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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACTGGAAACCAAATGGTGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagaggaaatatttttgaaggttttcgggccagcattcttgctcaaagttttgcaatcttattgtttcag

Basic information

species Oryza sativa
transcript LOC_Os03g49420.2
intron # 3
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g49420.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G033619_T01 (Zea mays), 5'ss of exon 3
ACTGGAAACCAAATGGTGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagaggaaatatttttgaaggttttcgggccagcattcttgctcaaagt---tttgcaatcttattgtttcag
||||| ||||||||||||||||||| |||||||||||||||||||||||| |||||||||||||||||| |  ||||||||   || ||    |||  |  | |||  |     ||  |   ||| ||||||||||  |||||
ACTGGGAACCAAATGGTGCAAGAAGCTGCTTTAACTGCTTTAGCATCAGCAGCAGATTCTTCTCAGgtagatcaggaaatacagttcaat-ccttcttgttaacatagtaatctaacataaattttcaatcttatttattcag

upper sequence: LOC_Os03g49420.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA19G29010.1 (Glycine max), 5'ss of exon 4
ACTGGAAACCAAATGGTGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtaca----agaggaaatatttttgaaggttttcgggccagcattcttgctcaaagttt------tgcaatcttattgtttcag
| ||| || |||||||| |||||||| ||||| || || |||||||| | ||||||||||||  |||| |       ||  |||||| |  |  ||  | |     || ||   | |  |   ||      || |||   ||  |  |||
AATGGGAAGCAAATGGTTCAAGAAGGGGCTTTGACAGCCTTAGCATCTGTTGCAGATTCTTCAGAGgtgctttatgtagccaatattctccatagtaat-gacaatgcttttaagttttatacttaatacgtgaaatgccatgttaacag

upper sequence: LOC_Os03g49420.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA05G28950.2 (Glycine max), 5'ss of exon 6
ACTGGAAACCAAATGGTGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagaggaaatatttt------tgaaggttttcgggccagcat-tcttgctcaaagttttgcaatcttattgtttcag----
| ||| || || ||||||||||||||||| ||||||||||| ||||||| ||| |||||||||||||||       || |  |||      | ||  |||       |   | | ||| |||    |||  | | |||| || |       
AATGGTAAGCAGATGGTGCAAGAAGGTGCCTTAACTGCTTTGGCATCAGTTGCTGATTCTTCTCAGgtattttgttaacttctttgttcaatcaacatttataatttattttcttttgatcactcattta-attattatggtctttcttag

upper sequence: LOC_Os03g49420.2 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA08G12120.1 (Glycine max), 5'ss of exon 4
ACTGGAAACCAAATGGTGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagaggaaatatttt------tgaaggttttcgggccagcat-tcttgctcaaa-gttttgcaatcttattgtttcag--
| ||| || || ||||||||||||||||| ||||||||||| ||||||| ||| |||||||||||||||      ||| |  |||      | ||  | | |     |   | | ||| |||    |||    ||  | || ||||    
AATGGTAAGCAGATGGTGCAAGAAGGTGCCTTAACTGCTTTGGCATCAGTTGCTGATTCTTCTCAGgtattttgtgaacttctttgttcaatcaacatatgcaatttattttcttttgatcactcatttaattattatgttctttcttag

upper sequence: LOC_Os03g49420.2 (Oryza sativa), 5'ss of exon 3
lower sequence: AT5G19820.1 (Arabidopsis thaliana), 5'ss of exon 4
ACTGGAAACCAAATGGTGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtac-----aagaggaaatatt---tttgaaggttttcgggccagca-ttcttgctcaaagttttgca-atcttattgtttcag
| ||| || ||||||||||||||||| |||||||||||| | || ||||  || ||||| || ||||||      |||| |   | ||   | |   | ||| |   |  |||  ||||| || |||| |  || |   ||   ||  ||
AATGGTAAACAAATGGTGCAAGAAGGAGCTTTAACTGCTCTTGCTTCAGTGGCTGATTCATCACAGgtatttgtaaagaagttgtgttgcatctattgttttccctacatgcaactcttgatctaagtctaacataatctaaatttgtag

upper sequence: LOC_Os03g49420.2 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv06s0004g00500.t01 (Vitis vinifera), 5'ss of exon 4
ACTGGAAACCAAATGGTGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagaggaaatatttttgaaggttttcgggccagcattcttgctcaaagttttgcaatcttattgtttcag----------
| |||||| |||||||||||||| || || || ||||||||||| || | ||| ||||| |||||||||  |      |||||||  ||  |  |      |   || |  || | |  |  |||  || |   |||             
AATGGAAAACAAATGGTGCAAGAGGGGGCCTTGACTGCTTTAGCGTCTGTTGCTGATTCATCTCAGgtattat-----atattttaaaatatgcttccattatggtttt--cttataaatgagcagcctaacacttttgagtatcaatag

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|29679231|gb|CB675506.1|CB675506
EST:     TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAC                         GAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA
genomic: TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagagg ... attgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA
EST: gi|571970|gb|D41481.1|D41481
EST:     TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAG                         GA-CACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA
genomic: TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagagg ... attgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA
EST: gi|569698|gb|D40547.1|D40547
EST:     TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAG                         GAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA
genomic: TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagagg ... attgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA
EST: gi|29629840|gb|CB634849.1|CB634849
EST:     TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAG                         GAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA
genomic: TGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagagg ... attgtttcagGAACACTTCCAAAAATATTATGATGCAGTCATGCCATATCTCAAGTCTATA

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
ACTGGAAACCAAATGGTGCAAGAAGGTGCTTTAACTGCTTTAGCATCAGCTGCAGATTCTTCTCAGgtacaagaggaaatatttttgaaggttttcgggccagcattcttgctcaaagttttgcaatcttattgtttcag

- - - - - - - -  GCAAGA
- - - - - - - - -  AAGAAG
- - - - - - - - - - - - - - - - - - - - - -  TCAGCT
- - - - - - - - - - - - - - - - - - - - - - - CAGCTG
- - - - - - - - - - - - - - - - - - - - - - -  AGCTGC
- - - - - - - - - - - - - - - - - - - - - - - -  CTGCAG
- - - - - - - - - - - - - - - - - - - - - - - - -  GCAGAT