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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtctttctagcatttgttttttgattggcttgtgctccttttatttccttatgttatctttttccttttcattgattattgaactatccacattattagGTCAAGTATTTGTGGCTTCTTTTTGATTTGGCTGCGGGTTCGGACAACCTTGTTGAAAATGGGCCATACAA

Basic information

species Vitis vinifera
transcript Vv05s0020g04650.t01
intron # 15
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: LOC_Os01g56670.2 (Oryza sativa), 3'ss of exon 14
tgtctttctag-catttgttttttgattggcttgtgctccttttatttccttatgttatctttttccttttcattgat-tattgaactatccacat-tattagGTCAAGTATTTGTGGCTTCTTTTTGATTTGGCTGCGGGTTCGGACAACCTTGTTGAAAATGGGCCATACAA
| | |  |||   |        |  |     ||   || | | | |||| ||  | |||  | |    ||   |  || || | || |||   |   |   ||||||| ||| | ||||||||||||||||| ||||| ||  | || ||  ||||||||||||||||||| ||
tctttgcctaaataaccagcaatgcaacaattta--ctgcatat-tttcgttgagctattctctattgttggttaaatctaattaattattagcgcattccagGTCAAATATCTCTGGCTTCTTTTTGATTTAGCTGCAGGCCCTGATAATATTGTTGAAAATGGGCCATATAA

upper sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GRMZM2G173868_T02 (Zea mays), 3'ss of exon 13
tgtctttcta-gcatttgttttttgattggcttgtgctccttttatttccttatgttatctttttccttt-tcattgattattgaactatccacat-tattagGTCAAGTATTTGTGGCTTCTTTTTGATTTGGCTGCGGGTTCGGACAACCTTGTTGAAAATGGGCCATACAA
  |||      ||| |  ||||| |    |   | | |   |  ||  | || |  | | ||| |||| | |   |||  ||  ||||| |  ||  ||  ||||||||||| | ||||||||||||||||| ||||| ||  | |||||  ||||||||||||| ||||| ||
-atctagaagtgcactcttttttgggacagagggcg-taaatacatgccattttcctttatttatcctctattgctgaa-atctaactacctgcacataccagGTCAAGTATCTCTGGCTTCTTTTTGATTTAGCTGCTGGCCCTGACAATATTGTTGAAAATGGACCATATAA

upper sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA10G32320.1 (Glycine max), 3'ss of exon 13
tgtctttctagcatttgttttttgattggcttgtgctccttttatttccttatgttatctttttccttttcat---tgattattgaactatccacattattagGTCAAGTATTTGTGGCTTCTTTTTGATTTGGCTGCGGGTTCGGACAACCTTGTTGAAAATGGGCCATACAA
  |     || ||||||| ||    ||    | |  || |||     |||  | |||| | |||       |        || | | |||| |  |  |||||||||||||| |||||||||| ||||||||||||| |||| | ||||| ||||| ||||||||||| |||||
-ctaccattaacatttgtcttgcctttcatattttgtcttttccccccctc-tattatttatttaaaagaaaaatgctgctactaacctatgc-tacaattagGTCAAGTATCTGTGGCTTCTGTTTGATTTGGCTGTGGGTCCTGACAATCTTGTGGAAAATGGGCCTTACAA

upper sequence: Vv05s0020g04650.t01 (Vitis vinifera), 3'ss of exon 15
lower sequence: GLYMA20G35290.1 (Glycine max), 3'ss of exon 10
---------tgtctttctagcatttgttttttgattggcttgtgctcctt--ttatttccttatgttatctttttccttttcattgattattgaactatccacattattagGTCAAGTATTTGTGGCTTCTTTTTGATTTGGCTGCGGGTTCGGACAACCTTGTTGAAAATGGGCCATACAA
           |||| |||||||| |  |||   ||| |||   | |||   ||||||  | |    |    ||              || | | |||| |  |  |||||||||||||| |||||||||| |||||||||  ||     | || ||  |  ||                  
taaactatgcctcttactagcattagcatttgtcttgccttccccccctctattatttattcaaaagaaaaattct----------gctactaacctatgc-tacaattagGTCAAGTATCTGTGGCTTCTGTTTGATTTG--TGGAAAATGGGCCATACAAGTGA----------------


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttccttatgttatctttttccttttcattgattattgaactatccacattattagGTCAAGTATTTGTGGCTTCTTTTTGATTTGGCTGCGGGTTCGGACAACCTTGTTGAAAATGGGCCATACAA
                         cattgat  putative branch site (score: 4)
                     ttttcattgattatt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtctttctagcatttgttttttgattggcttgtgctccttttatttccttatgttatctttttccttttcattgattattgaactatccacattattagGTCAAGTATTTGTGGCTTCTTTTTGATTTGGCTGCGGGTTCGGACAACCTTGTTGAAAATGGGCCATACAA

- - - - - gcatttg
- - - - - - - - - - - tgattgg
- - - - - - - - - - - - - - -cttgtgc