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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCATGACACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAGgtacattcttgtccatttgcgcgcatatttttatcatcttgttcgtatatggttttggactagtaattttatttatttatttaattgttttcagtacatt...

Basic information

species Vitis vinifera
transcript Vv01s0011g05370.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: LOC_Os03g50480.2 (Oryza sativa), 5'ss of exon 3
GCATGACACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAGgtacattcttgtccatttgcgcgcatatttttatcatcttgttcgtatatggttttggactagtaattttatt-tatttatttaattgttttcagtacatt-----
|    ||  ||||||| ||||||||||||||||||||||||||||||||  ||||||||  || |  |  ||| |  | |||  || |       ||    | | || |  |  | |   |||||| || ||| | |  | ||| ||  |     ||     
GTGCAACCATTGTTGTGTCTGGTGATGGCCGCTATTTCTCGAAGGATGCTGTTCAGgtaatttatgattgattaggcctcatggttct-----tgtgcaattttgtgatcctt-attgtcaattttgttatatatttgcagttgcttctacggatttccctt

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G109383_T01 (Zea mays), 5'ss of exon 3
GCATGACACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAGgtacattcttgtccatttgcgcgcatatttttatcatct-tgttcgtatatggttttggactag-taattttatttatttatttaattgttttcagtacatt
|    ||| ||||||| ||||||||||||||||||||||| || |||||  |||||||   ||    | | | | |     | || |  |   |        ||  ||       |   | |||||   |    | |  | |  |   |||   ||  
GTGCAACAATTGTTGTCTCTGGTGATGGCCGCTATTTCTCAAAAGATGCTGTTCAGgtgatttagaatac-tctccatctttgttatggttggcaacacctataggtgccggcaaaggggctaattaggtgggataagatcaagggggtcaaatcag-

upper sequence: Vv01s0011g05370.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G023289_T03 (Zea mays), 5'ss of exon 3
GCATGACACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAGgtacattct-----tgtccatttgcgcgcatattttt-------atcatcttgttcgtatatggttttgg-actagtaattttatttatttatttaattgttttcagtacatt-------------------------------------------------------------------------------------
|    ||  ||||||| ||||||||||||||||||||||| || |||||  |||||||   ||       |  |   |  |    |||||||        ||| | |  ||  ||||  | ||||  | |||  ||| ||    |  |||    ||         ||||                                                                                     
GTGCAACCATTGTTGTCTCTGGTGATGGCCGCTATTTCTCAAAAGATGCTGTTCAGgtgatttagaacagtaccatctcccttatatattttctaaccccatcttataatttttatactgctttgatagtagctattgtagacttgaattccgatgcagatgtagcattgttgtcttctccctgaggtcgagtttttttaatagacttggtgttcatgaactacattgaatcccattgattttgcttgttacag

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|30133485|gb|CB918824.1|CB918824
EST:     CACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAG                         ATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
genomic: CACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAGgtacattctt ... aaactgccagATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
EST: gi|71862440|gb|DT011495.1|DT011495
EST:     CACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAG                         ATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
genomic: CACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAGgtacattctt ... aaactgccagATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
EST: gi|351015349|gb|FQ445633.1|FQ445633
EST:     CGAAGGATGCCATTCAG                         ATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
genomic: CGAAGGATGCCATTCAGgtacattctt ... aaactgccagATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
EST: gi|32270931|gb|CD720090.1|CD720090
EST:     CACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAG                         ATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
genomic: CACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAGgtacattctt ... aaactgccagATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
EST: gi|32268210|gb|CD717369.1|CD717369
EST:     CACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAG                         ATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
genomic: CACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAGgtacattctt ... aaactgccagATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
EST: gi|77583444|gb|DV220763.1|DV220763
EST:     CACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAG                         ATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
genomic: CACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAGgtacattctt ... aaactgccagATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
EST: gi|161715336|gb|FC066459.1|FC066459
EST:     CACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAG                         ATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
genomic: CACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAGgtacattctt ... aaactgccagATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
EST: gi|349810189|gb|FQ401635.1|FQ401635
EST:     CGAAGGATGCCATTCAG                         ATTATAATTAAGATGGCGGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
genomic: CGAAGGATGCCATTCAGgtacattctt ... aaactgccagATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
EST: gi|349818554|gb|FQ403189.1|FQ403189
EST:     CGAAGGATGCCATTCAG                         ATTATAATTAAGATGGCAGCTGCAAATGGGGTGAGATCTGTCTGGGTTGGT
genomic: CGAAGGATGCCATTCAGgtacattctt ... aaactgccagATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
EST: gi|349827300|gb|FQ421573.1|FQ421573
EST:     CGAAGGATGCCATTCAG                         ATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
genomic: CGAAGGATGCCATTCAGgtacattctt ... aaactgccagATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
EST: gi|349810979|gb|FQ405967.1|FQ405967
EST:     CGAAGGATGCCATTCAG                         ATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
genomic: CGAAGGATGCCATTCAGgtacattctt ... aaactgccagATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
EST: gi|349810186|gb|FQ401632.1|FQ401632
EST:     CGAAGGATGCCATTCAG                         ATTATAATTAAGATGGCGGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT
genomic: CGAAGGATGCCATTCAGgtacattctt ... aaactgccagATTATAATTAAGATGGCAGCTGCAAATGGAGTGAGATCTGTCTGGGTTGGT

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCATGACACTTGTTGTTTCTGGTGATGGCCGCTATTTCTCGAAGGATGCCATTCAGgtacattcttgtccatttgcgcgcatatttttatcatcttgttcgtatatggttttggactagtaattttatttatttatttaattgttttcagtacatt

- - - - - - - - - - - - - - - - - - - - - AGGATG