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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgtcggtttgttttcttaaatccattatgattcatgtattttgttgcttttgtagttctctgagtcttctttattacctgttctggttgagcag

Basic information

species Vitis vinifera
transcript Vv12s0035g01740.t01
intron # 19
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: LOC_Os02g50550.1 (Oryza sativa), 5'ss of exon 19
AAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgt---cggtttgttttcttaaatccattatgattcatg-tattttgttgcttt-------tgtagttctctgagtcttctttattacc-tgttctggttgagcag
 |  ||||| ||||| |||||||| || || ||||||||||||||||| ||||||||||| || |||||| |||||||  | || || ||||| ||||| ||   |  ||     ||  || |   | |  | ||||  |||||| |    |          | ||  |    |   |  ||||||   | || |   ||| |||
GAAGCCTGCTGATCCTGAAGAAGAACTTCGGTGGATGTCTCAAGAAGTTCGTGGTTATGTAGAGGCTGTTTTGAACAGTTTGGCAGCAAATGTTCCAAAGgtttacatttgaacctcacaattgtttcaacagtcatactattttttaaactcaatttaacatggtcatagttgcaattgttattattgtctttttcatgatcag

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 5'ss of exon 19
AAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgtcggtttgttttcttaaatccattatgattcatgtattttgttgcttttgtagttctctgagtcttctttattacctgttctggttgagcag
 |||||||| ||||| |||||||| ||  |||||||||| || ||||| |||||||||||||| |||||| |||| || || || || ||||||||||| ||   |   ||     ||| | |  ||   |||| |  || |   || |  | ||        |||| ||  ||        |   | | |||
GAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCCCATGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTCCCAAAGgtt--tacattaaaaaaaagctagcattgctcatttcattggaccctgtcattgtggcaatgttcttattgttttttccccttctcttatcag

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: LOC_Os08g32920.1 (Oryza sativa), 5'ss of exon 19
-AAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgtcggtttgttttcttaaatccattatgattcatgtattttgttgcttttgtagttctctgagtcttctttattacctgttctggttgagcag
 ||  || |  ||||| || ||||||||   |||||| ||||||||||| ||||| ||||| ||||||||||| | ||| ||||| || |||||||| ||  |  |  ||| |  |    | | | |   ||| ||      ||  | ||| ||| |   ||  |     | |||    | ||  ||||||   
GAAAGCCAGTAGATCCTGAGGAAGAGCTTAAATGGATATCTCAAGAAGTCCGTGGGTATGTGGAAGCTGTTCTCAGCAGTCTTGCGGCAAATGTCCCCAAgttaagcatgtctggtgtcttgcttaagctttcctg------gtctcctttctagcttcttgcattaatatcatt----gatcctgttgag---

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GRMZM5G870253_T01 (Zea mays), 5'ss of exon 3
AAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgtcggtttgttttcttaaatccattatgattcatgtattttgttgcttttgtagttctctgagtcttctttattacctgttctggttgagcag
 || ||||| ||||| |||||||| || |||||||||||||||||||| ||||||||||||||||||||| |||||||  | ||||| ||||| |||||    |||||||  || ||  | || |    |   || |  ||||   || || |||    |   | || | | || | ||  | |         
GAGGCCTGCTGATCCTGAAGAAGAACTTCGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTTTGAACAGTTTGGCTGCAAATGTTCCAAA----Ggtttgtactcgtagcttcagttgattctttgaaccttgtgatttgtggagtaacgttc-ttttgtcttttgcatgaccag---------

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GRMZM5G811223_T01 (Zea mays), 5'ss of exon 7
AAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgtcggtttgttttcttaaatccattatgattcatgtattttgttgcttttgtagttctctgagtcttctttattacctgttctggttgagcag
 ||||| || ||||| |||||||| ||  ||||||||||||||||||| |||||||||||||| |||||| |||| || || || || ||||| || || ||   | |  ||   | ||||  ||        |  ||    |||  |||||     ||  | | |  ||  ||  |||| || |||      
GAGACCAGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTTGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCGAAGgttcatattgttctgttaatcagtt--------taaatggccttgtatttgtg----tcaaattttcattgcttgtctgtacttgttag----

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GRMZM2G157462_T01 (Zea mays), 5'ss of exon 19
AAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgtcggtttgttttcttaaatccattatgattcatgtattttgttgcttttgtagttctctgagtcttctttattacctgttctggttgagcag
 |||||||| ||||| |||||||| ||  ||||||||||||||||||| ||||||||||| || |||||| |||| || || || || ||||| |||||    ||||  | ||  |   || |  |   || |  |    | ||  || |||      |  | |||| ||  ||  |||| || |||      
TAGACCTGCTGATCCTGAAGAAGAACTTAGATGGATGTCTCAAGAAGTTCGTGGTTATGTCGAGGCTGTTTTGAATAGTCTGGCAGCAAATGTTCCAAA----Ggttcatattggtctgtcaacca--gtttaaatggccttttatttgtgt------caaattcttattgtttgtctgtacttgttag----

