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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATTTGACCTTCTGGATGTTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGTCAGgtattctgccatattgctttgtgatttctttagctaccttttttttttttttctgatgaggaaggttagatctgatttctttagctacttgtgtcttggt...

Basic information

species Vitis vinifera
transcript Vv06s0004g07380.t01
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv06s0004g07380.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: LOC_Os03g18590.1 (Oryza sativa), 5'ss of exon 3
ATTTGACCTTCTGGATGTTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGTCAGgtattctgccatattgctttgtgatttctttagctaccttttttttttttttctgatgaggaaggttagatctgatt-tctttagctacttgtgtcttggt
 | |||| |  ||||| |||||| ||||||||||||||||||||| || || || ||  | |||||||| || |    |      |  |   | ||| |   |     |||   || || |       ||   || ||   ||| | |      |  ||||| ||  |
GTATGACTTGTTGGATTTTTGCACCAATGGACCAAAAGAAAAGCTTGACTCGACAGTAATCAGTCAGgt-ttgtagatttcaaagtcatttctccttcatgcattccatttggcttcttatccatgtaaatactaaatagtattatttgctatgaactgtgttttttt

upper sequence: Vv06s0004g07380.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GRMZM2G029543_T01 (Zea mays), 5'ss of exon 3
ATTTGACCTTCTGGATGTTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGTCAGgtattctgccatattgctttgtgatttctttagctaccttttttttttttttctgatgaggaaggttagatctgatttc--tttagct-acttgtgtcttggt
|| |||| | |||||| |||||| ||||||||||||||||||||| || || ||  |  | |||||||||    |   | |   |      |   |||  | |    |    |   |   | || |      ||   | |  ||||  || | || | || | || |   
ATATGACTTGCTGGATCTTTGCACCAATGGACCAAAAGAAAAGCTTGACTCAACAATGATCAGTCAGgtaagtagatttctgagtcccaagtaattttcaccagtggtgacatgcatagttaattaacttaattcattttcttttccattcaacttatttttctcct---

upper sequence: Vv06s0004g07380.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA11G29490.1 (Glycine max), 5'ss of exon 3
ATTTGACCTTCTGGATGTTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGTCAGgtattctgccatattgctttgtgatttctttagctaccttttttttttttttctgatgaggaaggttagatctgattt--ctttagctacttgtgtcttggt-------
 ||||| ||||| ||| | ||||||||||| |||||||||||||||||||| |||||| | || |||||||  | |  || ||||||      | |  | |||  | ||   | |    ||    |   ||| | | ||| || |  | |   ||| |  ||              
GTTTGATCTTCTTGATATATGCATCAATGGGCCAAAAGAAAAGCTAGATTCAACTGTTATCAGCCAGgtata-tactttaatgcttt------tgtcaaactatgtgttcagtataaa-ctagcaatctaggct-gttctcatctggcatagactattgatggaacaacgggatat

upper sequence: Vv06s0004g07380.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: GLYMA18G06500.1 (Glycine max), 5'ss of exon 3
ATTTGACCTTCTGGATGTTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGTCAGgtattctgccatattgctttgtgatttctttagctaccttttttttttttttctgatgaggaaggttagatctgattt--ctttagctacttgtgtcttggt-------
 ||||| ||||| ||| | ||||||||||| |||||||||||| ||||||| || ||| | || |||||||        ||   ||  || |||  ||||   || | ||   | |   ||    |   ||| ||  ||| ||||  | |  |||| |  |               
GTTTGATCTTCTTGATATATGCATCAATGGGCCAAAAGAAAAGTTAGATTCCACCGTTATTAGCCAGgtat--------atgctttaatgcttttcttagactccgtgttcagtataaactaccaatctaggctat-tctcatttggcgtaggctattgatagaacaaagggatat

upper sequence: Vv06s0004g07380.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ07045 (Selaginella moellendorffii), 5'ss of exon 3
ATTTGACCTTCTGGATGTTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGTCAGgtat-tctgccatattgctttgtgatttctttagctaccttttttttttttttctgatgaggaaggttagatctgatttctttagctacttgtgtcttggt
 |  |||||||| ||||||||||| ||||| ||||| || ||||| || ||||||||  | || ||||| | |      |||||  ||   ||   |  ||||| || |||  |  |                                                   
CTACGACCTTCTCGATGTTTGCATGAATGGTCCAAAGGAGAAGCTCGACTCTACTGTCATCAGCCAGgtttgtgaattctattggctttgtatgagtaaagctaactatttgatcgtag-------------------------------------------------

upper sequence: Vv06s0004g07380.t01 (Vitis vinifera), 5'ss of exon 3
lower sequence: EFJ18856 (Selaginella moellendorffii), 5'ss of exon 3
ATTTGACCTTCTGGATGTTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGTCAGgtat-tctgccatattgctttgtgatttctttagctaccttttttttttttttctgatgaggaaggttagatctgatttctttagctacttgtgtcttggt
 |  || ||||| ||||||||||| ||||| ||||| || ||||| |||||||||||  | || ||||| | |      |||||  ||   ||   |  ||||| || |||  |  |                                                   
GTACGATCTTCTCGATGTTTGCATGAATGGGCCAAAGGAGAAGCTCGATTCTACTGTCATCAGCCAGgtttgtgaattctattgtctttgtatgagtaaagctaactatttgatcgtag-------------------------------------------------

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|161710827|gb|FC059885.1|FC059885
EST:     TTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGCCAG                         CCGGCCATATATGTCACAAGCCTAGCTGCAGTAGAGGTGCTTCGTGCTCGT
genomic: TTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGTCAGgtattctgcc ... ttaattgcagCCGGCCATATATGTCACAAGCCTAGCTGCAGTAGAGGTGCTTCGTGCTCGT
EST: gi|161714260|gb|FC063524.1|FC063524
EST:     TTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGCCAG                         CCGGCCATATATGTCACAAGCCTAGCTGCAGTAGAGGTGCTTCGTGCTCGT
genomic: TTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGTCAGgtattctgcc ... ttaattgcagCCGGCCATATATGTCACAAGCCTAGCTGCAGTAGAGGTGCTTCGTGCTCGT
EST: gi|110687429|gb|EE064834.1|EE064834
EST:     CTAGATTCTACTGTTTTAAGCCAG                         CCGGCCATATATGTCACAAGCCTAGCTGCAGTAGAGGTGCTTCGTGCTCGT
genomic: CTAGATTCTACTGTTTTAAGTCAGgtattctgcc ... ttaattgcagCCGGCCATATATGTCACAAGCCTAGCTGCAGTAGAGGTGCTTCGTGCTCGT
EST: gi|30128526|gb|CB913865.1|CB913865
EST:     TTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGCCAG                         CCGGCCATATATGTCACAAGCCTAGCTGCAGTAGAGGTGCTTCGTGCTCGT
genomic: TTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGTCAGgtattctgcc ... ttaattgcagCCGGCCATATATGTCACAAGCCTAGCTGCAGTAGAGGTGCTTCGTGCTCGT
EST: gi|161713818|gb|FC063453.1|FC063453
EST:     TTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGCCAG                         CCGGCCATATATGTCACAAGCCTAGCTGCAGTAGAGGTGCTTCGTGCTCGT
genomic: TTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGTCAGgtattctgcc ... ttaattgcagCCGGCCATATATGTCACAAGCCTAGCTGCAGTAGAGGTGCTTCGTGCTCGT
EST: gi|71872032|gb|DT021087.1|DT021087
EST:     TTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGCCAG                         CCGGCCATATATGTCACAAGCCTAGCTGCAGTAGAGGTGCTTCGTGCTCGT
genomic: TTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGTCAGgtattctgcc ... ttaattgcagCCGGCCATATATGTCACAAGCCTAGCTGCAGTAGAGGTGCTTCGTGCTCGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ATTTGACCTTCTGGATGTTTGCATCAATGGACCAAAAGAAAAGCTAGATTCTACTGTTTTAAGTCAGgtattctgccatattgctttgtgatttctttagctaccttttttttttttttctgatgaggaaggttagatctgatttctttagctacttgtgtcttggt

- - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaggaag