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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGTCGGTGGCCTCCTCGGCTTCGGCGTCGGCCTCCCCCTCGGCATCGCCGTCGCCTACCTCGTCTACCTCCGCTTGTTCGCCCCTCGCCGCCGTCTCCAGgtcagtccatccatcgcctccttccttctcgatccttcccgtcctgtactaatcctagcaatttagtggttagttgaacgcattcatcgttagcaattcg...

Basic information

species Oryza sativa
transcript LOC_Os06g47130.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g47130.2 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G140443_T02 (Zea mays), 5'ss of exon 1
CGTCGGTGGCCTCCTCGGCTTCGGCGTCGGCCTCCCCCTCGGCATCGCCGTCGCCTACCTCGTCTACCTCCGCTTGTTCGCCCCTCGCCGCCGTCTCCAGgtcagtccatccat-cgcctc------cttccttctcgatccttcccgtcctgtactaatcctagcaatttagtggttagttgaacgcattcatcgttagcaattcg
|||||| ||  || |||||||| || ||||||||||| ||||| |||||| ||| ||| |||||||||||||||  |||||| |    ||||| ||||||||  || |   |   |||| |      |     | ||    || |  |    |   | |      |  |    || |  | |     || | |||| | |       
CGTCGGCGGTGTCGTCGGCTTCTGCCTCGGCCTCCCCATCGGCCTCGCCGCCGCGTACTTCGTCTACCTCCGCTACTTCGCCGCCGCTCGCCGCCTCCAGgtacgtacgcgcgcgcgccgcgcgcagcacttgtttctgaactgctagctgggagttgaattccccgctacgttgctgcgctagttccaataatcgatgg-------
















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|29661300|gb|CB657575.1|CB657575
EST:     TCGCCTACCTCGTCTACCTCCGCTTGTTCGCCCCTCGCCGCCGTCTCCAG                         GATCCTATTATTAGACCACTACGCGACTTGGATTCTGAGACATTACAGACA
genomic: TCGCCTACCTCGTCTACCTCCGCTTGTTCGCCCCTCGCCGCCGTCTCCAGgtcagtccat ... acttttgcagGATCCTATTATTAGACCACTACGCGACTTGGATTCTGAGACATTACAGACA
EST: gi|117246883|gb|CT843715.1|CT843715
EST:     TCGCCTACCTCGTCTACCTCCGCTTGTTCGCCCCTCGCCGCCGTCTCCAG                         GATCCTATTATTAGACCACTACGTGACTTGGATTCTGAGACATTACAGACA
genomic: TCGCCTACCTCGTCTACCTCCGCTTGTTCGCCCCTCGCCGCCGTCTCCAGgtcagtccat ... acttttgcagGATCCTATTATTAGACCACTACGCGACTTGGATTCTGAGACATTACAGACA
EST: gi|88580938|gb|CI697901.1|CI697901
EST:     TCGCCTACCTCGTCTACCTCCGCTTGTTCGCCCCTCGCCGCCGTCTCCAG                         GATCCTATTATTAGACCACTACGCGA
genomic: TCGCCTACCTCGTCTACCTCCGCTTGTTCGCCCCTCGCCGCCGTCTCCAGgtcagtccat ... acttttgcagGATCCTATTATTAGACCACTACGCGA
EST: gi|88340084|gb|CI650531.1|CI650531
EST:     TCGCCTACCTCGTCTACCTCCGCTTGTTCGCCCCTCGCCGCCGTCTCCAG                         GATCCTATTATTAGACCACTA
genomic: TCGCCTACCTCGTCTACCTCCGCTTGTTCGCCCCTCGCCGCCGTCTCCAGgtcagtccat ... acttttgcagGATCCTATTATTAGACCACTA
EST: gi|88307559|gb|CI643407.1|CI643407
EST:     TCGCCTACCTCGTCTACCTCCGCTTGTTCGCCCCTCGCCGCCGTCTCCAG                         GATCCTATTATTAGACCACTACGCGACTTGG
genomic: TCGCCTACCTCGTCTACCTCCGCTTGTTCGCCCCTCGCCGCCGTCTCCAGgtcagtccat ... acttttgcagGATCCTATTATTAGACCACTACGCGACTTGG

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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
CGTCGGTGGCCTCCTCGGCTTCGGCGTCGGCCTCCCCCTCGGCATCGCCGTCGCCTACCTCGTCTACCTCCGCTTGTTCGCCCCTCGCCGCCGTCTCCAGgtcagtccatccatcgcctccttccttctcgatccttcccgtcctgtactaatcctagcaatttagtggttagttgaacgcattcatcgttagcaattcg

- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - cgcctcc
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - -cccgtcc