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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AACATTAGACATGACATATTCTGTTAAATGGATTCCTACTACTGTCACTTTTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAGgtgaatttcttattggtactcaccaaattagaaaaatgaatagggctattagttgcaactttcttcaatgcacttccctcttaattgccccatgtgttta...

Basic information

species Vitis vinifera
transcript Vv12s0035g00280.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os02g34690.1 (Oryza sativa), 5'ss of exon 6
AACATTAGACATGACATATTCTGTTAAATGGATTCCTACTACTGTCACTTTTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAGgt--gaatttcttattggtactca----ccaaattagaaaaatgaa---tagggctattagttgcaactttcttcaa-------tgcacttccctcttaattgccccatgtgttta-------------------------------------------
  |||| || |||||||||||||| || |||   || || | ||| || |||||||  || |||||||| || || || |||||||||||||||||||||||  ||| |   | |  | | | |    |    |  | |   ||     || |  | ||  |  ||| ||||  ||        |   | |   |  | | |  ||||||| | |                                            
GGCATTGGATATGACATATTCTGTCAAGTGGGAACCAACCAATGTAACATTTGCTCACCGCTTTGATGTATACCTTGACTACCCTTTCTTTGAACACCAGgtaagaactcagtttctgcaattaaagcctggttctgcaccttggttcttatgtattttgttgccaattttccacataaaaaattatgccttgattctcaatttcccatgtatatcttgcagcatttcctctgaccacagataatccattttatggcag

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G165631_T01 (Zea mays), 5'ss of exon 5
AACATTAGACATGACATATTCTGTTAAATGGATTCCTACTACTGTCACTTTTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAGgtgaatttcttattggtactcaccaaattagaaaaatgaatagggct--attagttgcaactttctt-------caatgcacttccctc---ttaattgc--cccatgtgttta----------------------------------------------------
  |||| || |||||||||||||| ||||||   || || |   | || |||||||  ||||||||||| |||||||| || |||||||||||||||||||| |  |   |||   |  |  |  |||||   | ||   |   |||    |  | | || |    |       || |  | || | ||   |||  |||   | |  |||||                                                     
GGCATTGGATATGACATATTCTGTCAAATGGGAACCAACAAACATAACATTTGCTCACCGTTTTGATGTGTATCTGGACTATCCTTTCTTTGAACACCAGgtaatataggtatatatttttgc--aattaaggagatctttgcagcttggctcctcgtaattacaatacagaaccagtataattacttcccattagctgcgttctacatgtttgaaagagcctgaatcatatcttcttaatttctagttatttcttgtacttgcag

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G026231_T01 (Zea mays), 5'ss of exon 6
AACATTAGACATGACATATTCTGTTAAATGGATTCCTACTACTGTCACTTTTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAGgtgaatttcttattggtactcaccaaattagaaaaatgaatagggctatt-agttgcaactttc--ttcaatgcacttccc----tcttaattgccccatgtgttta----------
 | | | || ||||||||||| || || ||| |  | ||   |||  | ||||| || |||||||| || || ||||| || |||||||||||||||||||||| |   || || | |  ||    |  |||||  |        ||||| || || | ||| |  || ||   |||        || |||   |      | |||           
GAAACTGGAAATGACATATTCAGTGAAGTGGGTAGCAACAGATGTGTCATTTGCACGCCGTTTTGAAGTGTACCTGGACTATCCTTTCTTTGAACACCAGgtga-tactttgtttgcagaca----accagaaactttctagtttctattcagctgtatcttcccttttaactaactattagaaatcctaagctctgttcatatttctcattttcag

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G420310_T01 (Zea mays), 5'ss of exon 6
AACATTAGACATGACATATTCTGTTAAATGGATTCCTACTACTGTCACTTTTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAGgtgaa---tttcttattggtactcaccaaattagaaaaatgaatagggctattagttgcaactttcttcaatgcacttccctcttaattgc-cccatgtgttta--------
 | ||| || ||||||||||| || || ||| |  | |||  |||  | ||||| || |||||||| || || ||||| || ||||||||||||||||||||||    ||  || | |  |  |  ||| ||   |   |   |   ||| |   || |   ||   |   |          || |  |     ||| | | |         
GAAATTGGAAATGACATATTCAGTGAAGTGGGTAGCGACTGATGTGTCATTTGCACGCCGTTTTGAAGTGTACCTGGACTATCCTTTCTTTGAACACCAGgtgatactttgtttgtagacaaccgacaacttcctagtttctgttcagctgtaccttcccttttaactagctattagaagtcctaagctctgttcatatttctcatttccag

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA08G20100.1 (Glycine max), 5'ss of exon 6
AACATTAGACATGACATATTCTGTTAAATGGATTCCTACTACTGTCACTTTTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAGgtgaatttc-ttattggta------ctcaccaaattagaaaaatgaatagggcta-ttagttgcaactttcttcaatgcacttccctcttaattgccccatgtgttta------------------------------
| | || ||||||||||||||||| ||||||  |||||| | |||||||||||  || || |||||||| || ||||| || || |||||||| || ||||||||  || ||  || ||            | |||  | |  ||  ||  | |  |||  ||| | | | |||| | ||  |   || ||  |   ||||||   |                               
ATCTTTGGACATGACATATTCTGTCAAATGGTCTCCTACGAATGTCACTTTTGGACGCCGATTTGATGTATACCTGGACTATCCGTTCTTTGAGCATCAGgtgaaaatcattgctgctagctttgtattttagattgaagaggtgtttattgttggttacctgcta-tgtgttcagt-catgtggatcctatcttagccatgtcactgagagaactttgatccgttttctttctgtag

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA12G29120.1 (Glycine max), 5'ss of exon 6
AACATTAGACATGACATATTCTGTTAAATGGATTCCTACTACTGTCACTTTTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAGgtgaatttc-ttattggta------ctcaccaaattagaaaaatgaatagggcta-ttagttgcaactt--tcttcaatgcacttccc-tcttaattgcccca-tgtgttta------------------------
| | || ||||||||||||||||| ||||||  |||||| | |||||||||||  || || |||||||| || ||||| || || |||||||| || ||||||||  || ||  || ||            | |||  | |  ||  ||  | |  |||  ||| || |  || |  |||    |||  |||||       || || |   |                        
ACCTTTGGACATGACATATTCTGTCAAATGGTCTCCTACGAATGTCACTTTTGGACGCCGATTTGATGTATACCTGGACTATCCGTTCTTTGAGCATCAGgtgaaaatcattgctgctagatttgtattttagattgaagaggtgtttattgttggttacctgctacgtgttcattcatgtggatcctatcttagccatgtcactgagcgaactttgatcatttttctttctgtag

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA08G13370.1 (Glycine max), 5'ss of exon 6
AACATT-AGACATGACATATTCTGTTAAATGGATTCCTACTACTGTCACTTTTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAGgt--gaatttcttattggtactcaccaaattagaaaaatgaatagggctattagt-tgcaactttcttcaatgcacttccctcttaattgcc-ccatgtgttta-------------------------
 |||||  ||||||||||||||| | ||||||  | |||| | |||||||||||  ||||| |||||||| || |||||| | ||||||||||| || |||||   | |||  | ||   | | |     |       |||  | ||   |||  | || |    ||     ||  | | ||   |   || | |   || |||                          
-ACATTTGGACATGACATATTCTATCAAATGGGATTCTACCAATGTCACTTTTGGGCGTCGCTTTGATGTCTACCTGGATCATCCTTTCTTTGAGCATCAGgtacaactttgcttttaaaattgaaatggtgttgtttatggtttggtgaattgctatgtattcatccatgttggtcctaccatatctctgtcactgagtattttgctcctttgttttctttttccctag

