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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...ctttgagttacttcatcaaagatgtagtattttaattagttttgcttggctgcatcagaaatgacatccagttctaagtgtatttagtcataatttgcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA

Basic information

species Vitis vinifera
transcript Vv18s0166g00300.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os01g13190.1 (Oryza sativa), 3'ss of exon 8
ctttgagttactt-catcaaagatgtagtattttaattagttttgcttggctgcatcagaa--atgacatccagttctaagtgtatttagtcataatttgcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA
   ||  ||| || ||  |    | |  | |  | |||  ||         ||  |||     || |  |   ||  | |   ||| || |     |||| |||| ||||| || ||||| |||||||||||||||||||||||||||||||||||||| || 
-aatgctttagttgcactagtatttttctgtactcatttattcataacaattgtgtcatttccattatttgtggtgatcaacttatatactgtc--tttgtagGTTGAAAAAATATTTGGACCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTTCAG

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GRMZM2G058584_T01 (Zea mays), 3'ss of exon 10
-ctttgagttacttcatcaaagatgtagtattttaattagtt-ttgcttggctgcatcagaaatgacatccagttctaagtgtatttagtcataatttgcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA
 |    |||| || || ||    | ||  ||||    || |   ||        |||   |    | | |   | |||| |  |||      |    | ||||  || ||||||||||| ||||| || |||||||| || ||||| ||||||||||| || 
tcaccaagtt-ctacagcatttttttatgatttcctgtattggctgtgcactctcattcaaccacataacttttgctaacttcattacaatgtc-catacagGCTGAGAAGATTTTTGGACCTGGTAACCAGTATGTAACAGCTGCCAAAATGATTCTTCAG

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G02960.1 (Glycine max), 3'ss of exon 8
ctttgagtta-cttcatcaaagatgtagtattttaattagttttgcttggctgcatcagaaatgacatccagttctaagtgt-atttagtcat--aatttgcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA
 | ||| | | |   |   ||||||||  | || ||  ||      |       ||  ||  | |  |  | || ||| ||| | || || ||  || | | |||| ||||||||||||||||||||||| || |||||||| |||||||||||||| || |||
ttgtgattaaaccgtacttaagatgta--acttcaacaagaaaacttcatacttatttga--tcatttttaattttaattgtgaatttgtgatgaaactagtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA15G13910.1 (Glycine max), 3'ss of exon 8
--ctttgagttactt-catcaaagatgtagtattttaattagttttgcttggctgcatcagaaatgacatccagttctaagtgt--attta-gtcataatttgcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA
   | ||| | | |   |   ||||||||  | || ||  |    | | |   |   |     || |  |  | ||  || |||  ||||  |    || ||| |||| ||||||||||||||||||||||| || |||||||| |||||||||||||| || |||
tcttgtgaatgaatcgtacttaagatgta--acttcaacaaaaccttcatacttagtt----gatcatttttaatttaaattgtgaatttgtggtgaaacttgtagGTTGAAAAGATTTTTGGCCCTGGAAACCAATATGTCACTGCTGCAAAAATGATACTTCAA

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA08G08630.1 (Glycine max), 3'ss of exon 7
ctttgagttacttcatcaaagatgtagtattttaattagtttt--gcttggctgcatcagaaatgacatccagttctaagtgtatttagtcataattt-gcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA
     ||| || | |   |  || |   ||||   |||   |     ||   | | ||| |  |   |     ||   |   | | | || ||| ||| | |||| || || ||||||||||| ||||| || |||||||| |||||||||||||| || |||
-acatagtgacataac--attatttgaaatttaggttaacataaaatttaaatacttcatagttcttaaattttttgcataatttcttgtaatacttttgtagGTTGAGAAAATTTTTGGCCCAGGAAACCAATATGTCACAGCTGCAAAAATGATACTACAA

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G63890.1 (Arabidopsis thaliana), 3'ss of exon 7
--------------------------------------ctttgagttacttcatcaaagatgtagtattttaattagttttgcttggctgcatcagaaatgacatccagttctaagtgtatttagtcataatttgcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA
                                        | | | |  |   |      | ||  ||| ||   | ||    || | |      |  ||  |  |||   |   | | |   | || |  |    |||| || ||||||||||| ||||| || ||||||||||| ||||| || |||||||| |  
gtgtgtctgtgttagttttttttcgcttatgttttcatgctggtgattgtattttttctctctaagattgtagacatttcgattttgttttgcagGCTATAGCTGCCATGGCCTGGGGGACAGATTCTTG-TCCAAAGGTTGAGAAGATTTTTGGTCCTGGGAACCAGTATGTCACAGCTGCTAAGATGATTCTTC--

upper sequence: Vv18s0166g00300.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S233_40V6.1 (Physcomitrella patens), 3'ss of exon 9
ctttgagttacttcatcaaa-gatgtagtattttaattagttttgcttggctgcatcagaaatga--catccagttctaagtgtatttagtcataattt-gcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA
 |||   ||| |   |   |  || | | |  | ||   || |   ||       |||    | |  |    |||| | |    || |    ||  ||  ||||||||| ||  ||||||| ||||||||||||||||| ||||||||||||||| | || || 
-ttt---ttaatgtgtaggataatttggaaaatcaagccgtgtctgttaaggttttcaatcgttatccgcttagttttgacgaaatatcaaaatgcttgagcagGTGGATAAAGTTTTTGGACCTGGAAATCAGTATGTTACGGCTGCAAAAATGTTGCTTCAG

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|30251428|gb|CB969161.1|CB969161
EST:     GCCATTGCTGCCATGGCATGGGGGACAACATCATGCCCTAAG                         GTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATG
genomic: GCCATTGCTGCCATGGCATGGGGGACAACATCATGCCCTAAGgtaatagttc ... taatttgcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATG
EST: gi|351054495|gb|FQ450579.1|FQ450579
EST:     GCCATTGCTGCCATGGCATGGGGGACAACATCATGCCCTAAG                         GTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATG
genomic: GCCATTGCTGCCATGGCATGGGGGACAACATCATGCCCTAAGgtaatagttc ... taatttgcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttggctgcatcagaaatgacatccagttctaagtgtatttagtcataatttgcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA
                                   tatttagtcataattt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ctttgagttacttcatcaaagatgtagtattttaattagttttgcttggctgcatcagaaatgacatccagttctaagtgtatttagtcataatttgcagGTGGAAAAGATTTTTGGCCCTGGAAATCAGTATGTCACGGCTGCAAAAATGATTCTCCAA

- - - - - - tcatcaa
- - - - - - - - - - - - - - - - - - - - - - - - -ctgcatc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -acatcca