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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtcatttatcttgtttgacatgtttacatgctatggattatcttgtatagcctgctatggcttattttgtatcacctgcctaatctttgtgctggtatcatgttatagCCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATTCAGGAGAACCATGATGAGTTCCTTCAGTTAATAAATGAGCCCTTTGATG

Basic information

species Oryza sativa
transcript LOC_Os02g08300.1
intron # 9
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g08300.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G143462_T06 (Zea mays), 3'ss of exon 9
gtcatttatcttgtttgacatgtttacatgctatggattatcttgtatagcctgctatggcttattttgtatcacctgcctaatctttgtgctggtatcatgttatagCCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATTCAGGAGAACCATGATGAGTTCCTTCAGTTAATAAATGAGCCCTTTGATG
                            |  |||   || | |||  |  | | ||||||||| || |||| ||||||||| | |||| |||||||| |||||||||||||||||||   ||  |||||||| ||||||||||| |||| ||||||||| ||||||| ||||||||||| ||||||||| |||||||||||||||| |
-------------------------gttttgtattctttgttttggcttacattctatggcttcttatgtagcacctgcctgaactttttgctggtaccatgttatagCCTATGCTCGTTGAGTTGAGCAAGCAGAATCCTCAAATTCTAAGGTTGATTGAGGAGAATCATGATGAGTTTCTTCAGTTACTAAATGAGCCCTTTGAAG

upper sequence: LOC_Os02g08300.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G79650.3 (Arabidopsis thaliana), 3'ss of exon 8
gtcatttatcttgtttgacatgtttacatgctatggattatcttgtatagcctgctatggcttattttgtatcacctgcctaatctttgtgctggta-tcatgttat-agCCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATTCAGGAGAACCATGATGAGTTCCTTCAGTTAATAAATGAGCCCTTTGATG----------
         || ||||     |||  | || |   |  ||  |||||   | |   |   || |||  | | |      || || || |  |   |  |  |||||  |||| ||||| ||||||||  | ||| | || ||||||||||||||| | ||||| || ||||| |  ||||| ||||||||| |||||||||||| ||| |          
---------ctagttt---tcgttatcctggtccag--tagtttgtaagacttctca---ctgattccgaacc-----tcttatgttggaacaactgcttttgttaccagcccatgcttcagGAACTTGGAAAGCAAAACCCTCAACTTCTGAGGCTAATTCAAGAAAACCAGGCAGAGTTTCTTCAGTTAGTAAATGAGCCCTATGAGGGTTCTGACGG

upper sequence: LOC_Os02g08300.1 (Oryza sativa), 3'ss of exon 9
lower sequence: AT1G79650.1 (Arabidopsis thaliana), 3'ss of exon 9
--gtcatttatcttgtttgacatgtttacatgctatggattatcttgtatagcctgctatggcttattttgtatcacctgcctaatctttgtgctggta-tcatgttat-agCCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATTCAGGAGAACCATGATGAGTTCCTTCAGTTAATAAATGAGCCCTTTGATG
     | |  ||| ||||     |||  | || |   |  ||  |||||   | |   |   || |||  | | |      || || || |  |   |  |  |||||  |||| ||||| ||||||||  | ||| | || ||||||||||||||| | ||||| || ||||| |  ||||| ||||||||| |||||||||||| ||| |
gtaagactcgtctagttt---tcgttatcctggtccag--tagtttgtaagacttctca---ctgattccgaacc-----tcttatgttggaacaactgcttttgttaccagCCCATGCTTCAGGAACTTGGAAAGCAAAACCCTCAACTTCTGAGGCTAATTCAAGAAAACCAGGCAGAGTTTCTTCAGTTAGTAAATGAGCCCTATGAGG

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|88976735|gb|CI257507.1|CI257507
EST:     TTTCAGGCGCTTCGGGAAATGGTTCATACTAACCCACAAATATTGCAG                         CCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATT
genomic: TTTCAGGCGCTTCGGGAAATGGTTCATACTAACCCACAAATATTGCAGgtcatttatc ... catgttatagCCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATT
EST: gi|66923978|gb|CX110826.1|CX110826
EST:     TTTCAGGCGCTTCGGGAAATGGTTCATACTAACCCACAAATATTGCAG                         CCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATT
genomic: TTTCAGGCGCTTCGGGAAATGGTTCATACTAACCCACAAATATTGCAGgtcatttatc ... catgttatagCCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATT
EST: gi|88980844|gb|CI022534.1|CI022534
EST:     GGGAAATGGTTCATACTAACCCACAAATATTGCAG                         CCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATT
genomic: GGGAAATGGTTCATACTAACCCACAAATATTGCAGgtcatttatc ... catgttatagCCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATT
EST: gi|58676620|gb|CK065307.1|CK065307
EST:     TTTCAGGCGCTTCGGGAAATGGTTCATACTAACCCACAAATATTGCAG                         CCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATT
genomic: TTTCAGGCGCTTCGGGAAATGGTTCATACTAACCCACAAATATTGCAGgtcatttatc ... catgttatagCCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATT
EST: gi|88966384|gb|CI119519.1|CI119519
EST:     ACCCACAAATATTGCAG                         CCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATT
genomic: ACCCACAAATATTGCAGgtcatttatc ... catgttatagCCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATT
EST: gi|88991630|gb|CI019808.1|CI019808
EST:     TCGGGAAATGGTTCATACTAACCCACAAATATTGCAG                         CCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATT
genomic: TCGGGAAATGGTTCATACTAACCCACAAATATTGCAGgtcatttatc ... catgttatagCCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATT


 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

gctatggcttattttgtatcacctgcctaatctttgtgctggtatcatgttatagCCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATTCAGGAGAACCATGATGAGTTCCTTCAGTTAATAAATGAGCCCTTTGATG
                        gcctaat  putative branch site (score: 3)
        ttattttgtat  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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
gtcatttatcttgtttgacatgtttacatgctatggattatcttgtatagcctgctatggcttattttgtatcacctgcctaatctttgtgctggtatcatgttatagCCTATGCTCCAGGAACTGAGCAAGAAGAATCCTCAACTTCTGAGGTTGATTCAGGAGAACCATGATGAGTTCCTTCAGTTAATAAATGAGCCCTTTGATG

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - AGGAGA
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -  GGAGAA