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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aacatctgaatgctccatcattttatctttttatgttctgtttgcttgattattattttccaaataatatgcattgctctgatagccatccacatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAAGAGTGGTTATGGTGTGAATCATGGTGCGGAAATGCTACAAAATCCAAGG

Basic information

species Vitis vinifera
transcript Vv12s0034g02230.t01
intron # 36
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 36
lower sequence: LOC_Os02g44510.1 (Oryza sativa), 3'ss of exon 15
aacatctgaatgctccatcattttatctttttatgttctgtttgcttgattattattttccaaataatatgcattgctctgatagccatccacat-ttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAAGAGTGGTTATGGTGTGAATCATGGTGCGGAAATGCTACAAAATCCAAGG
 ||||      |       |  |||       |   |            ||   |  |   ||    | || ||   |        || |   || |||||||||| ||||| | |||||||||||| |||||||| || || || || ||||| ||| ||||||||||||| ||||| |||||||| |||||  | |  |
-acatgctgtggtgtgcagagattaatggaagaaactacacaaatgcagtttacagatgtgaacatgtgtgaatgcttacttgcaacacctttatattcagGATCTCCCAAATTATGCTCAGCATACTGTGCCCATATTCTCTCTCCCTCAAGAATGGCTATGGTGTGAATCTTGGTGTGGAAATGCCACAAAGGCAAGAG

upper sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 36
lower sequence: GRMZM5G846198_T01 (Zea mays), 3'ss of exon 8
aacatctgaatgctccatcattttatctttttatgttctgtttgcttgattattattttccaaata-atat-gcattgctc---tgatagccatccacatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAAGAGTGGTTATGGTGTGAATCATGGTGCGGAAATGCTACAAAATCCAAGG
 |||| ||||   ||  |  ||||   ||| | | |  ||||  | | ||||||  | |  ||||  || | ||| ||||    ||  |  |||  | ||| |||||||| || || | ||| || ||||||||||| || || || ||||| ||||| ||| | ||||||||||| ||||| |||||||| |||||| | |  |
gacatttgaagattctgttttttt---tttctgtttcatgtt-acataattatttctgtataaatggatgttgcaatgcttacttggaacacattaatatt-cagGATCTCCCGAATTATGCCCAACATACGGTGCCTATATTCTCTCTTCCTCAAGAATGGCTGTGGTGTGAATCTTGGTGTGGAAATGCCACAAAAGCAAGAG

upper sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 36
lower sequence: GLYMA05G30230.1 (Glycine max), 3'ss of exon 36
aacatctgaatgctccatcattttatctttttatgttctgtttgcttgattattattttccaaataatatgcattgctctgatagccatcc-----acatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAAGAGTGGTTATGGTGTGAATCATGGTGCGGAAATGCTACAAAATCCAAGG
    |   ||||     ||   ||| | || | | || ||  ||| || || | |||||     | |  ||| ||  |   | |    |||     |   |  |||||||||| || | |||||||||||| ||||| || || ||  | || ||||||||| ||||||||||||||||||| || ||||||||||||| |||||
---cttccaatgtatt-tcccattagccttctctcttttgaatgcatgcttttgattttg-gtttgaggtgcctttttgctaaaattttccctgaaatggtctagGATCTTCCTAATTATGCTCAGCATACCGTGCCAATTTTCTCTTTGCCGCAAGAGTGGCTATGGTGTGAATCATGGTGTGGTAATGCTACAAAATACAAGG

upper sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 36
lower sequence: GLYMA08G13400.1 (Glycine max), 3'ss of exon 38
aacatctgaatgctccatcattttatctttttatgttctgtttgcttgattattattttccaaataatatgcattgct-ctgatagccatcc----acatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAAGAGTGGTTATGGTGTGAATCATGGTGCGGAAATGCTACAAAATCCAAGG
    |   |||  |   ||   ||| | || | | || ||  ||| || || || || |     | |  ||| ||  | || | |     ||    |   |  |||||||||| || | |||||||||||| ||||| || || ||  | || ||||||||| ||||||||||||||||||| || ||||||||||||| |||||
---gttccaat-ttatttcccattaaccttctgtcttttgaatgcatgttt-ttgttattggtttgaggtgcctttttgctaaaatttgcccctaaatggtctagGATCTTCCTAATTATGCTCAGCATACCGTGCCTATTTTCTCTTTGCCACAAGAGTGGCTATGGTGTGAATCATGGTGTGGTAATGCTACAAAATACAAGG

upper sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 36
lower sequence: GLYMA08G20020.1 (Glycine max), 3'ss of exon 35
--aacatctgaatgctccatcattttatctttttatgt-tctgtttgcttgattattattttccaaataatatgcattgctctgatagccatccacatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAAGAGTGGTTATGGTGTGAATCATGGTGCGGAAATGCTACAAAATCCAAGG
   || ||| ||||   || |  ||   |||  | | | ||  |||  ||  || || ||||   |   |  |    ||   |  | ||  || |   ||||||||||||| || | |||||||||||  || ||||| || || || || ||||| ||| | |||||||| |||||||| || |||||||||||||| ||||
tttacttct-aatgtagcacctgttgcccttggtgtatatcatttttttttttttttgttttttgacggaccttagctgaaat--ttgcattcaatggttcagGATCTTCCTAATTATGCTCAGCATATTGTTCCCATTTTCTCTCTGCCACAAGAATGGCTTTGGTGTGAGTCATGGTGTGGTAATGCTACAAAATCAAAGG

upper sequence: Vv12s0034g02230.t01 (Vitis vinifera), 3'ss of exon 36
lower sequence: AT1G71220.2 (Arabidopsis thaliana), 3'ss of exon 35
-----------------------------------------------------------------------aacatctgaatg-ctccatcatttta-tctttttatgttctgtttgcttgattattat--tttccaaataatatgcattgctctgatagccat-ccacatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAAGAGTGGTTATGGTGTGAATCATGGTGCGGAAATGCTACAAAATCCAAGG
                                                                          || |||| | ||    ||||| | ||||   ||   |  |   ||  ||  |||   || |    | | |   |||| |   ||  |  |      |||||||||||||| || | |||||||||||| || || || ||||||||||||||||||||||| ||||||||||| ||||| ||||| || |||||| ||||||
gcaagttgtataatatggttctctatacttagggctgtaacctttctttggtggtcacactatcgttttactttatttgaaaggcttttgcatttgactcttaccatacaccatgctctgaatctttagagttccaggttcaaacatattgatggcatgtcattattttgtttcagGATCTTCCTAATTATGCTCAGCATACTGTTCCTATATTTTCACTTCCCCAAGAGTGGTTGTGGTGTGAATCCTGGTGTGGAAACGCCACAAAAGCCAAGG

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|351019639|gb|FQ439456.1|FQ439456
EST:     TCTATGAAACTCTCAGCAAGGATCCGAACAGTCTATCAAATCTTGATCAG                         GATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAA
genomic: TCTATGAAACTCTCAGCAAGGATCCGAACAGTCTATCAAATCTTGATCAGgcaagtcacc ... cacatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAA
EST: gi|349827343|gb|FQ421616.1|FQ421616
EST:     TCTGTGAAACTCTCAGCAAGGATCCGAACAGTCTATCAAATCTTGATCAG                         GATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAA
genomic: TCTATGAAACTCTCAGCAAGGATCCGAACAGTCTATCAAATCTTGATCAGgcaagtcacc ... cacatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAA
EST: gi|351054907|gb|FQ440246.1|FQ440246
EST:     TCTATGAAACTCTCAGCAAGGATCCGAACAGTCTATCAAATCTTGATCAG                         GATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAA
genomic: TCTATGAAACTCTCAGCAAGGATCCGAACAGTCTATCAAATCTTGATCAGgcaagtcacc ... cacatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAA
EST: gi|352795524|gb|FQ480112.1|FQ480112
EST:     TCTATGAAACTCTCAGCAAGGATCCGAACAGTCTATCAAATCTTGATCAG                         GATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAG
genomic: TCTATGAAACTCTCAGCAAGGATCCGAACAGTCTATCAAATCTTGATCAGgcaagtcacc ... cacatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAA
EST: gi|110701698|gb|EE079566.1|EE079566
EST:     TCTATGAAACTCTCAGCAAGGATCCGAACAGTCTATCAAATCTTGATCAG                         GATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAA
genomic: TCTATGAAACTCTCAGCAAGGATCCGAACAGTCTATCAAATCTTGATCAGgcaagtcacc ... cacatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttgattattattttccaaataatatgcattgctctgatagccatccacatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAAGAGTGGTTATGGTGTGAATCATGGTGCGGAAATGCTACAAAATCCAAGG
                               ctctgat  putative branch site (score: 4)
     tattattttccaaata  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aacatctgaatgctccatcattttatctttttatgttctgtttgcttgattattattttccaaataatatgcattgctctgatagccatccacatttcagGATCTTCCAAACTTTGCTCAGCATACGGTGCCCATCTTTTCACTTCCCCAAGAGTGGTTATGGTGTGAATCATGGTGCGGAAATGCTACAAAATCCAAGG

- - -ctgaatg
- - - - - - ctccatc
- - - - - - - - - - - - - - - - - - - - - tgcttga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -aaataat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tgcattg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -agccatc