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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgtgctgaaacctttacatgctctgtaatatcaactgagttaaattgtcaaaaaaaagcatcactacattactttctctgtctctagcttccc...

Basic information

species Vitis vinifera
transcript Vv12s0057g01200.t01
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: LOC_Os09g07830.3 (Oryza sativa), 5'ss of exon 12
GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatattt-gtgctgaaacctttacatgctctgtaatatcaactgagttaaattgtcaaaaaaaagcatcactacattactttctctgtctctagcttccc
|||||| ||||||| ||||| || ||||| || || ||||||||||| || |||||||| || ||||| |||||||| ||  | || |||  |||     ||| |  |     || ||| | || |   ||  |||    | | |    |    ||       ||     | |    || |  |||  
GAAAAAATTAATGTACATGGAGGAGCTGTGTCTTTAGGACATCCTCTTGGATGCAGTGGTGCTCGAATTTTGGTCACCCTGCTTGGTgtaagttttaccttgagatgtccttttgttctatgattttctctctgttttcctatgattttatgagattctgctgttcaggacacctcatccatgttct-

upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM5G866758_T01 (Zea mays), 5'ss of exon 12
GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatt-tgtgctgaaacctttacat--gctctgtaatatcaactgagttaaattgtcaaaaaaaagcatcactacattactttctctgtctctagcttccc
|||||  ||||||| ||||| || ||||||||||| ||||||||||| || |||||||| || || || ||||| || ||| | || |||  || | |  | | |   ||   |   || |  | |  |||     ||   ||   |||||   |||    |    || |       |   | |  |   
GAAAAGATTAATGTTCATGGAGGAGCTGTATCCTTAGGACATCCTCTCGGGTGCAGTGGTGCTCGCATTTTGGTTACCCTTATTGGTgtaagttctatcttaagatgcttgttttaccttttgagttacaatcccttttgtttaaaaaaaatgtgcaatgtttttctagtaaaaaaatagatggtct---

upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GRMZM5G830250_T01 (Zea mays), 5'ss of exon 11
GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgtgctgaaacctttacatgctctgtaatatcaactgagttaaattgtcaaaaaaaagcatcactacattactttctctgtctctagcttccc
|||||   |||||| |||||||| |||||||| || ||||||||||| || |||||||| || || || ||||| || ||| | || ||| |||        |  ||| | ||| |   | |   |||     ||   || |   | |     ||   || ||| || | | |  |  |        
GAAAAGACTAATGTTCATGGTGGAGCTGTATCTTTAGGACATCCTCTTGGGTGCAGTGGTGCTCGCATTTTGgttactcttcttggtgtaaattct------agtcttaagatgtttgttta---caatctgttttgtttatgttatatgtatatttatatattcctatgtatacccattt------

upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA14G00760.2 (Glycine max), 5'ss of exon 10
GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatat-ttgtgctgaaacctttacatgctctgtaatatcaactgagttaaattgtcaaaaaaaagcatcac----tacattactttctctgtctctagcttccc
|||||||| || || |||||||| |||||  |  |||| |||||||| ||||||||||| || || ||  |||| |||||||||||||||| |  |  | | | | ||||  ||  | | ||||||  | |    |  || ||  | | |  || |       |  |  |     ||| ||  |||      
GAAAAAGTAAACGTACATGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGGgtatgtgctcagttcataactttg-attttttataatatatagtagaatgcat-gttgacagattgccttgtgttttgtagaaaaaagtctatca-tagtgct--

upper sequence: Vv12s0057g01200.t01 (Vitis vinifera), 5'ss of exon 13
lower sequence: GLYMA02G47860.2 (Glycine max), 5'ss of exon 11
GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatat-ttgtgctgaaacctttacatgctctgtaatatcaactgagttaaattgtcaaaaaaaagcatcactacattactttctctgtctctagcttccc
|||||||| ||  | || ||||| |||||  |  |||| |||||||| ||||||||||| || || ||  |||| |||||||||||||||| |  |  | | | | |||    |  | |  |||||  | |    |  || ||  ||| |  || |        ||        |||| |       |
GAAAAAGTAAACTTACACGGTGGAGCTGTTGCACTGGGTCATCCTCTTGGTTGCAGTGGTGCTCGCATTCTGGTGACACTTTTGGGGgtatgtgctcagttcataacttcgattattttacaatatataatagcatgcat-gttgaaagattgccttgtgtttgtataaaaaaagtctatcatagtgc

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|352790687|gb|FQ475445.1|FQ475445
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GCACTGAGGCAGAAAGATGGGAAATATGGAGTCAGTGGTGTTTGCAATGGT
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
EST: gi|30130059|gb|CB915398.1|CB915398
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
EST: gi|71876405|gb|DT025460.1|DT025460
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
EST: gi|110700654|gb|EE077500.1|EE077500
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGAGGCACAAAGATGGCAAATATGCAGTCCGTGGTGTTTGCAATGTT
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
EST: gi|349833317|gb|FQ416695.1|FQ416695
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGAAGCAGAAAAATGGG
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGG
EST: gi|110368276|gb|EC932247.1|EC932247
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGAGGCAGAAAGATGGGAAATATGGAGTCAGTGGTGTTTGCAATGGT
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
EST: gi|33402805|gb|CF208432.1|CF208432
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGAGGCAGAAAGATGGGAAATATG-ATGTCAGTGGTGTTTGCAATAG
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGA-GTCGGTGGTGTTTGCAATGG
EST: gi|110361968|gb|EC925474.1|EC925474
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGAGGCAGAAAGATGGGAAATATGGAGTCAGTGGTGTTTGCAATGGT
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
EST: gi|30133750|gb|CB919089.1|CB919089
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
EST: gi|26259676|gb|CA810739.1|CA810739
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
EST: gi|110361336|gb|EC924802.1|EC924802
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGAGGCAGAAAGATGGGAAATATGGAGTCAGTGGTGTTTGCAATGGT
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
EST: gi|110362059|gb|EC925566.1|EC925566
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
EST: gi|110357331|gb|EC920800.1|EC920800
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
EST: gi|32246227|gb|CD712046.1|CD712046
EST:     GACATCCTTTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
EST: gi|33403297|gb|CF208924.1|CF208924
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGAGGCAGAAAGATGGGAAATATGGAGTCAGTGGTGTTTGCAATGGT
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTGCAATGGT
EST: gi|110723122|gb|EE100072.1|EE100072
EST:     GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGG                         GTACTGANGCAGAAAGATGGGAAATATGGAGTCNGTGGTGTTTGGCA-TGG
genomic: GACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgt ... ggtgttgcagGTACTGAGGCAGAAAGATGGGAAATATGGAGTCGGTGGTGTTTG-CAATGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GAAAAAGTTAATGTGCATGGTGGTGCTGTATCCTTGGGACATCCTCTAGGTTGCAGTGGAGCCCGAATCTTGGTCACACTTTTGGGGgtatatttgtgctgaaacctttacatgctctgtaatatcaactgagttaaattgtcaaaaaaaagcatcactacattactttctctgtctctagcttccc

- - - - - - - - - - - - - - - - - - - - - - - - - - - AGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aaaaaaa