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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...acgcaaccatacatatatttgtaaattctttctttattgagatgagttgttgttaaatgttatgtctttgttctatttatattttccatattgcttgcagGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA

Basic information

species Vitis vinifera
transcript Vv14s0066g02540.t01
intron # 10
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: LOC_Os03g48300.3 (Oryza sativa), 3'ss of exon 10
acgcaaccatacatatatttgtaaattctttctttattgagatgagttgttgttaa--atgttatgtctttgttctatttatattttcc-atattgcttgc------agGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA
         |     |  || | | |  | | || ||    |     |   ||| |  ||  ||| || |  |  |  |  ||| |||  ||||  ||||       |||||||||| |||||||||||  | ||||| ||| | |||||||| ||||| || ||||||||||| ||||||||||||||  ||||
--------gtttgcttgcttctca-tcttcttttcatgataaccgccttgcgtttatcatagtatttcctaatattcctattatgttctgatatgacttgtttccatagGTTTGTGGTTTTGATCTCTTAAGGTGTGATGGAAGATCATATGTTTGTGACGTTAATGGATGGAGCTTTGTGAAGAACTCGTACAA

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA19G02260.1 (Glycine max), 3'ss of exon 8
acgcaaccatacatatatttg-taaattctttct-ttattgagatgagttgttgttaaatgttatgtctttgttctatttatattttccatattgcttgcagGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA
 | |      | ||  |||   | || ||||||| | | | | |  |  |  | |      |  | |   |||  || |   | |||   | ||||||||||||||||||||||||||| ||| |  || |||||||||||||||| |||||||||||||||||||| ||||| || || ||  ||||
tctctttagaatatggattaaatgaaatctttctgtgactaaaagaaaataatttgtctgatcctcttcatgtgatactataaattt--gtgttgcttgcagGTTTGTGGGTTTGATCTATTGAGAAGTCAGGGACGCTCATATGTTTGTGATGTGAATGGATGGAGCTTTGTTAAAAATTCATACAA

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA13G05060.1 (Glycine max), 3'ss of exon 11
acgcaaccatacatatatttg-taaattctttct-ttattgagatgagttgttgttaaatgttatgtctttgttctatttatattttccatattgcttgcagGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA
 | |      | ||  |||   | || ||||||| | | | | |  |  |  | |      |  | |   |||  || |   | |||   | ||||||||||||||||||||||||||| ||| |  || |||||||||||||||| |||||||||||||||||||| ||||| || || ||  ||||
tctctttagaatatggattaaatgaaatctttctgtgactaaaagaaaataatttgtccgatcctcttcatgtgatactataaattt--gtgttgcttgcagGTTTGTGGGTTTGATCTATTGAGAAGTCAGGGACGCTCATATGTTTGTGATGTGAATGGATGGAGCTTTGTTAAAAATTCATACAA

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA09G37610.1 (Glycine max), 3'ss of exon 8
----acgcaaccatacatatatttgtaaattctttctttattgagatgagttgttgttaaatgttatgtctttgttctatt-tatattttccatattgcttgcagGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA
    | | |  | || | ||  ||     |   ||  | |   | |  |  |||| |||| | |  |    || | ||| | ||  |  | | | |||||||||||||||||| |||||||||||| | || ||||||||||| ||||| ||||| |||||||||||||| ||||| || ||||| |||||
gaggatgaagtcttaaaaatggtt-----tgtcttagtgaagaaaagaaaatgtttttaagtctgctcctcttctcctactataggtcattcttgttgcttgcagGTTTGTGGATTTGATCTCTTGAGATGCGAGGGACGCTCCTATGTTTGTGACGTGAATGGATGGAGCTTTGTTAAAAACTCACACAA

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: GLYMA18G49000.1 (Glycine max), 3'ss of exon 10
acgcaaccatacatatatttgtaaattctttctttattgagatgagt-tgttgttaaatgttatgtctttgttctatt-tatattttccatattgcttgcagGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA
  |          | ||    |   || | ||  |   || | ||   |  | |||| | || | |  || |  || | ||  |  | | | ||||||||||||||||||||||||||||||| | || |||||||| || ||||| ||||| |||||||||||||| ||||| || || || |||||
--gaggatgaggttttaaaaatggtttgtctcagtgaagaaaagaaaataattttaagtcttctcttcttctcttactataggtcattcttgttgcttgcagGTTTGTGGGTTTGATCTCTTGAGATGCGAGGGACGATCCTATGTTTGTGACGTGAATGGATGGAGCTTTGTTAAAAATTCACACAA

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT5G15070.2 (Arabidopsis thaliana), 3'ss of exon 11
-----acgcaaccatacatatatttgtaaattctttctttattgagatgagttgttgttaaatgttatgtctttgttctatttatattttccatattgcttgcagGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA
               |   ||  ||   || | ||   |||    ||  |||||  | ||  | || | |  | |   || |   ||| |    || |  |||||||||| || ||||||||| | || | ||||||| | |||||||| ||||| || ||||||||||||||||||||||||||  | ||
gtgtagtttgtttgaaggaatgattacgaaatgttg--ttacctggaaaagttgaagatat-tattgtataat-gcattagtggaattattttcat-gtctgcagGTTTGCGGTTTTGATCTCCTACGATCTGAGGGAAGTTCATATGTTTGTGACGTAAATGGATGGAGTTTTGTGAAGAACTCCTATAA

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: AT3G01310.1 (Arabidopsis thaliana), 3'ss of exon 11
-------------------acgcaaccatacatatat-ttgtaaattct---ttctttattgagatgagttgttgttaaatgttatgtctttgttctatttatattttccatattgcttgcagGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA
                      |  |  |   ||| | ||| |    |    | | ||||   | |  ||| |  ||   ||  ||| | | ||  | | |  |   |   |     || ||||| ||||||||||||||  | || | ||||||  | |||||||| |||||||| ||||||||||||||||||||||||||  ||||
gtatgttgtgaatccaatcctccggctctcattatgtcttgcagggccgtaatcccttataatggtacgttctgatttcgtgcaatgacgtagtaatttcttcaacatttttcacatttccagGTCTGTGGGTTTGATCTTCTACGATCTGAGGGCTGTTCATATGTTTGTGATGTCAATGGATGGAGTTTTGTGAAGAACTCATACAA

upper sequence: Vv14s0066g02540.t01 (Vitis vinifera), 3'ss of exon 10
lower sequence: PP1S70_284V6.1 (Physcomitrella patens), 3'ss of exon 10
------------------------------------------------------------------------------------acgcaaccatacatatatttgtaaattctttctttattgagatgagttgttgttaaatgttatgtctttgttctatttatattttccatatt--gcttgcagGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA
                                                                                    | ||   |||  |  |   |  | | |  |    || |  ||| | ||    |     | ||  ||    | ||  | | |      ||| |  || ||||||||||||| |||||| |  | || |   | || || |||||||| ||||| || ||||| ||||||||||| ||||||||| ||||
gtgagcactattttttaacagacccttttagtatttaaaaagaaagagaaaaagaagagaaagaagttaaattccaaaacctcaaggcttacatgaacgtgcgta-agacttctgacatactaggattacttacc-tgctccggtacttcgaaatgcttctgacaaaagggataattggcctgcagGTTTGTGGATTTGATTTGCTTCGATCGCAAGGCCGGTCATATGTGTGTGACGTTAATGGGTGGAGTTTTGTTAAGAACTCTTACAA


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gttgttgttaaatgttatgtctttgttctatttatattttccatattgcttgcagGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA
                         ttctatttatattttc  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
acgcaaccatacatatatttgtaaattctttctttattgagatgagttgttgttaaatgttatgtctttgttctatttatattttccatattgcttgcagGTTTGTGGGTTTGATCTCTTGCGTTGTGAGGGACGCTCATATGTCTGTGATGTGAATGGATGGAGTTTTGTGAAGAACTCTCACAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAC
- - - ccataca