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GLYMA07G40300.1 (Glycine max), 5'ss of exon 19
AAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgtcggtttgttttcttaaatccattatgattcatgtattttgttgcttttgtagttctctgagtcttctttattacctgttctggttgagcag
|| |||||| ||||||||||| |||||| ||||||||||||||||||||||||||||||||||||||||||| |||||||| ||||| ||||| ||||||||  |||| |||| | ||  | |  ||  ||| | | || || |  |   |  ||| | ||||     || | |        ||  |||||||
AAAACCTGCAGATCCAGAAGAGGAGCTCAGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTCGCTGCAAATGTTCCAAAAgtgagtttattttatcaa--ctaccatagttcttctcttctgat-ttgacgcggtt-tgtgagatgatttcact-------ttgactgagcag

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: GLYMA17G00480.1 (Glycine max), 5'ss of exon 19
AAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgtcggtttgttttcttaaatccattatgattcatgtattttgttgcttttgtagttctctgagtcttctttattacctgttctggttgagcag
 | |||||| |||||||| || |||||| ||||||||||||||||||| ||||||||||||||||||||||| ||||||||||| || ||||| ||||||||  |||| |||| | ||  | |  ||  ||| | | || || |  |  ||| ||| | ||||     || | |        |||||||||||
GAAACCTGCAGATCCAGAGGAGGAGCTCAGATGGATGTCTCAAGAAGTCCGTGGTTATGTTGAAGCTGTTCTTAACAGCCTTGCAGCTAATGTTCCAAAAgtgagtttattttatcaa--ctaccatagttcttctcttctgat-ttgatgtggtt-tgtgagatcatttcact-------ttggttgagcag

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: AT1G10290.1 (Arabidopsis thaliana), 5'ss of exon 19
AAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgtcggtttgttttcttaaatccattatgattcatgtattttgttg-----cttttgtagttctctgagtcttctttattacctgttctggttgagcag---------------
 | |||   |||||||||||| |||||||| |||||||| |||||||| || ||||| |||||||||||||| ||||||||||| |||||||| ||||| ||    |    || |  ||    |    |    |  ||||| |||     || || |   |  | |||  | ||   | |         |    |                  
GAAACCCATCGATCCAGAAGAGGAGCTCCGGTGGATGTCCCAAGAAGTACGGGGTTACGTTGAAGCTGTTCTTAACAGCCTTGCAGCCAATGTTCCAAAGgtgaactatccttatgcaaaagctcgaaagctctaaattttcttgtccatctcttttctcttacagagattcctcggtcatgctactaagcgatgtgaattgaccatgaacag

upper sequence: Vv12s0035g01740.t01 (Vitis vinifera), 5'ss of exon 19
lower sequence: AT1G59610.1 (Arabidopsis thaliana), 5'ss of exon 19
AAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgtcggtttgttttcttaaatccattatgattcatgtattttgttgcttttgtagttctctg--agtcttctttattacctgttctgg---ttgagcag
 | ||| | ||| || ||||| ||  | || |||||||| |||||||| || |||||||||||||||||||| ||||| || ||||||||||| ||||| || |  | ||    ||     | |    |||| |  |||    |||   | | | | |     | ||      |||||    ||||    || | |||
GAAACCGGTCGACCCGGAAGAGGAATTACGGTGGATGTCCCAAGAAGTACGGGGTTATGTTGAAGCTGTTCTCAACAGTCTAGCTGCCAATGTTCCAAAGgtggactagtcacttt----tcttgtgaattcttaaattcccatgccaatatcgcttttcattactcgatcacattactaaatctgtgacttcaacag

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|30135425|gb|CB920763.1|CB920763
EST:     GTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAA                         GCAGTTGTCCTTTGCCAAGTAGAAAAATCCAAGGAAGATATGCTTAATCAG
genomic: GTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgtcggtttgt ... ggttgagcagGCAGTTGTCCTTTGCCAAGTAGAAAAATCCAAGGAAGATATGCTTAATCAG




















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AAGACCTGCCGATCCAGAAGAAGAGCTCCGATGGATGTCTCAAGAAGTGCGTGGTTATGTTGAAGCTGTTCTGAACAGCCTTGCTGCCAATGTCCCAAAAgtcggtttgttttcttaaatccattatgattcatgtattttgttgcttttgtagttctctgagtcttctttattacctgttctggttgagcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GCTGTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGCTGC