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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

TCCAGCTGTGGTGAGCAAATTATACAAGGCGATAAATCGAAATGGAGGTGTGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttctccattttgtctcagaaatatgaattaattctgcctaaggcttttagctaagaaatacgaattgtaattaaatggcacacttctacggaat...

Basic information

species Vitis vinifera
transcript Vv00s0250g00020.t01
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: LOC_Os03g01750.2 (Oryza sativa), 5'ss of exon 8
TCCAGCTGTGGTGAGCAAATTATACAAGGCGATAAATCGAAATGGAGGTGTGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttctcca-ttttgtctcagaaatatgaattaattctgcctaaggcttttagctaagaaatacga-attgtaattaaatggcacacttctacggaat
||| |||||| | |||||| |  |||||    | || |  ||||| || || || ||||||||||| || ||||||||||||||||||||||| ||| | ||| | |||     | || |||      | |      | |     |||    ||||| |    | ||  | |||||  |    |  |    |      |   
TCCTGCTGTGATTAGCAAACTGCACAAGCTTGTCAACCATAATGGTGGGGTAACATATATACACTGTACCGCTGGACTTGGGAGAGCTCCTGCTGTGACAgtaggtttccatggtcttttcttttttgtttcccaagaattcttataataggtttaggtttacattataatattgtcttcttctttcctgttcagttagt--

upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GRMZM2G052546_T01 (Zea mays), 5'ss of exon 8
TCCAGCTGTGGTGAGCAAATTATACAAGGCGATAAATCGAAATGGAGGTGTGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttctccattttgtctcagaaatatgaattaattctgcctaaggcttttagctaagaaatacgaattgtaattaaatggcacacttctacggaat
||| |||||||| ||||||||  ||||    || ||  | ||||| ||||| || |||||||| || || ||||||||||| ||||||||||| || || ||| | ||           | |   ||| |   ||      | | |    || |  |  |||      |  | |   || |   |    | || | | | 
TCCTGCTGTGGTTAGCAAATTGCACAAACTTATCAACTGTAATGGTGGTGTAACATATATACATTGTACTGCTGGACTTGGAAGAGCTCCTGCTGTTGCAgtaggtttacatgccacccccccctaatttttgtttcccaagacaacttattgtttcacagattccttatgtttgtctagagatccttttgcttcagtag

upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA10G34370.2 (Glycine max), 5'ss of exon 7
TCCAGCTGTGGTGAGCAAATTATACAAGGCGATAAATCGAAATGGAGGTGTGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttctccattttgtctcagaaatatgaattaattctgcctaaggcttttagctaagaaatac-gaattgtaattaaatggcacacttctacggaat---
||||||||| || ||||||||||||||||| ||||||   ||||||||||| || |||||||| ||||| ||||||||||| |||||||| || || ||||||||  |||   |||  | |  |  ||   | ||| |    |  |     |||| || | |  |   |  ||  |  ||  |     |     |   | |   
TCCAGCTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctcttggtttcttttatgtgatgcaagttact----cacagaatatttacctgaaatgttttgggttagatctaggtaaggtaaaggaaataatttcc

upper sequence: Vv00s0250g00020.t01 (Vitis vinifera), 5'ss of exon 8
lower sequence: GLYMA20G33190.1 (Glycine max), 5'ss of exon 8
TCCAGCTGTGGTGAGCAAATTATACAAGGCGATAAATCGAAATGGAGGTGTGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttctccattttgtctcagaaatatgaattaattctgcctaaggcttttagctaagaaatacgaattgtaattaaatggcacacttctacggaat-------
||||| ||| || ||||||||||||||||| ||||||   ||||||||||| || |||||||| ||||| ||||||||||| |||||||| || || ||||||||  |||   |||  | |  |  ||   | ||| |    |  |     |||| ||  |||||     |||| | |    || | |  |  | | |||       
TCCAGTTGTAGTTAGCAAATTATACAAGGCAATAAATTCCAATGGAGGTGTAACATATATACATTGCACTGCTGGACTTGGAAGAGCTCCAGCTGTTGCGgtatgtctcttagtttcttttatgtgatgcaagttact----cacagaatatttacct--gaaatgttttttgttagttctgggta-aggtaaaggaaataatttcc

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|37188932|gb|CF608281.1|CF608281
EST:     TGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCG                         TTGGCATACATGTTCTGGGTTCAGGGCTATAAACTTAATGAAGCTCACAGT
genomic: TGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttct ... tgaattacagTTGGCATACATGTTCTGGGTTCAGGGCTATAAACTTAATGAAGCTCACAGT
EST: gi|30252735|gb|CB970286.1|CB970286
EST:     TGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCG                         TTGGCATACATGTTCTGGGTTCAGGGCTATAAACTTAATGAAGCTCACAGT
genomic: TGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttct ... tgaattacagTTGGCATACATGTTCTGGGTTCAGGGCTATAAACTTAATGAAGCTCACAGT
EST: gi|110731715|gb|EE106367.1|EE106367
EST:     TGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCTGTGGCG                         TTGGCATACATGTTCTGGGTTCAGGGCCTA-AAACTTAATGAAGCTCACAG
genomic: TGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttct ... tgaattacagTTGGCATACATGTTCTGGGTTCAGGGC-TATAAACTTAATGAAGCTCACAG
EST: gi|110725728|gb|EE102561.1|EE102561
EST:     GACTTATATACACTGCACAGCTGGGACT-GGGAGAGCTCCTGCTGTGGCG                         TTGGCATACATGTTCTGGGTTCAGGGCTATAAACTTAATGAAGCTCACAGT
genomic: GACTTATATACACTGCACAGCTGG-ACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttct ... tgaattacagTTGGCATACATGTTCTGGGTTCAGGGCTATAAACTTAATGAAGCTCACAGT
EST: gi|110390476|gb|EC955386.1|EC955386
EST:     TGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCG                         TTGGCATACATGTTCTGGGTTCAGGGCTATAAACTTAATGAAGCTCACAGT
genomic: TGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttct ... tgaattacagTTGGCATACATGTTCTGGGTTCAGGGCTATAAACTTAATGAAGCTCACAGT
EST: gi|27582920|gb|CB005615.1|CB005615
EST:     TGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCTGTGGCG                         TTGGCATACATGTTCTGGGTTCAGGGCTATAAACTTAATGAAGCTCACAGT
genomic: TGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttct ... tgaattacagTTGGCATACATGTTCTGGGTTCAGGGCTATAAACTTAATGAAGCTCACAGT
EST: gi|110719002|gb|EE096483.1|EE096483
EST:     TGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCG                         TTGGCATACATGTTCTGGGTTCAGGGCTATAAACTTAATGAAGCTCACAGT
genomic: TGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttct ... tgaattacagTTGGCATACATGTTCTGGGTTCAGGGCTATAAACTTAATGAAGCTCACAGT
EST: gi|110723499|gb|EE100881.1|EE100881
EST:     TGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCTGTGGCG                         TTGGCATACATGTTCTGGGTTCAAGGCTATAAACTTAATGAAGCTCACAGT
genomic: TGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttct ... tgaattacagTTGGCATACATGTTCTGGGTTCAGGGCTATAAACTTAATGAAGCTCACAGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
TCCAGCTGTGGTGAGCAAATTATACAAGGCGATAAATCGAAATGGAGGTGTGACTTATATACACTGCACAGCTGGACTTGGGAGAGCTCCTGCCGTGGCGgtatgcttctccattttgtctcagaaatatgaattaattctgcctaaggcttttagctaagaaatacgaattgtaattaaatggcacacttctacggaat

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cttctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agaaata
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -taagaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aattaaa