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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatatatcattgttttctttttcttttgcttttatagctttatgtcttccattggaggataatgcccagtatgcacttatgcaacctccgaacagGCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCTGCGAAGCAG

Basic information

species Vitis vinifera
transcript Vv11s0052g01710.t01
intron # 20
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0052g01710.t01 (Vitis vinifera), 3'ss of exon 20
lower sequence: GLYMA17G07380.1 (Glycine max), 3'ss of exon 19
gtaatatatcattgttttctttttcttttgcttttatagctttatgtcttccattggaggataatgcccagtatgcacttatgcaacctccgaacagGCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCTGCGAAGCAG
|||| ||    |  |  |   |||   ||||    |||  ||  || |||  || |     |  ||  |  |||| |    ||   ||     | |||||||||||||||| |||||| |||| |||||||| | || |||||||||||| ||||||||| |||||||||| |||
gtaaaat----tcttcctacattttccttgccaaaata-tttagtgccttttatggttaact--tgatcgatatgga----tgttgcc-----atagGCTGGTAAGGCTGACTTTGAACTGCTTGAGAAGAAGGTCAAGGAATGGGGAGAACCAAAGGTTGCTTCTGCGAAACAG
















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|351031975|gb|FQ460232.1|FQ460232
EST:     TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAG                         GCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
genomic: TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAGgtaatatatc ... ctccgaacagGCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
EST: gi|351032492|gb|FQ458857.1|FQ458857
EST:     TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAG                         GCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
genomic: TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAGgtaatatatc ... ctccgaacagGCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
EST: gi|349809734|gb|FQ398359.1|FQ398359
EST:     TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAG                         GCTGGGTAAG-CTGATTTTGAAATGCTAGAAAAGAAAGCCAATG-AATGGG
genomic: TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAGgtaatatatc ... ctccgaacagGCTGG-TAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCA-TGGAATGGG
EST: gi|349811710|gb|FQ409707.1|FQ409707
EST:     TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAG                         GCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
genomic: TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAGgtaatatatc ... ctccgaacagGCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
EST: gi|349812955|gb|FQ411195.1|FQ411195
EST:     TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAG                         GCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
genomic: TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAGgtaatatatc ... ctccgaacagGCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
EST: gi|351032512|gb|FQ458877.1|FQ458877
EST:     TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCANATAGAG                         GCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
genomic: TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAGgtaatatatc ... ctccgaacagGCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
EST: gi|22015436|gb|BQ800470.1|BQ800470
EST:     TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAG                         GCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
genomic: TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAGgtaatatatc ... ctccgaacagGCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
EST: gi|349820047|gb|FQ404769.1|FQ404769
EST:     TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAG                         GCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
genomic: TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAGgtaatatatc ... ctccgaacagGCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
EST: gi|29784962|gb|CB341547.2|CB341547
EST:     TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAG                         GCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA
genomic: TTCGCAAGCGATATCAGAGTTTTGACACTGAAATCGGGGCTCAAATAGAGgtaatatatc ... ctccgaacagGCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tatgtcttccattggaggataatgcccagtatgcacttatgcaacctccgaacagGCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCTGCGAAGCAG
                                            cctcc  CT-rich tract
                  ataat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtaatatatcattgttttctttttcttttgcttttatagctttatgtcttccattggaggataatgcccagtatgcacttatgcaacctccgaacagGCTGGTAAGGCTGATTTTGAAATGCTAGAGAAGAAAGCCATGGAATGGGGAGAGCCAAAGGTTCCTTCTGCGAAGCAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CATGGA