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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agtttcttccagcttggttcatgatcatggttgttagcagcaatcaaaatgaataacataaatcagatattcacgagtcctattccatgtcattatacagATTGGTGTCCTTGAGGATACAAGAAACCACACTCTCCATGGCATTTTACGTGTTCAAAGTTGCTTCAGAGGTCACCAAGCTCGTTGTCATCTCAGGGATC

Basic information

species Vitis vinifera
transcript Vv10s0071g00210.t01
intron # 19
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA09G42180.1 (Glycine max), 3'ss of exon 18
---agtttcttccagcttggttcatgatcatggttgttagcagcaatcaaaatgaataacat-aaatcagatattcacgagtcctattcc-atgtcattatacagATTGGTGTCCTTGAGGATACAAGAAACCACACTCTCCATGGCATTTTACGTGTTCAAAGTTGCTTCAGAGGTCACCAAGCTCGTTGTCATCTCAGGGATC
     | ||| | |      | | | || |  | ||| || ||||   |||||   ||   | |||  | || |  |    | ||  |   |||  |||   ||||||||||| ||||| ||||| ||||| |  || |||||||||||||||||||| |||||||| ||||| ||| ||||||| |||  |  ||||| |||||
atttatatctgctattcctttcctttatgaaaggtgt-aggagca--taaaatttttatttttaaaatatatttcaatttatgctgctttgatggaattg--cagATTGGTGTGCTTGAAGATACTAGAAATCGTACCCTCCATGGCATTTTACGTGTCCAAAGTTGTTTCAGGGGTTACCAAGCACGTCATTCTCTCAAGGATC

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA20G00320.1 (Glycine max), 3'ss of exon 20
----agtttcttccagcttggttcatgatcatggttgttagcagcaatcaaaatgaataacataaatcagatattcacgagtcctattcc-atgtcattatacagATTGGTGTCCTTGAGGATACAAGAAACCACACTCTCCATGGCATTTTACGTGTTCAAAGTTGCTTCAGAGGTCACCAAGCTCGTTGTCATCTCAGGGATC
      | ||| | |      | | | || |  | ||| || |||| | | | |  ||    ||||| |  |    |    | ||  |   |||  |||   ||||||||||| ||||| ||||| ||||| |  || |||||||||||||||||||| |||||||| ||||| |||  |||||| ||| ||  ||||| |||||
tatttatatctgctattcctttcctttatgaaaggtgt-aggagca-taagattttattttttaaat-attttccaatttatgctgctttgatggaattg--cagATTGGTGTGCTTGAAGATACTAGAAATCGTACCCTCCATGGCATTTTACGTGTCCAAAGTTGTTTCAGGGGTTTCCAAGCACGTCGTTCTCTCAAGGATC

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA20G23660.1 (Glycine max), 3'ss of exon 20
agtttcttccagcttggttcatgatcatggttgttagcagcaatcaaaatgaataaca---taaatcagatattca-cgagtcctattccatgtcattatacagATTGGTGTCCTTGAGGATACAAGAAACCACACTCTCCATGGCATTTTACGTGTTCAAAGTTGCTTCAGAGGTCACCAAGCTCGTTGTCATCTCAGGGATC
    || |  |  | | || ||   || ||   | ||    ||    | | | |       |  ||    | || |    |     ||   ||| |||   |||||||| || ||||| ||||| ||||| |  || || |||||  |||||||||| |||||||||||||| ||| ||| |||||||||| ||| || ||| |
-aagtcgttgaaatagttttattcccaaggcc-taagtttaaactttatttactcttcttttgcattgtgtctttaataggatgcgttaactgtgattg--cagATTGGAGTGCTTGAAGATACCAGAAATCGTACCCTGCATGGAGTTTTACGTGTGCAAAGTTGCTTCAGGGGTTACCGAGCTCGTTGTTATCGCAAGGAGC

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: GLYMA10G43230.1 (Glycine max), 3'ss of exon 18
agtttcttccagcttggttcatgatcatggttg----ttagcagcaatcaaaatgaataacataaatcagatattca-cgagtcctattccatgtcattatacagATTGGTGTCCTTGAGGATACAAGAAACCACACTCTCCATGGCATTTTACGTGTTCAAAGTTGCTTCAGAGGTCACCAAGCTCGTTGTCATCTCAGGGATC
    || |  |  | | || ||   || ||       |||      ||  |      |    |  ||    | || |    |     ||   ||| |||   |||||||| || ||||| ||||| ||||| |  || || |||||  |||| ||||| |||||||||||||| ||| ||| |||||||||| ||| || ||| |
---gtcgttgaaatagttttattcccaaggcctaagtttaaactttatttactcctctcttttgcattgtctctttaatatgctgcgttgactgtgattg--cagATTGGAGTGCTTGAAGATACCAGAAATCGTACCCTGCATGGAGTTTTGCGTGTGCAAAGTTGCTTCAGGGGTTACCGAGCTCGTTGTTATCGCAAGGAGC

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: AT1G50360.1 (Arabidopsis thaliana), 3'ss of exon 20
agtttcttccagcttggttcatgatcatggttgttagcagcaatcaaaatgaataacataaatcagatattcacga-gtcctattcc-atgtcattat-acagATTGGTGTCCTTGAGGATACAAGAAACCACACTCTCCATGGCATTTTACGTGTTCAAAGTTGCTTCAGAGGTCACCAAGCTCGTTGTCATCTCAGGGATC
               |    || |  |  || ||  |  |   | |   |      || |||| ||| ||||     |   ||| |     |||  ||  |||||||| || ||||| |||||||| || | |||||| ||||||||||||||| |||||||||  || ||||| ||||||||||| |||| ||| |  || |
---------------gtactataacta--gtcgtctgatgtcttgactttaggggccacaaattagacattcttactgcagtatacttgcttcaccattgcagATTGGGGTTCTTGAAGATACAAGGAATCGCACTCTGCATGGCATTTTACGTCTTCAAAGTTATTTTAGAGGGCACCAAGCTCGCTGTCGTCTAAAAGAGC

upper sequence: Vv10s0071g00210.t01 (Vitis vinifera), 3'ss of exon 19
lower sequence: AT3G19960.1 (Arabidopsis thaliana), 3'ss of exon 20
agtttcttccagcttggttcatgatcatggttgttagcagcaatcaaaatgaataacataaatcagatattcacgagtcctattccatgtcattatacagATTGGTGTCCTTGAGGATACAAGAAACCACACTCTCCATGGCATTTTACGTGTTCAAAGTTGCTTCAGAGGTCACCAAGCTCGTTGTCATCTCAGGGATC
                ||  |  | | ||   | | |   |||   |  |  ||   ||||     |     | |||||  ||    || ||||   |||||||| || |||||||| ||||| ||||  |||||||| ||||||||||||||||||||||  || |||||  ||||||| || ||||  || | ||| |
----------------gtataatagcttgtcggctggtgtcaaa-gacttttattttataaggggcaggaataagagtctcat---gtg-cattg--cagATTGGGGTTCTTGAGGACACAAGGAACCGTACTCTCCACGGCATTTTACGTGTTCAAAGTTCTTTTAGAGGATACCAAGCACGCTGTCTCCTGAAGGAAC


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

aaaatgaataacataaatcagatattcacgagtcctattccatgtcattatacagATTGGTGTCCTTGAGGATACAAGAAACCACACTCTCCATGGCATTTTACGTGTTCAAAGTTGCTTCAGAGGTCACCAAGCTCGTTGTCATCTCAGGGATC
     gaataac  putative branch site (score: 2)
      aataacataaatca  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agtttcttccagcttggttcatgatcatggttgttagcagcaatcaaaatgaataacataaatcagatattcacgagtcctattccatgtcattatacagATTGGTGTCCTTGAGGATACAAGAAACCACACTCTCCATGGCATTTTACGTGTTCAAAGTTGCTTCAGAGGTCACCAAGCTCGTTGTCATCTCAGGGATC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CAAGCT
- - - ttccagc
- - - - - - - - - -catgatc
- - - - - - - - - - - - - -tggttgt
- - - - - - - - - - - - - - - - - - - -gcaatca
- - - - - - - - - - - - - - - - - - - - - - - - - gaataac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - aatcaga
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -tattcac