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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTCCGCCATGAGGTCGAGGAGTATGCAAAACAATTCCCAACTATTGGTTTTGAGAAAGAAACAATGAAATATAAAGATTGAAGTAGTCTTTAAGGACAAGgtatgtcacactctggatcgcgaaacagacatttgtgatagttgtcattttgtctgtagaattgaagcaataaaatcacatctagagatgaggtattgga...

Basic information

species Vitis vinifera
transcript Vv18s0001g07960.t01
intron # 15
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: LOC_Os03g52840.3 (Oryza sativa), 5'ss of exon 12
CTCCGCCATGAGGTCGAGGAGTATGCAAAACAATTCCCAACTATTGGTTTTGAGAAAGAAACAATGAAATATAAAGATTGAAGTAGTCTTTAAGGACAAGgtatgtcacactctggatcgcgaaacagacatttgtgatagttgtcattttgtctgtagaattgaagcaataaaatcacatctagagatgaggtattgga-----
    ||||||| || ||||| ||||||||||| ||||| || ||||| |||||||||||||| ||||| || ||  | | ||| |   || || |  |  | | |  |   ||  ||  |  |||  | |     |  |  ||  |||  ||  || || ||   ||      |  |         ||| | | |          
----GCCATGATGTGGAGGAATATGCAAAACAGTTCCCCACAATTGGGTTTGAGAAAGAAACCATGAAGTACAAGAACT-AAGAAACTTTGAATGGAACAGCAAGgtattgtcctgacagataaattggctccatttttttttagcatgctgcatgcagtatattagttgcctaggccttggctccgatcatgaaccatgtttac

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GRMZM2G135283_T04 (Zea mays), 5'ss of exon 15
----CTCCGCCATGAGGTCGAGGAGTATGCAAAACAATTCCCAACTATTGGTTTTGAGAAAGAAACAATGAAATATAAAGATTGAAGTAGTCTTTAAGGACAAGgtatgtcaca-ctctggatcgcgaaacagacat---ttgtgatagttgtcattttgtctgtagaattgaagcaataaaatcacatctagagatgaggtattgga-----------------------------
    || |||||||| || ||||| | |||||||||||||||||| ||||| ||||||||||| || |||||||| ||  | | |  |     |  | |||||||||||    | || || |  |   |      ||   || | |||      |  |    |||  ||  |  | |    |     | ||   | |    || | |                              
AAAGCTTCGCCATGATGTAGAGGAATTTGCAAAACAATTCCCAACAATTGGATTTGAGAAAGAGACCATGAAATACAAGAACTAATAT----CTGGATGACAAGgtatgctctatctttgcacggtttagtcattatgcattctaatatacagtagctcagttgtgaaag-ggggtaccggagctggaactgccgttttcttacttggctgagcgcttccctcttatccatttgcag

upper sequence: Vv18s0001g07960.t01 (Vitis vinifera), 5'ss of exon 15
lower sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 15
----CTCCGCCATGAGGTCGAGGAGTATGCAAAACAATTCCCAACTATTGGTTTTGAGAAAGAAACAATGAAATATAAAGATTGAAGTAGTCTTTAAGGACAAGgtatgtcaca-ctctggatcgcgaaacagacat---ttgtgatagttgtcattttgtctgtagaattgaagcaataaaatcacatctagagatgaggtattgga--------------------------------
    || |||||||| || ||||| | |||||||||||||||||| ||||| ||||||||||| || |||||||| ||  | | |  |     |  | |||||||||||    | || || |  |   |      ||   || | |||      |  |    |||  ||  |  | |    |     | ||   | |    || | |                                 
AAAGCTTCGCCATGATGTAGAGGAATTTGCAAAACAATTCCCAACAATTGGATTTGAGAAAGAGACCATGAAATACAAGAACTAATAT----CTGGATGACAAGgtatgctctatctttgcacggtttagtcattatgcattctaatatacagtagctcagttgtgaaag-ggggtaccggagctggaactgccgttttcttacttggctgagcgcttccctcttatccatttgcagaag

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|110361032|gb|EC924482.1|EC924482
EST:     TGAGAAAGAAACAATGAAATATAAAGATTGAAGTAGTCTTTAAGGACAAG                         GCAGGCTATCACTGTGGCTCTCTAAGTTCTCGGACGTTGAAGGCAAGGAGA
genomic: TGAGAAAGAAACAATGAAATATAAAGATTGAAGTAGTCTTTAAGGACAAGgtatgtcaca ... ttgtttccagGCAGGCTATCACTGTGGCTCTCTAAGTTCTCGGACGTTGAAGGCAAGGAGA
EST: gi|351022221|gb|FQ438806.1|FQ438806
EST:     TGAGAAAGAAACAATGAAATATAAAGATTGAAGTAGTCTTTAAGGACAAG                         GCAAGCTATCACTGTGGCTCTCTAAGTTCTCGGACGTTGAAAGCAAGGAGA
genomic: TGAGAAAGAAACAATGAAATATAAAGATTGAAGTAGTCTTTAAGGACAAGgtatgtcaca ... ttgtttccagGCAGGCTATCACTGTGGCTCTCTAAGTTCTCGGACGTTGAAGGCAAGGAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTCCGCCATGAGGTCGAGGAGTATGCAAAACAATTCCCAACTATTGGTTTTGAGAAAGAAACAATGAAATATAAAGATTGAAGTAGTCTTTAAGGACAAGgtatgtcacactctggatcgcgaaacagacatttgtgatagttgtcattttgtctgtagaattgaagcaataaaatcacatctagagatgaggtattgga

- - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaaacag
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aataaaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agatgagg