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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GCAGGTGTCGTATCGGGTGGTAAGAGATGAAAATGGGAATGTCAAACTCGAGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattttctttggtttggtgcagttgaattatatttggtacatattttatgttatttgagtgtgaggatatttgttttctttgggggcattttgaa...

Basic information

species Vitis vinifera
transcript Vv17s0000g03310.t01
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g03310.t01 (Vitis vinifera), 5'ss of exon 1
lower sequence: GLYMA12G28750.1 (Glycine max), 5'ss of exon 1
GCAGGTGTCGTATCGGGTGGTAAGAGATGAAAATGGGAATGTCAAACTCGAGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattttctttggtttggtgcagttgaattatatttggtacatattttatgttatttgagtgtgaggatatttgttttctttgggggcattttgaa--
|||||| || ||  | ||  | ||||| || || || || ||||||||||| ||||| || || || || |||||||| ||||| |||||||| ||||||||     | |  | |   |   | |   | | ||||  ||| |  ||   | ||    ||  |    |     | |||| |  | |   ||   |  | |  
GCAGGTCTCTTACAGAGTCATCAGAGACGACAACGGCAACGTCAAACTCGACTGCCCCGCCATTGGCAAACAGTTCGCTGCCGAGGAAATTTCTGCCCAGgtctctctgtcgtctccgtcaatacttgtta-ttattgttgat-tattgataatacctttacaactggtactgaattgtatgttatataggttctgaggaag
















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|110688337|gb|EE066777.1|EE066777
EST:     AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAG                         GTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
genomic: AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
EST: gi|110698482|gb|EE076028.1|EE076028
EST:     AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAG                         GTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAA-GTC
genomic: AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
EST: gi|110707989|gb|EE085014.1|EE085014
EST:     GTGCCCAGCGATCGGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAG                         GTACTAAAAAAGCTTGTTGATGATGCCTCGAAATTTCGGAATGATAAA-TC
genomic: GTGCCCAGCGATCGGG-AAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
EST: gi|110360709|gb|EC924030.1|EC924030
EST:     AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAG                         GTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
genomic: AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
EST: gi|110701600|gb|EE079356.1|EE079356
EST:     AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAG                         GTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
genomic: AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
EST: gi|110685528|gb|EE062329.1|EE062329
EST:     AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAG                         GTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
genomic: AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
EST: gi|110376029|gb|EC941068.1|EC941068
EST:     TGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAG                         GTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
genomic: TGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
EST: gi|110374685|gb|EC939606.1|EC939606
EST:     AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAG                         GTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
genomic: AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
EST: gi|161717811|gb|FC065964.1|FC065964
EST:     AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAG                         GTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
genomic: AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
EST: gi|37187864|gb|CF607215.1|CF607215
EST:     AGTGCCCAGCAATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAG                         GTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
genomic: AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
EST: gi|110710029|gb|EE086007.1|EE086007
EST:     GTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCCGGCCAAG                         -TACTAAAAAAGCTTGTTGATGAAGCCTCGAAATTCCCGAATGAGAAAGT
genomic: GTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTC-GGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGT
EST: gi|110699471|gb|EE076498.1|EE076498
EST:     AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAG                         GTACTAAGAAAGCTTGTTGATGATGCCTCGAAAGTT-CTGAATGATAA-GT
genomic: AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAA-GTTTCTGAATGATAAAGT
EST: gi|294964596|gb|GW838399.1|GW838399
EST:     AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAG                         GTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
genomic: AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
EST: gi|110730008|gb|EE106596.1|EE106596
EST:     AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAG                         GTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
genomic: AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
EST: gi|161717131|gb|FC065919.1|FC065919
EST:     AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAG                         GTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
genomic: AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
EST: gi|110700950|gb|EE078055.1|EE078055
EST:     AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAATAAATTTCGGCCCAG                         GTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC
genomic: AGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattt ... ttcttattagGTACTAAGAAAGCTTGTTGATGATGCCTCGAAGTTTCTGAATGATAAAGTC

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
GCAGGTGTCGTATCGGGTGGTAAGAGATGAAAATGGGAATGTCAAACTCGAGTGCCCAGCGATCGGGAAGCAGTTCGCGGCCGAAGAAATTTCGGCCCAGgtaatcattttctttggtttggtgcagttgaattatatttggtacatattttatgttatttgagtgtgaggatatttgttttctttgggggcattttgaa

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -gaggata