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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AGGCATGCCCCTTTTGCAGGAGAGTTCGAGAGGCCATAACTGAGCTTGATCTTTCTGTAGAGgtgagcaatgacttctatagacatgatttattttgattatcattgactgttattttcatcaataatctatatcctctgttttctagggaactatactcca...

Basic information

species Vitis vinifera
transcript Vv18s0001g06900.t01
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0001g06900.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G086971_T04 (Zea mays), 5'ss of exon 4
AGGCATGCCCCTTTTGCAGGAGAGTTCGAGAGGCCATAACTGAGCTTGATCTTTCTGTAGAGgtgagcaa---tgacttctatagacatgatttattttgattatcattgactgtta----ttttcatcaataatctatatcctctgttttctagggaactatactcca-------------------------------------------------------------
||||||| ||||| || ||||||||||| |||||||| || |||||||| ||||||| |||||||  |||   || |||  || |        | | |  |||   |   ||  | |     ||| | |  ||     | | || ||  ||| ||  |    |   |                                                               
AGGCATGTCCCTTCTGTAGGAGAGTTCGGGAGGCCATGACCGAGCTTGACCTTTCTGCAGAGgtgctcaaccttgtcttacattgttccttcatttctgcattcgaagcaaccatgaaaccattttacctgtaccggctctact-tgcattccagttagtgctggccattgatgtagcattctgacgctgtcttcttagtggcgccaatttttattcctaactgtttcag

upper sequence: Vv18s0001g06900.t01 (Vitis vinifera), 5'ss of exon 4
lower sequence: GRMZM2G086971_T05 (Zea mays), 5'ss of exon 3
AGGCATGCCCCTTTTGCAGGAGAGTTCGAGAGGCCATAACTGAGCTTGATCTTTCTGTAGAGgtgagcaatgacttctatagacatgatttattttgattatcattgactgttattttcatcaataatctatatc--ctctgttttctagggaacta-tactcca
||||||| ||||| || ||||||||||| |||||||| || |||||||| ||||||| |||||||  |||     |||       |   ||  |||    ||      |    ||         | | || || |  ||||  || |     |  || | ||   
AGGCATGTCCCTTCTGTAGGAGAGTTCGGGAGGCCATGACCGAGCTTGACCTTTCTGCAGAGgtgctcaaccttgtcttacattgttccttcatttctgcattcgaagcaaccatgaaaccattttacctgtaccggctctacttgcattccagttagtgct---
















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|110384554|gb|EC948998.1|EC948998
EST:     TTTGCAGGAGAGTTCGAGAGGCCATAACTGAGCTTGATCTTTCTGTAGAG                         GTCTATCCTTGTCCAAAAGGTTCTGTAAGACACAGGGAAATGGTTAGAAGA
genomic: TTTGCAGGAGAGTTCGAGAGGCCATAACTGAGCTTGATCTTTCTGTAGAGgtgagcaatg ... gtatctacagGTCTATCCTTGTCCAAAAGGTTCTGTAAGACACAGGGAAATGGTTAGAAGA
EST: gi|110396178|gb|EC961859.1|EC961859
EST:     TTTGCAGGAGAGTTCGAGAGGCCATAACTGAGCTTGATCTTTCTGTAGAG                         GTCTATCCTTGTCCAAAAGGTTCTGTAAGACACAGGGAAATGGTTAGAAGA
genomic: TTTGCAGGAGAGTTCGAGAGGCCATAACTGAGCTTGATCTTTCTGTAGAGgtgagcaatg ... gtatctacagGTCTATCCTTGTCCAAAAGGTTCTGTAAGACACAGGGAAATGGTTAGAAGA
EST: gi|22013797|gb|BQ798831.1|BQ798831
EST:     GCAGAAGAGTTCGAGAGGCCATAACTGAGC-TGATCTTTCTGTAGAG                         GTCTAT-CTTGTCCAAAA-GTTCTGTAAGACACAGGGAAATGG-TAGNAAG
genomic: GCAGGAGAGTTCGAGAGGCCATAACTGAGCTTGATCTTTCTGTAGAGgtgagcaatg ... gtatctacagGTCTATCCTTGTCCAAAAGGTTCTGTAAGACACAGGGAAATGGTTAG-AAG
EST: gi|352765203|gb|FQ465900.1|FQ465900
EST:     TTTGCAGGAGAGTTCGAGAGGCCATAACTGAGCTTGATCTTTCTGTAGAG                         GTCTATCCTTGTCCCAAAGGTTCTGTAAGACACNGGGAAATGGTTAGAA
genomic: TTTGCAGGAGAGTTCGAGAGGCCATAACTGAGCTTGATCTTTCTGTAGAGgtgagcaatg ... gtatctacagGTCTATCCTTGTCCAAAAGGTTCTGTAAGACACAGGGAAATGGTTAGAA
EST: gi|352772878|gb|FQ470493.1|FQ470493
EST:     TTTGCAGGAGAGTTCGAGAGGCCATAACTGAGCTTGATCTTTCTGTAGAG                         GTCTATCCTTGTCCAAAAGGTTCTGTAAGACACAGGGAAATGGTTAGAAGA
genomic: TTTGCAGGAGAGTTCGAGAGGCCATAACTGAGCTTGATCTTTCTGTAGAGgtgagcaatg ... gtatctacagGTCTATCCTTGTCCAAAAGGTTCTGTAAGACACAGGGAAATGGTTAGAAGA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AGGCATGCCCCTTTTGCAGGAGAGTTCGAGAGGCCATAACTGAGCTTGATCTTTCTGTAGAGgtgagcaatgacttctatagacatgatttattttgattatcattgactgttattttcatcaataatctatatcctctgttttctagggaactatactcca

- - - - - - - -  AGGAGA
- - - - - - - - - - - - -  GAGAGG
- - - - - - - - - - - - - - - - - - - -  GAGCTT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - agggaac