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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...cacatgctttctgataattcaaatattatacttataatgaattatgactgcttactcattccttcattctgatttaaatgtgcttaattaattgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATAAGGAGCTACAAGGGTTTGATGGTCTCTGAAAAGATGACTTCTAACAAAC

Basic information

species Vitis vinifera
transcript Vv04s0008g03810.t01
intron # 5
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv04s0008g03810.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GRMZM2G157332_T03 (Zea mays), 3'ss of exon 3
----cacatgctttctgata-----attcaaatattatacttataatgaattatgactgcttactcattccttcattctgatttaaatgtgcttaattaattgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATAAGGAGCTACAAGGGTTTGATGGTCTCTGAAAAGATGACTTCTAACAAAC
        | ||  ||||||     | | || |  |  |||| | || | ||| || |  | ||  |     ||| |  ||||   ||||  ||  |    || | ||||||||||||||||| ||||| |||||||| |||||||  || || || || ||||||||||||||| | ||||||   || ||||||||||| ||||| |
gatgttggtactacctgataaaataactgaactgctgaacttttgat-agtta-gaatattgacataacagatcactg-gatt---atgtttttcttc---tgtttcagAAACGTAGGGAAGAGATGGAGAGGCTTGAGAAAGAGAAGCAGGCTGATATCAGGAGCTACAAGGGTCTAATGGTCCAAGAGAAGATGACTTCCAACAAGC

upper sequence: Vv04s0008g03810.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G08530.1 (Glycine max), 3'ss of exon 5
cacatgctttctgataattcaaatattatacttataatgaattatgactgcttactcattccttcattctgatttaaatgtgctta---attaattgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATAAGGAGCTACAAGGGTTTGATGGTCTCTGAAAAGATGACTTCTAACAAAC
 | |           |  | |   |  || ||   ||||||  |||    | |  | |||     ||| |   ||  || | |  |    ||  |  || ||||||||| |||| ||| ||| |||||||||||| |||| |||| ||||| | |||||||||||||||||||||||  | ||||| ||||| || |||||||
-atagttcaatctgcatatgatgaaaaatgctgg-aatgaaa-atggtaacgtttttattgaacaattgtttcttttatttacccacatgtttctccatccagAAACGTCGGGAGGAATTGGGAAGGCTTGAAAAGGAGAAACAAACAGAGCTTAGGAGCTACAAGGGTTTGATGGTTGCAGAAAATATGACATCCAACAAAC

upper sequence: Vv04s0008g03810.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G08640.1 (Glycine max), 3'ss of exon 5
-cacatgctttctgata-attcaaatattatacttataatgaattatgactgcttactcattccttcattctgatttaaatgtgcttaattaattgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATAAGGAGCTACAAGGGTTTGATGGTCTCTGAAAAGATGACTTCTAACAAAC
    ||  ||     |  ||   || |  || ||   ||||||  |||||   ||  |    |  |  ||||  | |  |    | |  ||  |  || ||||||||  | || ||| |||||||||||||||| |||| |||| ||||| | |||||||||||||||||||||||  | ||||| ||||| || |||||||
gtttatagttcaatctgcatatgaaaaagatgctgg-aatgaaaaatgacgtttttattgaacaatttttcttttatttacccacatgtttc-tccatccagAAACGCCGTGAGGAATTGGAAAGGCTTGAAAAGGAGAAACAAACAGAGCTTAGGAGCTACAAGGGTTTGATGGTTGCAGAAAATATGACATCCAACAAAC

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|56409227|gb|CX017479.1|CX017479
EST:     CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAA                         AAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAAATA
genomic: CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAAgtaagtccca ... attgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
EST: gi|161720775|gb|FC070283.1|FC070283
EST:     CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAA                         AAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
genomic: CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAAgtaagtccca ... attgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
EST: gi|34549359|gb|CF517591.1|CF517591
EST:     CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAA                         AAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
genomic: CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAAgtaagtccca ... attgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
EST: gi|110715789|gb|EE094238.1|EE094238
EST:     CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAA                         AAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
genomic: CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAAgtaagtccca ... attgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
EST: gi|110383971|gb|EC948380.1|EC948380
EST:     CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAA                         AAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
genomic: CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAAgtaagtccca ... attgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
EST: gi|110710049|gb|EE086042.1|EE086042
EST:     CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAA                         AAACGTAGGGAAGAAATGGGAAGGCTTNGAAAA-GAGAGACAAGCAGAGAT
genomic: CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAAgtaagtccca ... attgatgcagAAACGTAGGGAAGAAATGGAAAGGCTT-GAAAAAGAGAGACAAGCAGAGAT
EST: gi|30128520|gb|CB913859.1|CB913859
EST:     CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAA                         AAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
genomic: CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAAgtaagtccca ... attgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
EST: gi|161721392|gb|FC070768.1|FC070768
EST:     CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAA                         AAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
genomic: CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAAgtaagtccca ... attgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
EST: gi|110357353|gb|EC920834.1|EC920834
EST:     CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTTAGAGATAAA                         AAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
genomic: CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAAgtaagtccca ... attgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
EST: gi|110374937|gb|EC939883.1|EC939883
EST:     CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAA                         AAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
genomic: CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAAgtaagtccca ... attgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
EST: gi|27583079|gb|CB005774.1|CB005774
EST:     CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAA                         AAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA
genomic: CAGTTAATGCAGCAGAAAGAGCTGAGAGAAAACTTCAGCTGAGAGATAAAgtaagtccca ... attgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gactgcttactcattccttcattctgatttaaatgtgcttaattaattgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATAAGGAGCTACAAGGGTTTGATGGTCTCTGAAAAGATGACTTCTAACAAAC
                          atttaaatgtgcttaa  TA-rich tract
















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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
cacatgctttctgataattcaaatattatacttataatgaattatgactgcttactcattccttcattctgatttaaatgtgcttaattaattgatgcagAAACGTAGGGAAGAAATGGAAAGGCTTGAAAAAGAGAGACAAGCAGAGATAAGGAGCTACAAGGGTTTGATGGTCTCTGAAAAGATGACTTCTAACAAAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
cacatgc
- - - - - - - - - -caaatat
- - - - - - - - - - - - - - - - - - - - - - tgactgc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatgtgc