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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcatgctgctgtaccgttacttttttttattataaagcctcaaaaacaatggctatttatctttgtcgctgaatgtcagctcgctagaatattg...

Basic information

species Oryza sativa
transcript LOC_Os02g15550.2
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g15550.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G120578_T02 (Zea mays), 5'ss of exon 7
CTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcatgctgctgtaccgttacttttttttattataaagcctcaaaaacaat-ggctatttatctttgtcgctgaatgtcagctc--gctagaatattg
||||||||||||| || ||||||||||||||||||||||||||||| ||||| |||||||| ||||| || |||||||| |||||||   ||  |    ||| ||    | |  |||    |||   |  ||||||  |            |||  |  |   ||||     |  
CTGTGGAGTTCTTGAGAAATGCTCCTGAAGGGACATATGATGCTATCATTGTTGATTCATCTGACCCAATAGgtgagcttatgctgcaacac-atagtatttcttgggaacattgccatggaaatttttagctattcttgggaacattgccatgcaaattttagctatgtctt--

upper sequence: LOC_Os02g15550.1 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G060896_T02 (Zea mays), 5'ss of exon 8
CTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcatgctgctgtaccgttacttttttttattataaagcctcaaaaacaatg-gctatttatctttgtcgctgaatgtcagctcgctagaatattg---
||||||||||||| || ||||||||||||||||||||||||||||| ||||| ||||| ||||| || || |||||||| |||||||  |    ||   ||| || |  | |   ||    |||   |  |||||   ||||||| | || || |||| ||  |  | | | |   
CTGTGGAGTTCTTGAGAAATGCTCCTGAAGGGACATATGATGCTATCATTGTTGATTCGTCAGATCCAATAGgtgagcttatgctgccatgg-attgtctttcttgaacacagtaccatggaaaggctttgctat--gtctttgttg-tgtatatcagttctgtgcattttggttt

upper sequence: LOC_Os02g15550.1 (Oryza sativa), 5'ss of exon 8
lower sequence: Vv16s0050g02670.t01 (Vitis vinifera), 5'ss of exon 8
CTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcatgctgctgtaccgttacttttt-tttattataaagcctcaaaaacaatggctatttatctt-tgtcgctgaatgtcagctcg-ctagaatattg--
|||| || ||  | ||  |||  ||||||||||  |||||||| |||||||| ||||||||||| ||  | |||  |  | |  |||  ||   || || ||| ||| ||   |||            ||| | | |||  | ||||  |||          |  | |||||     
CTGTTGAATTTCTTAGACATGTACCTGAAGGGAAGTATGATGCAATTATTGTTGATTCATCAGATCCTGTGGgtatgtcctt--tgccataatttttctatttatttcttgggaagtt---gggtgtgtgggtgtgtatagtgtgtccatgagcagggttggggttggaataaaaac

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|29664251|gb|CB660526.1|CB660526
EST:     ATTCATCAGACCCGATTG                         GGCCTGCCCAGGAAC-TGTGGGAGAAGCCATTTTTTGACACAATCGCAAGA
genomic: ATTCATCAGACCCGATTGgtgagctcat ... tctgttgcagGGCCTGCCCAGGAACTTGT-GGAGAAGCCATTTTTTGACACAATCGCAAGA
EST: gi|58695758|gb|CK084445.1|CK084445
EST:     TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG                         GGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
genomic: TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcat ... tctgttgcagGGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
EST: gi|218497953|gb|FG959345.1|FG959345
EST:     TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG                         GGCCTGCCCAGGAACTTGTGGAGAAGCCATTTGTTGACACAATCGCAAGAG
genomic: TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcat ... tctgttgcagGGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
EST: gi|29667241|gb|CB663516.1|CB663516
EST:     ACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG                         GGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
genomic: ACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcat ... tctgttgcagGGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
EST: gi|58695993|gb|CK084680.1|CK084680
EST:     TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG                         GGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
genomic: TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcat ... tctgttgcagGGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
EST: gi|33793719|gb|CF322742.1|CF322742
EST:     TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG                         GGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
genomic: TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcat ... tctgttgcagGGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
EST: gi|84117386|gb|CD151153.1|CD151153
EST:     TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG                         GGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
genomic: TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcat ... tctgttgcagGGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
EST: gi|38471600|gb|CF955731.1|CF955731
EST:     TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG                         GGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
genomic: TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcat ... tctgttgcagGGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
EST: gi|29657801|gb|CB654076.1|CB654076
EST:     CATCAGACCCGATTG                         GGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
genomic: CATCAGACCCGATTGgtgagctcat ... tctgttgcagGGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
EST: gi|58678117|gb|CK066804.1|CK066804
EST:     TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG                         GGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
genomic: TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcat ... tctgttgcagGGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
EST: gi|29619281|gb|CB624293.1|CB624293
EST:     TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG                         GGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
genomic: TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcat ... tctgttgcagGGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
EST: gi|33794317|gb|CF323046.1|CF323046
EST:     TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG                         GGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
genomic: TCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcat ... tctgttgcagGGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG
EST: gi|29672899|gb|CB669174.1|CB669174
EST:     ACATATGATGCTATTATTGTCGATTCATCAGACCCGATTG                         GGCCTGCCCAGGAACTTGTGGAGAAGCCA-TTTTTGACACAATCGCAAGAG
genomic: ACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcat ... tctgttgcagGGCCTGCCCAGGAACTTGTGGAGAAGCCATTTTTTGACACAATCGCAAGAG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CTGTGGAGTTCTTAAGGAATGCTCCTGAAGGGACATATGATGCTATTATTGTCGATTCATCAGACCCGATTGgtgagctcatgctgctgtaccgttacttttttttattataaagcctcaaaaacaatggctatttatctttgtcgctgaatgtcagctcgctagaatattg

- - - - - - - - - - - - CTGAAG