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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gttagtaaagtatcagttcatcactggatgtgccctttttgtattctttcattggttctttgcaccatttttgtctccatcaaatgtatcattgaattttaaaatgacagagtgccgtatttcatcaatatggttgtctttttgtttcacagCTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAG

Basic information

species Vitis vinifera
transcript Vv18s0089g00350.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os08g32920.1 (Oryza sativa), 3'ss of exon 15
gttagtaaagtatcagttcatcactggatgtgccctttttgtattctttcattggttctttgc---accatttttgtctccatcaaatgtatcattgaattttaaaatgacagagtgccgtatttcatcaat-atggttgtctttttgtttcacagCTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAG
                                                   |||| | | ||    | ||| ||     || |  || ||    |  |||||| |     | | ||    || | | |  || ||||     |   | ||   ||||||||||||||||| || |||||||| |||||||| || || ||||||| ||| |||
--------------------------------------------------gttggctttctgtttaagcatcttacatcccgt--aacgtcatttcaaattttca-----ctgggtttt-tactactttgatcatgggacaatgaattttatccagCTTGGTTACACCAAGAAACAAGAGGAGAGGCATTTTCGAGGCGTCATCAATTTGGAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os06g13820.1 (Oryza sativa), 3'ss of exon 15
gttagtaaagtatcagttcatcactggatgtgccctttttgtattctttcattggttctttgcaccatttttgtctccatcaaatgtatcattgaattttaaaatgacagagtgccgtatttcatcaatatggttgtctttttgtttca--cagCTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAG
|||| | |    ||| | |||||     |  |   | ||||| || || || |         ||  |    | ||   ||  ||| |||   || |||||   |||   || | |  |   |      | |||||  | || | |||    |||||||| ||||| || || |||||||| || ||||| ||||||||||||||| | |||
gttaatcagagttcaat-catcatctttta-gttttgtttgtctttttgcactaa-------caggaggaatatcaggat--aatttatttatgtattttccgatg---gacttctatgcatgggtggt-tggttaaccttctatttttatcagCTTGGCTACACGAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GRMZM2G157462_T01 (Zea mays), 3'ss of exon 15
gttagtaaagtat-cagttcatcactggatgtgccctttttgtattctttcattggttctttgcaccatttttgtctccatcaaatgtatcattgaattttaaaatgacagagtgccgta-tttcatcaatatggttgtctttttgtttcacagCTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAG
|||| | |  | | |||  |||  ||   | ||  || ||  | || ||| ||  ||   |   | |  ||  || |   ||||||||||       || |    ||| |    |  ||  ||| ||  || |   |||  |||   | | |||||||| ||||| || || |||||||| || ||||| ||||||||||||||| | |||
gttaatcagttcttcagaacatttct---tttgaactcttgat-ttgtttgatatgtatgtgaaagcccttaggttt---tcaaatgtatttcatggttcttgtttgatatgtgggtgtggttttattcat-tatctgttgtttctatgc-cagCTTGGGTACACAAAGAAACAAGAGGAGAGACATTTTCGTGGTGTCATCACTCTTGAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA12G37100.1 (Glycine max), 3'ss of exon 15
gttagtaaagtatcagttcatcactggatgtgccctttttgtattctttcattggttctttgcaccatttttgtctccatcaaatgtatcattgaattttaaaatgacagagtgccgtatttcatcaatatggttgtctttttgtttcacagCTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAG
                                               |   |||  ||||     ||||    |    || | || ||| ||||     |   |  |||   | | || |   ||  |  |  |   ||||    |||||||||||| || |||||||| ||||||||||| ||||| || ||||| || || ||||||
---------------------------------------------tctgtgttgcatcttgat-tcattcagat----atgagatatataattggccacttttaatacaatttactgtgtgatattgactt--taacctttcaacttcacagCTTGGATATACCAAAAAACAAGAGGAAAGACATTTTCGCGGTGTTATTACATTAGAG

upper sequence: Vv18s0089g00350.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA09G00430.2 (Glycine max), 3'ss of exon 15
gttagtaaagtatcagttcatcactggatgtgccctttttgtattctttcattggttctttgcaccatttttgtctccatcaaatgtatcattgaattttaaaatgacagagtgccgtatttcatcaatatggttgtctttttgtttcacagCTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAG
                                                ||  || | | |      |||  |    | || | || ||| ||||     |   |  |||   | | || |   ||  |  |   |  | |||   |||||||||||| ||||||||||| ||||||||||  ||||| || ||||| || || ||||||
-----------------------------------------------atctgtgatgcatcttg--attcattcagctatgagatatataattgtccacttttaatacaatttactgtgtgatattgacct---taacctttcacttcacagCTTGGGTACACCAAAAAACAAGAGGAAAAACATTTTCGCGGTGTTATTACATTAGAG

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|161719802|gb|FC065762.1|FC065762
EST:     CTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG                         CTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACT
genomic: CTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAGgttagtaaag ... tgtttcacagCTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACT
EST: gi|32270986|gb|CD720145.1|CD720145
EST:     CTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG                         CTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTGATCACT
genomic: CTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAGgttagtaaag ... tgtttcacagCTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACT
EST: gi|161714373|gb|FC063214.1|FC063214
EST:     CTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAG                         CTTGGTTACACCAAAAAGCAAGAGGAAAGACATTTCCGTGGTGTCATCACT
genomic: CTAATGGATGGAGCAGGCGATGGTTTGTTTTAAATGAAAAGACTGGCAAGgttagtaaag ... tgtttcacagCTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

tttaaaatgacagagtgccgtatttcatcaatatggttgtctttttgtttcacagCTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAG
                                    ttgtctttttgtttc  CT-rich tract
                    tatttcatcaatat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gttagtaaagtatcagttcatcactggatgtgccctttttgtattctttcattggttctttgcaccatttttgtctccatcaaatgtatcattgaattttaaaatgacagagtgccgtatttcatcaatatggttgtctttttgtttcacagCTTGGTTACACCAAAAAGCAAGAGGAAAGGCATTTCCGTGGTGTCATCACTTTAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGCAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGAGG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAGGA