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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGAAAAAGCCCAAAGAAGGTGATAGTGTTGTAGAAGAAGCACCAGCTGACATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattttgggtgccttggtttccttattcctatcttttgtattgcattcttgctttgactgcatgtaaaggtgagagctttttgttatttattcaatata...

Basic information

species Vitis vinifera
transcript Vv07s0031g01970.t01
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: LOC_Os03g63430.1 (Oryza sativa), 5'ss of exon 6
AGAAAAAGCCCAAAGAAGGTGATAGTGTTGTAGAAGAAGCACCAGCTGACATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattttgggtgccttggtttccttattcctatcttttgtattgcattcttgctttgactgcatgtaaaggtgagagctttttgtt--atttattcaatata
| || || || ||||||||||||| | ||||  | ||||| ||||| || || |||||  | |  ||  ||||||||||||||||||||||||||||| ||||| |       ||  ||     || | | ||| |  || |    |   | ||   | ||   ||  | || |  |||      |    |     ||||||
AAAAGAAACCGAAAGAAGGTGATAATATTGTTCAGGAAGCCCCAGCAGAGATACCTTCCCTCCTGGAACTGAAGCGCATCTACTATGAACTGATGATTCGgtatgtcttcctgctcagtgagactaattc-atcatgagt-tcatgtcgcttctagtaatgttggttgaagttaatgctaccccctcaggtcgcaaaatata

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G013750_T03 (Zea mays), 5'ss of exon 6
AGAAAAAGCCCAAAGAAGGTGATAGTGTTGTAGAAGAAGCACCAGCTGACATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattttgggtgccttggtttcc-------------------------ttattcc--tatcttttgt-attgcattcttgctt---tgactgcatgtaaaggtgagagctt-tttgttat-ttattcaatata---------------------------------------------------------
| || || || || || ||||| |   ||||  | || || || || || ||||||||  | | ||| |||||||| ||||||||||||||||||||| ||||| |   |   ||   | ||                           |||| |  | ||  |||| |||    ||| |  |   ||||| | | |  |  ||  |  || |||||| | ||   || |||                                                          
AAAAGAAACCAAAGGAGGGTGACAACATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatgcttctcaatctcaattagattaatgtactaccagtctgctatttcattgtcaattgtcattattctctcgtctacctgactacctctggaactgccaatttctttgttctattgaacactatggttcacaatgacattttatattggagccaatcataattcttcgttatctcatcacag

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GRMZM2G468717_T01 (Zea mays), 5'ss of exon 7
AGAAAAAGCCCAAAGAAGGTGATAGTGTTGTAGAAGAAGCACCAGCTGACATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattttgggtgccttggtttccttattcctatcttttgtattgcattcttgctttgactgcatgtaaaggtgagagctttttgttatttattcaatata-
| || || || || || ||||| |   ||||  | || || || || || ||||||||  | | ||| |||||||| ||||||||||||||||||||| ||||| |   |   ||   | ||  |     ||   |   || ||   |  |  ||| | ||    |     | |     |  | |   | | |   | |  
AAAAGAACCCAAAGGAGGGTGACAACATTGTTCAGGATGCTCCTGCAGATATTCCTTCCCTCCTAGAATTGAAGCGTATCTACTATGAACTGATGATTCGgtatgtcatgcttctcaatctcaattagattaatgtac-tactggtctgctattttcattgtcaattgtcattattcgctcgtctacctgactacctctgg

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA06G15330.1 (Glycine max), 5'ss of exon 6
AGAAAAAGCCCAAAGAAGGTGATAGTGTTGTAGAAGAAGCACCAGCTGACATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattttgggtgcc-ttggtttccttattcctatcttttgtattgcattcttgctttgactgcatgtaaaggtgagagct-ttttgttatttattcaatata
|||||||||| ||||||||||||| |||||| |||||||| || || || ||||| ||| | |||||||||||||| |||||||||||||| |||||| ||||  |      |   | |||  ||||||    |  ||     |||   || |  | |   |  |  ||| |||   | | || |||||  || | |     
AGAAAAAGCCTAAAGAAGGTGATAATGTTGTTGAAGAAGCTCCTGCAGATATTCCATCTCTACCAGAGTTGAAGCGGATCTACTATGAACTAATGATTCGgtaactgattctctacttgttgtcttattttgcttgttcaatatgctgcctgg--tagggggtgttaaaatgtggatgttgttctgttacatagttatcggt

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA04G39520.1 (Glycine max), 5'ss of exon 6
AGAAAAAGCCCAAAGAAGGTGATAGTGTTGTAGAAGAAGCACCAGCTGACATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattttgggtgcc-ttggtttccttattcctatcttttgtattgcattcttgctttgactgcatgtaaaggtgagagct-ttttgttatttatt-caatata
|||||||||| ||||||||||||| |||||| |||||||| || | ||| || || ||| | || ||||||||||| |||||||||||||| |||||| ||||         |   | |||  ||| ||    |  ||     ||| | || ||   |   |  |  ||| |||   | | || |||||   |     ||   
AGAAAAAGCCTAAAGAAGGTGATAATGTTGTTGAAGAAGCTCCTGTTGATATACCATCTCTACCGGAGTTGAAGCGAATCTACTATGAACTAATGATTCGgtaaccaattccctacttgttatcttgttttgcttgttcaatctgcttcctggcaggg---gtgttaaaatgtggatgttgttctgttacaaacagttatccg

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA08G15340.1 (Glycine max), 5'ss of exon 6
AGAAAAAGCCCAAAGAAGGTGATAGTGTTGTAGAAGAAGCACCAGCTGACATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattt---tgggtgccttggtttccttattcctatcttttgtattgcattcttgctttgactgcatgtaaaggtgagagctttttgttatttattcaatata---
|||||||||| ||||||||||||| |||||||||||| || || || || || || |||||||  ||||||||||  ||||| || ||||| |||||| |||| ||   |  || | |    || ||| ||  | | |||  | || ||| | || | |   ||||  ||    |     |||    || | ||||   |||    
AGAAAAAGCCTAAAGAAGGTGATAATGTTGTAGAAGAGGCCCCTGCAGATATACCATCTTTGCTGGAGTTGAAGCAAATCTATTACGAACTAATGATTCGgtaattgaatatgtacttcatgttgctt-tttttctttttcttgttccat-catgatgtagttgcaaata----ttgtgccttaaccttgtatatttggtatctct

upper sequence: Vv07s0031g01970.t01 (Vitis vinifera), 5'ss of exon 6
lower sequence: GLYMA05G32030.2 (Glycine max), 5'ss of exon 6
AGAAAAAGCCCAAAGAAGGTGATAGTGTTGTAGAAGAAGCACCAGCTGACATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattt---tgggtgccttggtttccttattcctatcttttgtattgcattcttgctttgactgcatgtaaag-gtgagagctttttgttatttattcaatata
|||||||||| ||||||||||||| |||||||||||| || || || || || || |||||||  ||||||||||  || || || ||||| |||||| |||| ||   |  || | |    || ||| ||    | | |||| ||    || || | |   | ||  ||  | |    | | || | |  |||        | 
AGAAAAAGCCTAAAGAAGGTGATAATGTTGTAGAAGAGGCTCCCGCAGATATACCATCTTTGCTGGAGTTGAAGCAGATATATTACGAACTAATGATTCGgtaattgaatatgtacttcatgttgctttttttcctttcttgtttta---tcatgatatagttacaaatattgtgccttaaccttgtatattttgcatctctt-

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|351035869|gb|FQ463714.1|FQ463714
EST:     ATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAG                         GTGTCACTCCCACAGCAATGATTACCTTGAAATTTGTCGTAGCTATAAGGC
genomic: ATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattttggg ... acttgtgtagGTATCACTCCCACAGCAATGATTACCTTGAAATTTGTCGTAGCTATAAGGC
EST: gi|110391070|gb|EC956024.1|EC956024
EST:     ATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAG                         GTATCACTCCCACAGCAATGATTACCTTGAAATTTGTCGTAGCTATAAGGC
genomic: ATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattttggg ... acttgtgtagGTATCACTCCCACAGCAATGATTACCTTGAAATTTGTCGTAGCTATAAGGC
EST: gi|110381624|gb|EC934958.1|EC934958
EST:     ATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAG                         GTATCACTCCCACAGCAATGATTACCTTGAAATTTGTCGTAGCTATAAGGC
genomic: ATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattttggg ... acttgtgtagGTATCACTCCCACAGCAATGATTACCTTGAAATTTGTCGTAGCTATAAGGC
EST: gi|27583566|gb|CB006261.1|CB006261
EST:     ATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAG                         GTATCACTCCCACAGCAATGATTACCTTGAAATTTGTCGTAGCTATAAGGC
genomic: ATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattttggg ... acttgtgtagGTATCACTCCCACAGCAATGATTACCTTGAAATTTGTCGTAGCTATAAGGC
EST: gi|349825795|gb|FQ423090.1|FQ423090
EST:     ATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAG                         GTATCACTCCCACAGCAATGATTACCTTGAAATTTGTCGTAGCTATAAGGC
genomic: ATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattttggg ... acttgtgtagGTATCACTCCCACAGCAATGATTACCTTGAAATTTGTCGTAGCTATAAGGC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGAAAAAGCCCAAAGAAGGTGATAGTGTTGTAGAAGAAGCACCAGCTGACATTCCTTCTTTGCCAGAGTTGAAGCGCATCTACTATGAACTGATGATTAGgtattttgggtgccttggtttccttattcctatcttttgtattgcattcttgctttgactgcatgtaaaggtgagagctttttgttatttattcaatata

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGAAGC