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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...gacctagaaatataggttacaattcacttccttctcctctgatttcccagcagcccaacagagggttaatttcattttgccaccacaatttgaagcgcagGTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATATTCGTGGAGGGAAGCGAAGAGGTGGAGGTGGACGTTTTCAAGAATCTGG

Basic information

species Vitis vinifera
transcript Vv17s0000g05650.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv17s0000g05650.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os01g40310.1 (Oryza sativa), 3'ss of exon 1
--gacctagaaatataggttacaattc-acttccttctcctctgatttcccagcagcccaacagagggttaatttcattttgccaccacaatttgaagcgcagGTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATATTCGTGGAGGGAAGCGAAGAGGTGGAGGTGGACGTTTTCAAGAATCTGG
   ||| ||  |   | |   |   || |||    |      ||  |||      |  | |   | ||   |||  | || |        ||| |  | |||||||||||| ||||| ||||| |||  |||  |||||||||| || || ||||||| |||||| ||||| ||||||||||||||||| |||||||| ||||
gtaaccaagctagccatgccccgtctcgactgaaattggagatgtgttcatccatgatccatccatggcggatt--aattggttg--gatattgggggtgcagGTGAACAGGTACGACGAGAAGTGGTCGAAGCAGTGGTTCGGGGCGGGGATATTCGCGGAGGGGAGCGAGGAGGTGGAGGTGGACGTGTTCAAGAAGCTGG

upper sequence: Vv17s0000g05650.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GLYMA04G34330.2 (Glycine max), 3'ss of exon 1
gacctagaaatataggttacaattcacttccttctcctctgatttcccagcagcccaacagagggttaa--tttcattttgccaccacaatttgaagcg-cagGTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATATTCGTGGAGGGAAGCGAAGAGGTGGAGGTGGACGTTTTCAAGAATCTGG
    |     | |         |   ||  |  |  |  ||||     |   |   |    | ||||||  ||| |||||        ||||  |   |  |||||||||  ||| |||| || |||||||| |||||||| ||||| || ||||||   ||||||||||| ||||||||||||||||| ||||||||  | |
---tttcttctttctcccttcttcttctatcagcaaccttgatgaattaagtggaaactcaaaggttaagatttgattttagttatggaattgaacttggtagGTGAACAAGTACAATGATAAGTGGAAGAAGGAGTGGTTTGGAGCGGGGATATTCTACGAGGGAAGCGAGGAGGTGGAGGTGGACGTGTTCAAGAAGATAG
















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|71870973|gb|DT020028.1|DT020028
EST:     TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAG                         GTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
genomic: TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAGgtaacttaat ... tgaagcgcagGTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
EST: gi|77579219|gb|DV218442.1|DV218442
EST:     TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAG                         GTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
genomic: TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAGgtaacttaat ... tgaagcgcagGTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
EST: gi|77585944|gb|DV222071.1|DV222071
EST:     TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAG                         GTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
genomic: TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAGgtaacttaat ... tgaagcgcagGTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
EST: gi|71865494|gb|DT014549.1|DT014549
EST:     TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAG                         GTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
genomic: TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAGgtaacttaat ... tgaagcgcagGTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
EST: gi|71865985|gb|DT015040.1|DT015040
EST:     TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAG                         GTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
genomic: TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAGgtaacttaat ... tgaagcgcagGTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
EST: gi|110395890|gb|EC961564.1|EC961564
EST:     TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAG                         GTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
genomic: TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAGgtaacttaat ... tgaagcgcagGTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
EST: gi|26267002|gb|CA818065.1|CA818065
EST:     TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAG                         GTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
genomic: TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAGgtaacttaat ... tgaagcgcagGTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
EST: gi|77584573|gb|DV221368.1|DV221368
EST:     TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAG                         GTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA
genomic: TTCCCGCCAAAAAGCCGTTAAGAATTCTCGCCATGGCCTCTAAGAAGAAGgtaacttaat ... tgaagcgcagGTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cccagcagcccaacagagggttaatttcattttgccaccacaatttgaagcgcagGTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATATTCGTGGAGGGAAGCGAAGAGGTGGAGGTGGACGTTTTCAAGAATCTGG
                  ggttaat  putative branch site (score: 4)
                    ttaatttcatttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gacctagaaatataggttacaattcacttccttctcctctgatttcccagcagcccaacagagggttaatttcattttgccaccacaatttgaagcgcagGTGAACAGATACGATGAGAATTGGAAGAAAGAGTGGTTCGGAGCAGGAATATTCGTGGAGGGAAGCGAAGAGGTGGAGGTGGACGTTTTCAAGAATCTGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GTGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGTGGA
- - -agaaata
- - - - - - - - - -caattca
- - - - - - - - - - - - - - -ccttctc
- - - - - - - - - - - - - - - - - - - - - - -cccagca
- - - - - - - - - - - - - - - - - - - - - - - - - - -cccaaca
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caccaca