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA05G30210.1 (Glycine max), 5'ss of exon 6
AACATT-AGACATGACATATTCTGTTAAATGGATTCCTACTACTGTCACTTTTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAGgtgaatttcttattggtactcaccaaattagaaaaatgaatagggctattagttgcaactt--tcttcaatgcacttccctct-taattgccccat---gtgttta-------------------------
 |||||  ||||||||||||||||| ||||||  | |||| | ||||||||| |  ||||| |||||||| || |||||  | ||||||||||| || |||||  |  | |  ||   |   |   || | |     |  || |     | | |||| |  |  || || |||    |||  |  ||  |   |||    |  |||                          
-ACATTTGGACATGACATATTCTGTCAAATGGGATTCTACCAATGTCACTTTCGGGCGTCGCTTTGATGTCTACCTGGACCATCCTTTCTTTGAGCATCAGgtacagctttgcttttaaa--attgaaatggtgttgtttatggtttggtgaattgctatgtattcatccatgttggtcctaccatagctctgccactgagaattttgctcctttgttttctttttccctag

upper sequence: Vv12s0035g00280.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: AT1G10950.1 (Arabidopsis thaliana), 5'ss of exon 6
AACATTAGACATGACATATTCTGTTAAATGGATTCCTACTACTGTCACTTTTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAGgtgaatttcttattggtactcaccaaattagaaaaatgaa-tagggctattagttgcaactttcttcaatgcacttccctcttaattgccccatgtgttta-----
|| | | ||| |||| ||||||||  |||||||||| || | |||||| |||||||| || ||||| || ||||||||||| || ||||||||||||||||| | |||     | | |  |    ||||||     |    |   |||| |   ||  | |        | ||||    | | |  |  | ||  ||  ||     
AAAAATGGACCTGACGTATTCTGTGCAATGGATTCCAACAAATGTCACATTTGCTCGCCGCTTTGACGTATATCTGGATTATCCGTTCTTTGAACACCAGgtaacttt-----tagcatgctatgaattagtcttgtacccttctgctactgtctgtgattccaaatggttcactggtttataatgtatcacac-tgaatacccca

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|351023401|gb|FQ432784.1|FQ432784
EST:     TTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAG                         ATTCATTGGTTCTCCATTTTTAATTCTTTCATGATGGTTATCTTCCTCACT
genomic: TTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAGgtgaatttct ... caatgtgcagATTCATTGGTTCTCCATTTTTAATTCTTTCATGATGGTTATCTTCCTCACT
EST: gi|28959529|gb|CB339765.1|CB339765
EST:     CTTTCTTTG-ACACCAG                         ATTCATTGGTTCTCCATTTTTAATTCTTTCATGATGGTTATCTTCCTCACT
genomic: CTTTCTTTGAACACCAGgtgaatttct ... caatgtgcagATTCATTGGTTCTCCATTTTTAATTCTTTCATGATGGTTATCTTCCTCACT
EST: gi|110728638|gb|EE104382.1|EE104382
EST:     TTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAG                         ATTCATTGGTTCTCCATTTTTAATTCTTTCAGGAGGGGTATCTTCCTCACT
genomic: TTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAGgtgaatttct ... caatgtgcagATTCATTGGTTCTCCATTTTTAATTCTTTCATGATGGTTATCTTCCTCACT
EST: gi|110708664|gb|EE086465.1|EE086465
EST:     TTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAG                         ATTCATTGGTTCTCCATTTTTAATTCTTTCATGATGGTTATCTTCCTCACT
genomic: TTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAGgtgaatttct ... caatgtgcagATTCATTGGTTCTCCATTTTTAATTCTTTCATGATGGTTATCTTCCTCACT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AACATTAGACATGACATATTCTGTTAAATGGATTCCTACTACTGTCACTTTTGCTCGTCGTTTTGATGTTTATCTGGATTACCCTTTCTTTGAACACCAGgtgaatttcttattggtactcaccaaattagaaaaatgaatagggctattagttgcaactttcttcaatgcacttccctcttaattgccccatgtgttta

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- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaataggg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttccctc