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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtgagcaattcttctttgactttacatctgccagttctgtgattcttagatgccatggtgtgtagttgagatgaaagtttcttttctttttgggttttcccttctggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG

Basic information

species Vitis vinifera
transcript Vv11s0016g02890.t01
intron # 4
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g02890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GRMZM2G051288_T01 (Zea mays), 3'ss of exon 3
gtgagcaattcttctttgactt-tacatctgccagttctgtgattcttagatgccatggtgtgtagttgagatgaaagtttcttttctttttgggttttcccttctggggaa----cagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG
             ||  || || | ||     ||        |   ||    ||| |    || | ||  ||  | |   |||    ||  | | ||   | |   |  | |    ||| |||||||||    ||  | ||||| ||||||||||||||||||||| ||||| | ||||| ||||||||  | ||||| |||
-------------ctacgatttatgcaatcagcacaaaaaaaacctttta--gcctt----tgaaattctgaatacacgctctcaaattggtagattcaacatatagctgcattttcagGGAATGCATCACAAGGCGGTACTACATATGTTCATTGTAAAGCTGGAAGAGGACGAAGCACCACTATTGTATTGTGCTACTTG

upper sequence: Vv11s0016g02890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA05G36020.1 (Glycine max), 3'ss of exon 3
gtgagcaattcttctttgactttacatctgccagttctg-------------tgattcttagatgccatggtgtgt---agttga-gatgaaagtttcttttctttttgggttttcccttctgg-ggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG
||| |   ||  | ||  | || |  || |  |  | ||             ||  | |  | | |  || | | |    ||||  | ||      | |  || | |  |  ||||| || |       ||||||||||| ||| ||||| ||||||||||||||| ||||||||||| || || ||||| ||||| ||||||||||| ||| ||
gtgggtgttttcttttcaatttaatttcgggaaagtgtggggtgtaaatgcatgtctatgtggttctttgttattttttggttgttggtggtgaaatatagtcgtatgtgtatttcctttgtattatggcagAGAATGCAACTTGCGGTAAAACTACTTATGTTCACTGTAAAGCTGGTCGGGGGAGGAGTACAACAATTGTGCTTTGTTATCTG

upper sequence: Vv11s0016g02890.t01 (Vitis vinifera), 3'ss of exon 4
lower sequence: GLYMA08G03600.1 (Glycine max), 3'ss of exon 4
--------------------------gtgagcaattcttctttgactttacatctgccagtt-ctgtgattcttagatgccatggtgtgtagttgagatgaaagtttcttttctttttgggttttcccttctggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG
                            | | || |       |   ||| ||    ||||   |||| ||||| | |    |  ||  |  | | | |||||  |  |  | | | |   |  |   |  |  ||  ||||||||||| ||| ||| | ||||||||||||||| ||||||||||| || || ||||| ||||| ||||||||||| ||| ||
gtgggtgttttcttttcaatttaatttcgggaaagtggggaagggggttaaatgcatcagtcattgtggttctttg-taattttttggttgttggtggtgaaatatagtcgtgtgtgtatttcctttgtattatgg--cagAGAATGCAACTTGCGGCAAAACTACTTATGTTCACTGTAAAGCTGGGCGGGGGAGGAGTACAACAATTGTGCTTTGTTATATG

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|156735982|gb|EV240103.1|EV240103
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|351032518|gb|FQ458883.1|FQ458883
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|351034943|gb|FQ458300.1|FQ458300
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|349809160|gb|FQ398901.1|FQ398901
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|351039844|gb|FQ464882.1|FQ464882
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|110379170|gb|EC944349.1|EC944349
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|351044066|gb|FQ452739.1|FQ452739
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|110388085|gb|EC952801.1|EC952801
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|351037982|gb|FQ465220.1|FQ465220
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|351052950|gb|FQ453937.1|FQ453937
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|349819705|gb|FQ402642.1|FQ402642
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|351037230|gb|FQ457063.1|FQ457063
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAAGCTGGACGA
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAA-GCTGGACGA
EST: gi|351038655|gb|FQ464521.1|FQ464521
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|351056738|gb|FQ443365.1|FQ443365
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|71856681|gb|DT005736.1|DT005736
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|351041750|gb|FQ455960.1|FQ455960
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|351041720|gb|FQ455930.1|FQ455930
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|30304523|gb|CB981317.1|CB981317
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|351038816|gb|FQ464682.1|FQ464682
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|110729962|gb|EE106494.1|EE106494
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
EST: gi|351037592|gb|FQ462575.1|FQ462575
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCGTCTTCCGGTAGAACTACTTATGTTCATTGTAAA
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAA
EST: gi|110689256|gb|EE065319.1|EE065319
EST:     TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATA                         AGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG
genomic: TTTTGCTCCTTCATTTGTGGATATTAGCCGTGCTGTAGATTTCATTCATAgtgagcaatt ... tggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtgtagttgagatgaaagtttcttttctttttgggttttcccttctggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG
                  tttcttttctttttgg  CT-rich tract
                  tttcttttcttttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtgagcaattcttctttgactttacatctgccagttctgtgattcttagatgccatggtgtgtagttgagatgaaagtttcttttctttttgggttttcccttctggggaacagAGAATGCATCTTCCGGTAGAACTACTTATGTTCATTGTAAAGCTGGACGAGGAAGGAGCACAACTATTGTGCTTTGCTATTTG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGCTG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GCTGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGCA