTTTGGAA-GGTGCTGCCCGCACTGAATGGGAAGT-AACCGGGC-TGT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTT-GGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGG-CATGT
EST: gi|110371235|gb|EC935092.1|EC935092
EST:     GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAG                         GCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT
genomic: GAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagct ... gatcatatagGCTGTTGGAAAGGTGCTGCCTGCACTGAATGGGAAGTTAACCGGCATGTCT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CCACACAGAAGACCGTTGATGGGCCATCAAGCAAGGACTGGAGAGGTGGAAGAGCTGCTTCCTTCAACATCATCCCCAGCAGCACTGGTGCTGCCAAGgtacttagcttagttatcgagcagaggtctatgatttccattagatcttccttgtattgggtctcaatgattttgatggtttgcacatcaaatcatccaaagtccaatccattttttgtgatcatatag

- - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGCTGC