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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tttctagctttataatgccttgcagttttaatccaggcatctgataattccaatataaactaaactgattggaacttattctgttttggccatccttcagGTTTGGAAAGTTGCTGATGTTCCGGAAAATGATAAATTCCAGTTCACATATTTTGCACACAAGATAAACAGCTTTGAAACTGCTCCCAGGAAGTTGTTGG

Basic information

species Vitis vinifera
transcript Vv08s0007g00480.t01
intron # 8
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv08s0007g00480.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA18G39880.1 (Glycine max), 3'ss of exon 8
---tttctagctttataatgcct-tgcagttttaatccaggcatctgataattc--caatataaactaaactgattggaacttattctgttttggccatccttcagGTTTGGAAAGTTGCTGATGTTCCGGAAAATGATAAATTCCAGTTCACATATTTTGCACACAAGATAAACAGCTTTGAAACTGCTCCCAGGAAGTTGTTGG
     | |  || ||| ||  ||     |||    |     || ||  |  | |  |||| | || ||   |  || ||| | |  |  ||       | |  ||| |||||| |||||||||||  ||  | || || |||||||||| |||  |||||||||||||||| ||||||||||| |||||||||| |||||||||| 
tttagtgtcactctatgatttctgcttggttgggttgtcatcaccttttgttccatcaatttgaattatttt--tttgaagtaa--ccattcccattctgca-caGATTTGGAGAGTTGCTGATGCCCCCAAGAAGGACAAATTCCAGTACACGCATTTTGCACACAAGATTAACAGCTTTGACACTGCTCCCAAGAAGTTGTTG-

upper sequence: Vv08s0007g00480.t01 (Vitis vinifera), 3'ss of exon 8
lower sequence: GLYMA07G15930.3 (Glycine max), 3'ss of exon 8
tttctagctttataat----gccttgcagttttaatccaggcatctgataattccaatataaactaaactgattggaacttattctgttttggccatccttcagGTTTGGAAAGTTGCTGATGTTCCGGAAAATGATAAATTCCAGTTCACATATTTTGCACACAAGATAAACAGCTTTGAAACTGCTCCCAGGAAGTTGTTGG
  | |  || ||| ||    || |    |  ||  ||    | | |  |  |  |||| | || |    |  |   || |||  |||| ||          ||| |||||| ||||||||||   ||| | || || || ||||||| |||  |||||||||||||||| ||||||||||| |||||||||| |||||||||||
--tgtcactgtatgatttccgcttcattgggttg-tcatcaccttttgttctagcaatttgaattgtttttttgttaagttac-ctgtgtttcattctgcacagATTTGGAGAGTTGCTGATACCCCGAAGAAGGACAAGTTCCAGTACACGCATTTTGCACACAAGATTAACAGCTTTGACACTGCTCCCAAGAAGTTGTTGG
















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|110716445|gb|EE091435.1|EE091435
EST:     AACCTTGTGACTTGGAAGGAGAGCCCCTTCCTGGCAGTGAACAAAAGGAG                         GTTTGGAGAGTTGCTGATGTTCCGGAAAATGATAAATTCCAGTTCACACAT
genomic: AACCTTGTGACTTGGAAGGAGAGCCCCTTCCTGGCAGTGAACAAAAGGAGgttagtcttt ... catccttcagGTTTGGAAAGTTGCTGATGTTCCGGAAAATGATAAATTCCAGTTCACATAT
EST: gi|22014866|gb|BQ799900.1|BQ799900
EST:     GCCCCTTCCTGGCAGTGAACAAAAGGAG                         GTTTGGAAAGTTGCTAATGTTCCGGAAAATGATAAATTCCAGTTCACATAT
genomic: GCCCCTTCCTGGCAGTGAACAAAAGGAGgttagtcttt ... catccttcagGTTTGGAAAGTTGCTGATGTTCCGGAAAATGATAAATTCCAGTTCACATAT
EST: gi|110382321|gb|EC939158.1|EC939158
EST:     AACCTTGTGACTTGGAAGGAGAGCCCCTTCCTGGCAGTGAACAAAAGGAG                         GTTTGGAGAGTTGCTGATGTTCCGGAAAATGATAAATTCCAGTTCACACAT
genomic: AACCTTGTGACTTGGAAGGAGAGCCCCTTCCTGGCAGTGAACAAAAGGAGgttagtcttt ... catccttcagGTTTGGAAAGTTGCTGATGTTCCGGAAAATGATAAATTCCAGTTCACATAT
EST: gi|110379349|gb|EC944536.1|EC944536
EST:     AACCTTGTGACTTGGAAGGAGAGCCCCTTCCTGGCAGTGAACAAAAGGAG                         GTTTGGAGAGTTGCTGATGTTCCGGAAAATGATAAATTCCAGTTCACACAT
genomic: AACCTTGTGACTTGGAAGGAGAGCCCCTTCCTGGCAGTGAACAAAAGGAGgttagtcttt ... catccttcagGTTTGGAAAGTTGCTGATGTTCCGGAAAATGATAAATTCCAGTTCACATAT
EST: gi|352777378|gb|FQ474012.1|FQ474012
EST:     AACCTTGTGACTTGGAAGGAGAGCCCCTTCCTGGCAGTGAACAAAAGGAG                         GTTTGGAAAGTTGCTGATGTTCCGGAAAATGATAAATTCCAGTTCACATAT
genomic: AACCTTGTGACTTGGAAGGAGAGCCCCTTCCTGGCAGTGAACAAAAGGAGgttagtcttt ... catccttcagGTTTGGAAAGTTGCTGATGTTCCGGAAAATGATAAATTCCAGTTCACATAT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aattccaatataaactaaactgattggaacttattctgttttggccatccttcagGTTTGGAAAGTTGCTGATGTTCCGGAAAATGATAAATTCCAGTTCACATATTTTGCACACAAGATAAACAGCTTTGAAACTGCTCCCAGGAAGTTGTTGG
                                            ccatccttc  CT-rich tract
      aatataaactaaact  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tttctagctttataatgccttgcagttttaatccaggcatctgataattccaatataaactaaactgattggaacttattctgttttggccatccttcagGTTTGGAAAGTTGCTGATGTTCCGGAAAATGATAAATTCCAGTTCACATATTTTGCACACAAGATAAACAGCTTTGAAACTGCTCCCAGGAAGTTGTTGG

- - - - - - taatgcc
- - - - - - - - - - tgcagtt
- - - - - - - - - - - - - - - - ccaggca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - aaactaa
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgattgg