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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

...aataaatctagacaacatcaatataaatgtgggaaatgatagaatgacttacattgtaaaacggaggaagtatttactgtgaataattctctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCTCTTGAACCTGGGAGGGTTACATTTGATGAGAAGATGGAGATAAGAAGAG

Basic information

species Oryza sativa
transcript LOC_Os12g16220.2
intron # 1
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g16220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GRMZM2G326116_T01 (Zea mays), 3'ss of exon 2
aataaatctagacaacatcaatataaatgtgggaaatgatagaatgacttacattgtaaaacggaggaagtatttactgtgaataattctctgcga--------gcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCTCTTGAACCTGGGAGGGTTACATTTGATGAGAAGATGGAGATAAGAAGAG
     |  |  ||   |     ||| |||| |   |  ||| ||  |   |||    || | | || | ||  | | | | |||||   |  |  |        |||||||||  | || || ||||| |||||||||||||| | ||||||| ||||||||||||| || ||||||||||||||||| ||||||||  ||||  | |
----gacatgtacgg-actctcatatatgtagttcaatatataa--ataaacaacaaaagatgaag-aggtgctgagtctaaataaacttacgttattgtggatgcagCGTTTTATACCATCGGAATTCGGCATGGATCCATCCAAGATGGGGCATGCTCTTGAACCAGGAAGGGTTACATTTGATGAAAAGATGGACCTAAGGCGTG

upper sequence: LOC_Os12g16220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: GLYMA09G34470.1 (Glycine max), 3'ss of exon 1
----aataaatctagacaacatcaatataaatgtgggaaatgatagaatgacttacattgtaaaacggaggaagtatttactgtgaataattctctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCTCTTGAACCTGGGAGGGTTACATTTGATGAGAAGATGGAGATAAGAAGAG
    | |   || | | || | |   || ||  ||    ||   | |||    || |||  ||           || | | | |  |   |  | |      |||||||| |||| ||||||||||||||||| ||  ||   |||||  |||| |||||||| || || || |||||||||||||| |||    |||| | ||
aaaaagttgttccaaataagaccttaattaaaatgttttatttcaaaat----tatattagaatcacatttttttaatcattatacaatttggtttttctctagCGTTTCTTGCCTTCAGAATTTGGCATGGACCCTGCACTTATGGGACATGCACTTGAACCGGGAAGAGTGACATTTGATGAGAAAATGACCGTAAGGAAAG

upper sequence: LOC_Os12g16220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0033g00260.t01 (Vitis vinifera), 3'ss of exon 1
--aataaatctagacaacatcaatataaatgtgggaaatgatagaatgacttacattgtaaaacggaggaagtatttactgtgaataattctctgcgag------cagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCTCTTGAACCTGGGAGGGTTACATTTGATGAGAAGATGGAGATAAGAAGAG
  ||||||   | | || | || |    || | |       || |||   | | |||| | ||      || |   ||  |  | ||||| | | | |       ||||| |||||||| ||||| ||||| ||||||||| |||| |||||  |||| |||||||| || || || |||||||||||||||||||   | || |  |
aaaataaa---aaataagaacatttcttattttgcttccattataat--ttgatattg-acaatatttaaaatggatatcg--attaattttttacaaattatttcagCGATTCCTGCCTTCAGAGTTTGGAATGGATCCAGCAAGAATGGGAGATGCACTTGAACCAGGAAGAGTGACATTTGATGAGAAGATGGTTGTGAGGAAGG

upper sequence: LOC_Os12g16220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0033g00270.t01 (Vitis vinifera), 3'ss of exon 1
---aataaatctagacaacatcaatataaatgtgggaaatgatagaatg-acttacattgtaaaacggaggaagtatttactgtgaataattctctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCTCTTGAACCTGGGAGGGTTACATTTGATGAGAAGATGGAGATAAGAAGAG
    |  ||| |   ||   |    ||     ||    || ||| | |  |   | ||   |            || | | | |||  ||     |  | | |||| ||| |||| ||||| ||||| ||||| ||||| || |||||  |||| |||||||| || || ||  |||||||||||||||||    | || |  |
tcttagtaatttccccactcttttgatgggcctg---cattataaattctatcaatatcaaactctaagattgatactaattttgagcaaaaaaatttg-gtagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCATCCAGAATGGGAGATGCACTTGAACCAGGAAGAGTGTCATTTGATGAGAAGATGATTGTGAGGAAGG

upper sequence: LOC_Os12g16220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv02s0033g00290.t01 (Vitis vinifera), 3'ss of exon 1
-----aataaat-ctagacaacatcaatataaatgtgggaaatgatagaatgacttacattgtaaaacggaggaagtatttactgtgaataattctctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCTCTTGAACCTGGGAGGGTTACATTTGATGAGAAGATGGAGATAAGAAGAG
     | ||| | |   ||    |  ||     ||   | | | ||   || |   ||||   ||           || | | |||| | ||   | ||   |||||| ||| |||| ||||| ||||| ||||| ||| ||||||||||  |||| |||||||| || || || ||||||||||||||||||    | || || |
ctcctagtaatttcctcacccttttgatgggcctgcctgtatttattctatca---acatcaaaatctaagattgataataattgtgtacaaaattttg---gcagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCAGCAAGGATGGGAGATGCACTTGAACCAGGAAGAGTAACATTTGATGAGAAGATGATTGTGAGGAGGG

upper sequence: LOC_Os12g16220.2 (Oryza sativa), 3'ss of exon 1
lower sequence: Vv17s0053g00460.t01 (Vitis vinifera), 3'ss of exon 1
-----aataaat-ctagacaacatcaatataaatgtgggaaatgatagaatgacttacattgtaaaacggaggaag-tatttactgtgaataattctctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCTCTTGAACCTGGGAGGGTTACATTTGATGAGAAGATGGAGATAAGAAGAG
     | ||| | |   ||    |  ||     ||   | | | ||   || |   ||||   ||| |  ||   | || | | ||||   || | |      |||||| ||| |||| ||||| ||||| ||||| ||| ||||||||||  |||| |||||||| || || || ||||||||||||||||||    | || |  |
ctcctagtaatttcctcacccttttgatgggcctgcctgtatttattctatca---acatcaaaaatctaagattgataataattgtgtcaaaatttt----ggcagCGATTCTTGCCTTCAGAGTTTGGAATGGACCCAGCAAGGATGGGAGATGCACTTGAACCAGGAAGAGTAACATTTGATGAGAAGATGATTGTGAGGAAGG

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|88357934|gb|CI650670.1|CI650670
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCT
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCT
EST: gi|88325588|gb|CI675397.1|CI675397
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCAGAATTTG
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCAGAATTTG
EST: gi|88571323|gb|CI662696.1|CI662696
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCA
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCA
EST: gi|88355439|gb|CI679156.1|CI679156
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCAGAATTTGGCATGG
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGG
EST: gi|88411764|gb|CI571256.1|CI571256
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCAGAATTTGGCATGGATCC
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCC
EST: gi|88345370|gb|CI656028.1|CI656028
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGT
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGT
EST: gi|88347930|gb|CI636023.1|CI636023
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCAGAATT
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCAGAATT
EST: gi|88296297|gb|CI669073.1|CI669073
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAGGGATGGGGAA
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAA
EST: gi|29660598|gb|CB656873.1|CB656873
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCT
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCT
EST: gi|88580829|gb|CI697786.1|CI697786
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCC
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCC
EST: gi|88851506|gb|CI670946.1|CI670946
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCAG
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCAG
EST: gi|88574644|gb|CI666413.1|CI666413
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCA
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCA
EST: gi|88392098|gb|CI683929.1|CI683929
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCT
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCT
EST: gi|29660599|gb|CB656874.1|CB656874
EST:     ATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCT
genomic: ATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCT
EST: gi|88449574|gb|CI579854.1|CI579854
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCAGAATTTGGCATGGATCCAT
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCAT
EST: gi|25799331|gb|CA755292.1|CA755292
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCT
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCT
EST: gi|38469582|gb|CF953713.1|CF953713
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCT
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCT
EST: gi|88340972|gb|CI638528.1|CI638528
EST:     TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAG                         CGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCT
genomic: TGCTCCAGCTCAAGCTTGTCGAGGCCATCAAAGAAGCTGGAAATGTCAAGgtaatttatt ... ctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gacttacattgtaaaacggaggaagtatttactgtgaataattctctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCTCTTGAACCTGGGAGGGTTACATTTGATGAGAAGATGGAGATAAGAAGAG
 gacttac  putative branch site (score: 2)
                                         ttctctgc  putative PPT
       attgtaaaa  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
aataaatctagacaacatcaatataaatgtgggaaatgatagaatgacttacattgtaaaacggaggaagtatttactgtgaataattctctgcgagcagCGTTTCCTGCCGTCAGAATTTGGCATGGATCCATCAAGGATGGGGAATGCTCTTGAACCTGGGAGGGTTACATTTGATGAGAAGATGGAGATAAGAAGAG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  AAGATG
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GATGGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  TGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - GGAGAT
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AAGAAG
- - - - - - -aacatca
- - - - - - - - - - - - - - - - - - - - - - - -cttacat
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - tttactg