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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtatccttctcacattaactcttttgccaagttcttatacttcctcaatatttatgtcttctagcaattccattttcacctaaggttttgttatccttattacttcatagAAGCCCTGAGGAAGGAGATGCTAAACCTCAACGAACAGGCCATCTTCCTGCATATGGCTTCAGTTTCAAGTGTGATGAGAGAGCTGAGAAACGAAAAGAA

Basic information

species Vitis vinifera
transcript Vv11s0016g05460.t01
intron # 5
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv11s0016g05460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA04G07100.1 (Glycine max), 3'ss of exon 5
-----------gtatccttctc--acattaactcttttgccaagt-----------tcttatac---ttcctcaatatttatgtcttctagcaattcc--attttcacctaaggttttg-----ttatccttattacttcatagAAGCCCTGAGGAAGGAGATGCTAAACCTCAACGAACAGGCCATCTTCCTGCATATGGCTTCAGTTTCAAGTGTGATGAGAGAGCTGAGAAACGAAAAGAA
            | ||||  |    ||||   |||| ||   ||            ||| |||    ||  |  |||||||| |  |       || |  |   |  |  |  || ||      ||||||||| | |  | |  ||| |||   | || |||||| |||||||   |    ||    |||||   |||||| ||||||||||||||||||||| ||||||||| | ||||||| 
gtatcctttttttttcctggttgagcattgtttcttgtggtgagaggcaatggggatctaatatggatttatttatatttatattataagtttgttactgagagtggcacagtgtatttatggtttatccttaat-ccacttgtaagTCCTACCGCAGAAGATGCCAAACCTCGCAGGGTGGGAGCACTTCCAAAATATGGATTCAGTTTCAAGTGTGATGAGCGAGCTGAGAGAAGAAAAGAG

upper sequence: Vv11s0016g05460.t01 (Vitis vinifera), 3'ss of exon 5
lower sequence: GLYMA06G07190.1 (Glycine max), 3'ss of exon 5
-----------------------gtatccttctca--cattaactcttttgccaagttcttat--acttcctca--atatttatgtcttctagcaattcc--attttcacctaaggt-tttgttatcc-ttattacttca--tagAAGCCCTGAGGAAGGAGATGCTAAACCTCAACGAACAGGCCATCTTCCTGCATATGGCTTCAGTTTCAAGTGTGATGAGAGAGCTGAGAAACGAAAAGAA
                       | ||  ||        | |       ||   || |  | |  | ||  | |   |||||||||  |       || |  |   |  |  |  || ||| |  |   |  ||| | ||  |  ||| |||   | || |||||| |||||||   |    ||    || ||   |||||| ||||||||||||||||||||| ||||||||| | ||||||| 
gtatccttttttttcctggttgagcattgtttatggtggtgagaggcaatggggagctaatgtggatttgtttatattatttatgttgttagtttgttactgagagtggcacagtgtatttatggtttatccttaatccagttgtaagTCCTACTGCAGAAGATGCCAAACCTCGCAGGGTGGGGGCGCTCCCAAAATATGGATTCAGTTTCAAGTGTGATGAGCGAGCTGAGAGAAGAAAAGAG


















 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gtcttctagcaattccattttcacctaaggttttgttatccttattacttcatagAAGCCCTGAGGAAGGAGATGCTAAACCTCAACGAACAGGCCATCTTCCTGCATATGGCTTCAGTTTCAAGTGTGATGAGAGAGCTGAGAAACGAAAAGAA
 atccttatt  putative branch site 
                                      tccttatt  putative PPT
                              ttttgttat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtatccttctcacattaactcttttgccaagttcttatacttcctcaatatttatgtcttctagcaattccattttcacctaaggttttgttatccttattacttcatagAAGCCCTGAGGAAGGAGATGCTAAACCTCAACGAACAGGCCATCTTCCTGCATATGGCTTCAGTTTCAAGTGTGATGAGAGAGCTGAGAAACGAAAAGAA

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGAGCT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGCTGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAAGAA