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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...tgtgctgacatttttctgtgtaatgaagaaagagattttgcaactagagttcatattattttatgtattgaatgatttttctttaaccttggtcaataagATCCTTGTACCCCTTCCGGAACCAGAAGCAAGAAGAGCCATGTTTGAGGAGCTCCTGCCATCAGTACCAGGTGAGGAGAAGCTTCCATATGATTTGATGG

Basic information

species Vitis vinifera
transcript Vv10s0003g03500.t01
intron # 9
splice site 3'
intron type U12 (go to U12 genes for details)

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA05G26100.1 (Glycine max), 3'ss of exon 9
-tgtgctgacattt---ttctgtgtaatgaagaaagagattttgcaact-agagttcatattattttatgtattgaatgatttttctttaaccttggtcaataagATCCTTGTACCCCTTCCGGAACCAGAAGCAAGAAGAGCCATGTTTGAGGAGCTCCTGCCATCAGTACCAGGTGAGGAGAAGCTTCCATATGATTTGATGG
   |||  | ||||   |  ||   ||| |  ||    || |||||| | | || ||  | |  ||| | || ||  ||  || || || ||| |       |||||||||||||| ||||| ||||||| |||||||||||| ||||| ||||| ||||| ||   |   || | ||||||   | | || |||||| |  |||
caatgc--atatttagatgatgcccaataagcaatcttatcttgcaattgaaagctctcagtccttt-tctaatggttg--ttgtccttgaccataaattgaaagATCCTTGTACCACTTCCAGAACCAGTAGCAAGAAGAGCAATGTTCGAGGAACTCCTTCCTCAACAGCCTGATGAGGAACCGATCCCCTATGATATACTGG

upper sequence: Vv10s0003g03500.t01 (Vitis vinifera), 3'ss of exon 9
lower sequence: GLYMA08G09050.1 (Glycine max), 3'ss of exon 9
tgtgctgacattt---ttctgtgtaatgaagaaagagattttgcaact-agagttcatattattttatgtattgaatgatttttctttaaccttggtcaataagATCCTTGTACCCCTTCCGGAACCAGAAGCAAGAAGAGCCATGTTTGAGGAGCTCCTGCCATCAGTACCAGGTGAGGAGAAGCTTCCATATGATTTGATGG
|      | ||||   |  ||   ||| |  ||   ||| || ||| | | || ||| | |  ||| | || ||||||  || || || ||| |  |  | |||||||||||||| ||||| |||||||  || |||||||| ||||| ||||| ||||| ||   |   || || |||||   | | || |||||| |  |||
tcaatgcatatttggatgatgcccaataagcaatctgatctttcaattgaaagctcacagtccttt-tctaatgaatg--ttgtccttgaccgtaattga-aagATCCTTGTACCACTTCCAGAACCAGTTGCGAGAAGAGCAATGTTCGAGGAACTCCTTCCTCAACAGCCTGGCGAGGAATCGATCCCCTATGATATACTGG
















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|32271159|gb|CD720318.1|CD720318
EST:     ATCTCCCATGGGAATTGGATGCAGCGATGCTCCGTCGCCTTGAAAAGAGA                         ATCCTTGTACCCCTTCCGGAACCAGAAGCAAGAAGAGCCATGTTTGAGGAG
genomic: ATCTCCCATGGGAATTGGATGCAGCGATGCTCCGTCGCCTTGAAAAGAGAgtatcctttt ... ggtcaataagATCCTTGTACCCCTTCCGGAACCAGAAGCAAGAAGAGCCATGTTTGAGGAG
EST: gi|27586367|gb|CB009062.1|CB009062
EST:     ATCTCCCATGGGAATTGGATGCAGCGATGCTCCGTCGCCTTGAAAAGAGA                         ATCCTTGTACCCCTTCCGGAACCAGAAGCAAGAAGAGCCATGTTTGAGGAG
genomic: ATCTCCCATGGGAATTGGATGCAGCGATGCTCCGTCGCCTTGAAAAGAGAgtatcctttt ... ggtcaataagATCCTTGTACCCCTTCCGGAACCAGAAGCAAGAAGAGCCATGTTTGAGGAG
EST: gi|110732627|gb|EE108077.1|EE108077
EST:     ATCTCCCATGGGAATTGGATGCAGCGATGCTCCGTCGCCTTGAAAAGAGA                         ATCCTTGTACCCCTTCCGGAACCANAANCAAGAAGAGCCTTGTTTGAGGAG
genomic: ATCTCCCATGGGAATTGGATGCAGCGATGCTCCGTCGCCTTGAAAAGAGAgtatcctttt ... ggtcaataagATCCTTGTACCCCTTCCGGAACCAGAAGCAAGAAGAGCCATGTTTGAGGAG


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

agagttcatattattttatgtattgaatgatttttctttaaccttggtcaataagATCCTTGTACCCCTTCCGGAACCAGAAGCAAGAAGAGCCATGTTTGAGGAGCTCCTGCCATCAGTACCAGGTGAGGAGAAGCTTCCATATGATTTGATGG
                                 ttctttaac  putative branch site 
     tcatattattttatgt  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
tgtgctgacatttttctgtgtaatgaagaaagagattttgcaactagagttcatattattttatgtattgaatgatttttctttaaccttggtcaataagATCCTTGTACCCCTTCCGGAACCAGAAGCAAGAAGAGCCATGTTTGAGGAGCTCCTGCCATCAGTACCAGGTGAGGAGAAGCTTCCATATGATTTGATGG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GAGGAG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGAAGC
- - ctgacat
- - - - - - - - - - - - gaagaaa
- - - - - - - - - - - - - - - - - - - -gcaacta