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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATCCGACGCGTGCGGCGGTGCGACGCCGGCCGGGGTGGGGGACGCCATGAGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGCgtacgccgcgcgctccgccgtgctccgagacctagcggctgcttctgctttgcttccgagtccctaactttcctccctgttgtttggcttcgcag

Basic information

species Oryza sativa
transcript LOC_Os01g54020.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g54020.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G177970_T02 (Zea mays), 5'ss of exon 1
AATCCGACGCGTGCGGCGGTGCGACGCCGGCCGGGGTGGGGGACGCCATGAGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGCgtacgccgcgcgctccgccgtgctccgagacctagcggctg------cttctgctttgcttccgagtccctaactt-----tcctccctgttgtttggcttcgcag
   | | |   | ||  || |   ||  |  |||||     ||||||||||||||| |||||||||||||| |||||||||| |||||||  || | ||   ||   |  ||   |||  |||||  |  | |||| |||       ||| |   | ||    ||  |   | |||     |   ||| |  |||||||  || ||
--GCAGCCAAATCCGAAGG-GTAGCGTAGCACGGGG---ACGACGCCATGAGCCGCGCGCTCCTCTCCCACGTCCTCCACCGTCCGCCGC-ACTTCGCGTACACCTGgtacggcacgctctgctc-aaaccttagccgcttatatatctttttactcgccgttgacgctgcatcttctgtttttcccccgccgtttggcgacgtag
















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|58604739|gb|CK015267.1|CK015267
EST:     AGCCGCACGCTCCTCTCCCACATTCTCCACCGCCCGCCGC-GCTCCTCGC                         GTCGAGGGGTGGTGGG
genomic: AGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGCgtacgccgcg ... ggcttcgcagGTCGAGGGGTGGTGGG
EST: gi|88341213|gb|CI639970.1|CI639970
EST:     AGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGC                         GTCGAGGGGTGGTGGGCGAGGAGGAGCGCTCCCGTCCCGCCTCCGCACTCT
genomic: AGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGCgtacgccgcg ... ggcttcgcagGTCGAGGGGTGGTGGGCGAGGAGGAGCGCTCCCGTCCCGCCTCCGCACTCT
EST: gi|88341927|gb|CI644264.1|CI644264
EST:     AGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGC                         GTCGAGGGGTGGTGGGCGAGGAGGAGCGCTCCCGTCCCGCCTCCGCACTCT
genomic: AGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGCgtacgccgcg ... ggcttcgcagGTCGAGGGGTGGTGGGCGAGGAGGAGCGCTCCCGTCCCGCCTCCGCACTCT
EST: gi|88407431|gb|CI586272.1|CI586272
EST:     AGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGC                         GTCGAGGGGTGGTGGGCGAGGAGGAGCGCTCCCGTCCCGCCTCCGCACTCT
genomic: AGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGCgtacgccgcg ... ggcttcgcagGTCGAGGGGTGGTGGGCGAGGAGGAGCGCTCCCGTCCCGCCTCCGCACTCT
EST: gi|88335142|gb|CI658149.1|CI658149
EST:     AGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGC                         GTCGAGGGGTGGTGGGCGAGGAGGAGCGCTCCCGTCCCGCCTCCGCACTCT
genomic: AGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGCgtacgccgcg ... ggcttcgcagGTCGAGGGGTGGTGGGCGAGGAGGAGCGCTCCCGTCCCGCCTCCGCACTCT
EST: gi|44667170|gb|CR280604.1|CR280604
EST:     AGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGC                         GTCGAGGGGTGGTGGGCGAGGAGGAGCGCTCCTGTCCCGCCTCCGCACTCT
genomic: AGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGCgtacgccgcg ... ggcttcgcagGTCGAGGGGTGGTGGGCGAGGAGGAGCGCTCCCGTCCCGCCTCCGCACTCT
EST: gi|88365129|gb|CI616548.1|CI616548
EST:     AGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGC                         GTCGAGGGGTGGTGGGCGAGGAGGAGCGCTCCCGTCCCGCCTCCGCACTCT
genomic: AGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGCgtacgccgcg ... ggcttcgcagGTCGAGGGGTGGTGGGCGAGGAGGAGCGCTCCCGTCCCGCCTCCGCACTCT

RNA-Seq data


 ATGC   Supported by RNA-Seq exonic block that spans over the splice site

 atgs   Truncated intron sequence

Each block is as long as the maximal overhang of any read spanning the junction.
The score is the number of alignments spanning the junction.


Found data for 1 RNA-Seqlibrary.


Block sizes: 47 (upstream exon), 71 (downstream exon)
Score: 9

AATCCGACGCGTGCGGCGGTGCGACGCCGGCCGGGGTGGGGGACGCCATGAGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGCgtacgccgcg ... ggcttcgcagGTCGAGGGGTGGTGGGCGAGGAGGAGCGCTCCCGTCCCGCCTCCGCACTCTCCGACTCAACTGCAGCGTGGCTGAAGCGACTGCCTCCGGCGACGAGGCG




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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 
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------| 
AATCCGACGCGTGCGGCGGTGCGACGCCGGCCGGGGTGGGGGACGCCATGAGCCGCACGCTCCTCTCCCACATCCTCCACCGCCCGCCGCCGCTCCTCGCgtacgccgcgcgctccgccgtgctccgagacctagcggctgcttctgctttgcttccgagtccctaactttcctccctgttgtttggcttcgcag

- - - - - - - - - - - - - - - - - - - - - - - - - - - - -  CTCCTC
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CTCCTC