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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...agaagcaaatgaagtcatctttcttgtttgttgagctaatcagttttttaaagttcatgtgggcttgtgattatcgttaactttgctttgcaacatgcagGTTCTATGTAGCAGAGGTTCTTCTTGCTCTTGAATACCTTCACATGCTTGGGATTGTTTATCGTGACCTGAAGCCAGAGAATGTCCTTGTGAGGGAAGAC

Basic information

species Vitis vinifera
transcript Vv19s0015g00770.t01
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv19s0015g00770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os08g38320.2 (Oryza sativa), 3'ss of exon 2
agaagcaaatgaagtcatctttcttgtttgttgagctaatcagttttttaaagttcatgtgggcttgtgattatcgttaactttg-----ctttgcaacatgcagGTTCTATGTAGCAGAGGTTCTTCTTGCTCTTGAATACCTTCACATGCTTGGGATTGTTTATCGTGACCTGAAGCCAGAGAATGTCCTTGTGAGGGAAGAC
   | ||| ||  ||   ||  ||  ||  ||   ||  |  |  | || ||   ||||   |  | |  | || |  |  ||||     || |      | |||||||||||| |||||||||||||||||  | |||||||| || |||||||||||| | || ||||| ||||| ||||| |||||||||||  |||| || 
--gatcaattgttgtttgctaactcattaatt---ctttttggcgtcttgaaaggcatggatgactcttctcattgaaacttttggtgatctcttggtatttcagGTTCTATGTGGCAGAGGTTCTTCTTGCATTAGAATACCTGCATATGCTTGGGATTATATACCGTGATCTGAAACCAGAAAATGTCCTTGTCCGGGAGGAT

upper sequence: Vv19s0015g00770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os09g08420.1 (Oryza sativa), 3'ss of exon 2
agaagcaaatgaagtcatctt-tcttgtttgttga-gctaatcagtttt-ttaaagttcatgtgggcttgtgattatcgttaactttgctttgcaacatgcagGTTCTATGTAGCAGAGGTTCTTCTTGCTCTTGAATACCTTCACATGCTTGGGATTGTTTATCGTGACCTGAAGCCAGAGAATGTCCTTGTGAGGGAAGAC
 |   |       ||  |||  | |  |    |||   || | |   ||  | ||||  | | | | |  || | || |||   ||   |        |||||||| ||||| || ||||| ||||||||||| |||||||| || |||||||| ||  | ||||| ||||| |||||||| ||||| |||||||| ||||| 
-gtgtctgccctggttttctggtatcatggagtgatagtactaaaccttgctcaagtctaagagag-tcatgttgat-gtttggttgattaattcttttgcagGTTTTATGTGGCTGAGGTGCTTCTTGCTCTAGAATACCTGCATATGCTTGGCATCATATATCGGGACCTTAAGCCAGAAAATGTTCTTGTGAGAGAAGAT

upper sequence: Vv19s0015g00770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: LOC_Os09g30150.3 (Oryza sativa), 3'ss of exon 2
agaagcaaatgaagtcatctttcttgtttgttgagctaatc---agttttttaaagttcatgtgggcttgtgatt-------atcgttaactttgctttgcaacatgcagGTTCTATGTAGCAGAGGTTCTTCTTGCTCTTGAATACCTTCACATGCTTGGGATTGTTTATCGTGACCTGAAGCCAGAGAATGTCCTTGTGAGGGAAGAC
              |  |  |   | ||||   |   ||||   | | |   |||||| |||   || | |   |        |  | ||  |     ||   | | |||||||||||||||||||||||| || ||  | || ||||| || |||||||| ||  | || ||||| ||||||||||| |||||||| ||  |||| |||
----------ctgtttgttatcagtctttgccaaatcaatcttcaatataaaaaagtttatgcaagcatttagcttaaactggtactcaatctcttgatgtttctttcagGTTCTATGTAGCAGAGGTTCTCCTAGCGTTGGAGTACCTGCATATGCTTGGTATCATATACCGTGATCTGAAGCCAGAAAATGTCCTAGTTCGGGAGGAC

upper sequence: Vv19s0015g00770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: AC217842.3_FGT001 (Zea mays), 3'ss of exon 1
agaagcaaatgaagtcatctttcttgtttgttgagctaat--cagttttttaaagt-tcatgtgggcttgtga-ttatcgttaactttgctttgcaacatgcagGTTCTATGTAGCAGAGGTTCTTCTTGCTCTTGAATACCTTCACATGCTTGGGATTGTTTATCGTGACCTGAAGCCAGAGAATGTCCTTGTGAGGGAAGAC
   |   |      |   ||  | || ||||   |  | |  ||  |     |||  | |        | |||  |   ||| || |        || ||||||||| |||||||||||||| ||||||||||| |||||||| ||||||||||| ||  | || |||||| | |||||||||||||| |||||||||||||| 
-atatttagcatgataggctgccctgattgtcatgtcatttgcaactgcaagaagccttaatcaaatctatgaacttatgttgacatcaa---aaaatatgcagGTTTTATGTAGCAGAGGTGCTTCTTGCTCTGGAATACCTGCACATGCTTGGTATCATATACCGTGACTTAAAGCCAGAGAATGTTCTTGTGAGGGAAGAT

upper sequence: Vv19s0015g00770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G026065_T01 (Zea mays), 3'ss of exon 2
agaagcaaatgaagtcatctttcttgtttgttgagctaatcagtttt-ttaaagttcatgtgggcttgtgattatcgttaactttgctttgcaacatg-cagGTTCTATGTAGCAGAGGTTCTTCTTGCTCTTGAATACCTTCACATGCTTGGGATTGTTTATCGTGACCTGAAGCCAGAGAATGTCCTTGTGAGGGAAGAC
     |  |   | | ||        |||||     ||      ||  |||||     | |    |  |    || | | |  |         |  |  |||||||||||| |||||||| || |||||  | |||||||| || |||||||||||| | || ||||| || || ||||| |||||||| ||  ||||||| 
--tttctgacctatttataaactagatttgtgctattatctgtcttcattaaaacgactttaaattatttggcattgattatctaataccttgatgtttcagGTTCTATGTGGCAGAGGTACTCCTTGCATTGGAATACCTGCATATGCTTGGGATTATATACCGTGATCTTAAACCAGAAAATGTCCTCGTTCGGGAAGAT

upper sequence: Vv19s0015g00770.t01 (Vitis vinifera), 3'ss of exon 1
lower sequence: GRMZM2G464985_T01 (Zea mays), 3'ss of exon 2
-agaagcaaatgaagtcatctttcttgtttgttgagctaatcagttttt-taaagttcatgtgggcttgtgattatcgttaactttgctttgcaacatg-cagGTTCTATGTAGCAGAGGTTCTTCTTGCTCTTGAATACCTTCACATGCTTGGGATTGTTTATCGTGACCTGAAGCCAGAGAATGTCCTTGTGAGGGAAGAC
  ||  |   ||  |  || ||| | | ||  ||   |  || || ||  | ||  | || |   ||| |  ||  || | |||  |  |    |  |  ||||||||| ||||| ||||| || |||||  | |||||||| || |||||||||||| | || ||||| || || ||||| |||||||| ||  ||||||| 
tggatactcttgt-gctatttttatagatttgtgctattttctgtcttcattaaaatgatttcaacttat--ttggcgctgactgggtatcttgatgtttcagGTTCTACGTAGCTGAGGTGCTCCTTGCATTGGAATACCTGCATATGCTTGGGATTATATACCGTGATCTCAAACCAGAAAATGTCCTCGTTCGGGAAGAT

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|110725621|gb|EE102334.1|EE102334
EST:     ACACTTAGGCAGAGGCAACCTGGGAAGCATTTTTCCGAGCAAGCTGTAAA                         GTTCTATGTAGCAGAGGTTCTTCTTGCTCTTGAATACCTTCACATGCTTGG
genomic: ACACTTAGGCAGAGGCAACCTGGGAAGCATTTTTCCGAGCAAGCTGTAAAgtatgatact ... caacatgcagGTTCTATGTAGCAGAGGTTCTTCTTGCTCTTGAATACCTTCACATGCTTGG
EST: gi|33405248|gb|CF210875.1|CF210875
EST:     ACACTTAGGCAGAGGCAACCTGGGAAGCATTTTTCCGAGCAAGCTGTAAA                         GTTCTATGTAGCAGAGGTTCTTCTTGCTCTTGAATACCTTCACATGCTTGG
genomic: ACACTTAGGCAGAGGCAACCTGGGAAGCATTTTTCCGAGCAAGCTGTAAAgtatgatact ... caacatgcagGTTCTATGTAGCAGAGGTTCTTCTTGCTCTTGAATACCTTCACATGCTTGG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

ttttaaagttcatgtgggcttgtgattatcgttaactttgctttgcaacatgcagGTTCTATGTAGCAGAGGTTCTTCTTGCTCTTGAATACCTTCACATGCTTGGGATTGTTTATCGTGACCTGAAGCCAGAGAATGTCCTTGTGAGGGAAGAC
                             cgttaac  putative branch site (score: 3)
                               ttaacttt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
agaagcaaatgaagtcatctttcttgtttgttgagctaatcagttttttaaagttcatgtgggcttgtgattatcgttaactttgctttgcaacatgcagGTTCTATGTAGCAGAGGTTCTTCTTGCTCTTGAATACCTTCACATGCTTGGGATTGTTTATCGTGACCTGAAGCCAGAGAATGTCCTTGTGAGGGAAGAC

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTGAAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - TGAAGC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAAGA
- aagcaaa
- - - - -tgaagtc
- - - - - - - - - - - - - - - - - - - - - - - - - - - -catgtgg
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - gcttgtg