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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...atgtgtggagcatttccttttcatcctttctcctttttttttcaccctttttgatagttttgttttactaattgctgtgccaaaaattgatttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTTTGGGGGAAACAACCGTGCACAGGCTTTCTTTAAGCAGCATGGATGGTCT

Basic information

species Vitis vinifera
transcript Vv02s0012g01330.t01
intron # 2
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: LOC_Os10g42420.1 (Oryza sativa), 3'ss of exon 2
atgtgtggagcatttccttttcatcctttctcctttttttttcaccctttttgatagttttgttttactaattgctgtgccaaaaattgatttgctc--cagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTTTGGGGGAAACAACCGTGCACAGGCTTTCTTTAAGCAGCATGGATGGTCT
  |  |  || |||| | |   |  |  | |      || ||      || ||    | || |||     |   | ||       | || |    ||  |||||| |||||||| || || ||||   |||| || || || ||||||   | ||| || |||||||||||||| |||||||| ||||||||||| ||| | 
--gactacagaatttacatgctaaacaatataagaacttcttgtttagttgtggccttcttttttgctggaaacccgttgagttgactgctgcaatctgcagGTCAACAAATTTGGATTCGTGGACCCCAGAACAATTGAAAATGATGGTTTATGGAGGTAACAACCGTGCACAAGCTTTCTTCAAGCAGCATGGTTGGACA

upper sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G134045_T02 (Zea mays), 3'ss of exon 2
-atgtgtggagcatttccttttcatcctttctcctttttttttcaccctttttgatagttttgttttactaattgctgtgccaaaaattgattt---gctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTTTGGGGGAAACAACCGTGCACAGGCTTTCTTTAAGCAGCATGGATGGTCT
 || | | | | | ||     |  | |  |  | |||||  || |  |  ||  | |   | |  | ||| | | |  | |  ||||     |      | |||||| |||||||| || ||||||| | |||| ||| | || ||||||  || ||| ||||||||||||||||| |||||||||||||||||||| ||| | 
tattttttgggaaatttaacatagttcactgacatttttactttatgcagttgcaca---tcgaatgactgaat-caatactgaaaaacagctacaatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAGCTGAAAATGATGGTCTATGGAGGAAACAACCGTGCACAAGCTTTCTTTAAGCAGCATGGTTGGACA

upper sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G094390_T01 (Zea mays), 3'ss of exon 2
atgtgtggagcatttccttttcatcctttctcctttttttttcaccctttttgatagttt-tgttttactaattgctgtgccaaaaattgatttgct--ccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTTTGGGGGAAACAACCGTGCACAGGCTTTCTTTAAGCAGCATGGATGGTCT
||   | |   | ||     |  | |  |  | |||||  || |  |  ||  | | |   ||  ||| | | | |||    ||||| || |    |   |||||| |||||||| || ||||||| | |||| ||  | || ||||||  || ||| ||||| |||||||| || |||||||||||||||||||| ||| | 
atcctttggaaagtttaacatagttcactaacatttttactttatgcagttgcacactgaatgacttaatcaatactga---aaaaactgctacaatatgcagGTCAACAAATTTGGATTCATGGACTCCAGAACAACTGAAAATGATGGTCTATGGCGGAAATAACCGTGCGCAAGCTTTCTTTAAGCAGCATGGTTGGACA

upper sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G176612_T01 (Zea mays), 3'ss of exon 2
atgtgtggagcatttccttt---tcatcctttctcctttttttttcaccctttttgatagtttt--gttttactaattgctgtgccaaaaattgatttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTTTGGGGGAAACAACCGTGCACAGGCTTTCTTTAAGCAGCATGGATGGTCT
        |  || || |||     | |  | |   | |  | |  |    |  |   | |||   |    ||||| |  |    |   |  ||  || | | ||||| || ||  | |||||||||| | |||| ||| | |||||||||   || || || |||||||| ||||| |||||||| ||||||||||||||| | 
----aataaatatctcatttaagcaagctctacatatatgatatatagaaatcgtagcaatttacgggcaaactaactagtaaaaccttatgtgtctttcgc-agGTCAACGAACCTCGACTCATGGACTCCAGACCAGCTGAAGATGATGGCATTCGGAGGCAACAACCGGGCACATGCTTTCTTCAAGCAGCATGGATGGACC

upper sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GRMZM2G083546_T01 (Zea mays), 3'ss of exon 2
atgtgtggagcatttccttttcatcctttctcctttttttttcaccctttttgatagttttgttttactaattgc---tgtgccaaaaattgatttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTTTGGGGGAAACAACCGTGCACAGGCTTTCTTTAAGCAGCATGGATGGTCT
  |     |   || |||  ||   |                ||   | |     |||  |||  |  | ||| |   |   ||  |  |   | |  | |||||| || ||  | |||||||||| | |||| ||| | || ||||||   || || || |||||||| ||||| |||||||| ||||||||||||||| ||
--gcacaaaat-ttccctactccctccaagaatagggcgcagcattgtctcgaccagtgatgtcgtgttgatttcatatagaccttatctgtgtcttttgcagGTCAACGAACCTCGACTCATGGACTCCAGATCAGCTGAAAATGATGGCGTTCGGAGGCAACAACCGGGCACATGCTTTCTTCAAGCAGCATGGATGGACT

upper sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA01G12340.2 (Glycine max), 3'ss of exon 3
atgtgtggagcatttccttttcatcctttctcctttttttttcaccctttttgatagttttgttttactaattgctgtgccaaaaattgatttgc-tccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTTTGGGGGAAACAACCGTGCACAGGCTTTCTTTAAGCAGCATGGATGGTCT
|||     | ||     | ||||     |      || ||            || |     | || |    |   |   | | |   |  | |   |  ||||||||||||||||||||||||||| | |||||  |||| | |||||||||||| |||||||| |||||||| | |||||||||||| ||||| ||| ||
atgaaacaaacacactatattcagaaagtaggaagttgttgaatagaaagaagacaaaaaagattgataggtaaata-actatatgctcttctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACGATGAGCTTTGGAGGAAACAATCGTGCACATGGTTTCTTTAAGCAACATGGTTGGACT

upper sequence: Vv02s0012g01330.t01 (Vitis vinifera), 3'ss of exon 2
lower sequence: GLYMA08G36700.2 (Glycine max), 3'ss of exon 2
--atgtgtggagcatttccttttcatcctttctcctttttttttcaccctttttgatagttttgttttactaattgctgtgccaaaaattgatttgctcca----gGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTTTGGGGGAAACAACCGTGCACAGGCTTTCTTTAAGCAGCATGGATGGTCT
   | |||| | ||     | ||||   | |      || ||   |         | ||   ||    | | || |||  |  || |  || | | ||  |    |||||||||||||||||||||||||| | |||||  |||| |  ||||||||||| |||||||| |||||||||| |||||||||||| ||||| |||  |
tattctgtgaaacacactatattcagaatgtaggaagttgttg--aatagaaagaacagaaatg----attgatagctaagtaaatatatgctcttctatatgtagGTCTACAAATTTAGACTCATGGAGTCCTGAGCAACTAAAAACAATGAGCTTTGGAGGAAACAATCGTGCACAGGTTTTCTTTAAGCAACATGGTTGGAAT

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|37183533|gb|CF602887.1|CF602887
EST:     GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAG                         GTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
genomic: GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaa ... tttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
EST: gi|161715518|gb|FC069460.1|FC069460
EST:     GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAG                         GTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
genomic: GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaa ... tttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
EST: gi|110706113|gb|EE083724.1|EE083724
EST:     GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAG                         GTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
genomic: GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaa ... tttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
EST: gi|71867456|gb|DT016511.1|DT016511
EST:     GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAG                         GTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
genomic: GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaa ... tttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
EST: gi|161710058|gb|FC060595.1|FC060595
EST:     GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAG                         GTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
genomic: GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaa ... tttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
EST: gi|110707454|gb|EE083867.1|EE083867
EST:     GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAG                         GTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
genomic: GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaa ... tttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
EST: gi|110732011|gb|EE106922.1|EE106922
EST:     GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAG                         GTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
genomic: GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaa ... tttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
EST: gi|71887093|gb|DT036148.1|DT036148
EST:     GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAG                         GTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
genomic: GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaa ... tttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
EST: gi|110721187|gb|EE097897.1|EE097897
EST:     GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAG                         GTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
genomic: GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaa ... tttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
EST: gi|110395731|gb|EC961401.1|EC961401
EST:     GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAG                         GTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
genomic: GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaa ... tttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
EST: gi|161712670|gb|FC062242.1|FC062242
EST:     GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAG                         GTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
genomic: GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaa ... tttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
EST: gi|110730947|gb|EE108607.1|EE108607
EST:     GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAG                         GTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
genomic: GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaa ... tttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
EST: gi|71855004|gb|DT004059.1|DT004059
EST:     GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAG                         GTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
genomic: GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaa ... tttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
EST: gi|71867980|gb|DT017035.1|DT017035
EST:     GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAG                         GTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT
genomic: GACTGCTCCGCCGTGCATAGGAGTCTTGGGGTTCACATCAGCTTCGTCAGgtgatttcaa ... tttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

cctttttgatagttttgttttactaattgctgtgccaaaaattgatttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTTTGGGGGAAACAACCGTGCACAGGCTTTCTTTAAGCAGCATGGATGGTCT
                                             tttgctcc  CT-rich tract
            ttttgttttactaatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
atgtgtggagcatttccttttcatcctttctcctttttttttcaccctttttgatagttttgttttactaattgctgtgccaaaaattgatttgctccagGTCTACAAATTTAGACTCATGGAGTGCAGAGCAGTTAAAGATGATGAGCTTTGGGGGAAACAACCGTGCACAGGCTTTCTTTAAGCAGCATGGATGGTCT

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CATGGA
-tgtgtgg
- - - - -gcatttc
- - - - - - - - - - tcatcct
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -ttgctgt
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - caaaaat