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 5'  3'   		2  
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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGTGTCCATCGTGCGCCGCGGCATGGCGCAGGCAGTGCAGAAGGAGTCGCGCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAACgtaactacgcgaaatggatctcttgctcggccaatgtacttcgccttgttgagtttaatggccgcgtgcgtgtgtgcag

Basic information

species Oryza sativa
transcript LOC_Os01g10850.1
intron # 1
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g10850.1 (Oryza sativa), 5'ss of exon 1
lower sequence: GRMZM2G382379_T01 (Zea mays), 5'ss of exon 1
GGTGTCCATCGTGCGCCGCGGCATGGCGCAGGCAGTGCAGAAGGAGTCGCGCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAACgtaactacgcgaa-atggatctcttgctcggccaatgtacttcgccttgttgagtttaatggccgcgtgcgtgtgtgcag------------------------------------------------
|  | ||||||||||||||||| ||||||  || || | |  |||| |||||||||| || ||| |||||||||||||||||||||||||||||||||| ||||     ||     |      | |  ||| || |  ||||||| |        |   | |    ||  || ||||| |                                                
GCAGCCCATCGTGCGCCGCGGCGTGGCGCGCGCCGTCCGGGCGGAGCCGCGCATGGGGGCGTCCCTCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAATgtaagacgacgggcgcgagggagtggagcggtcact-cacttcgcttcacgcctgtcggtcggtcggtcggtttgtgctggtcctctcctgacgtgtgtccgtgcgtgtggatggatatggatcgcag
















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|88422208|gb|CI689010.1|CI689010
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAC                         GGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGGGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAACgtaactacgc ... gtgtgtgcagGGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGGGAG
EST: gi|88582851|gb|CI700294.1|CI700294
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAC                         GGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGGGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAACgtaactacgc ... gtgtgtgcagGGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGGGAG
EST: gi|88587698|gb|CI704410.1|CI704410
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAC                         GGGTGCGACGCCTCCATCTTGCTCGACGACACG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAACgtaactacgc ... gtgtgtgcagGGGTGCGACGCCTCCATCTTGCTCGACGACACG
EST: gi|33798839|gb|CF325276.1|CF325276
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAC                         GGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGGGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAACgtaactacgc ... gtgtgtgcagGGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGGGAG
EST: gi|88451948|gb|CI694728.1|CI694728
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAC                         GGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGGGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAACgtaactacgc ... gtgtgtgcagGGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGGGAG
EST: gi|33798888|gb|CF325301.1|CF325301
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAC                         GGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGGGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAACgtaactacgc ... gtgtgtgcagGGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGGGAG
EST: gi|88357585|gb|CI623639.1|CI623639
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAC                         GGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGGGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAACgtaactacgc ... gtgtgtgcagGGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGGGAG
EST: gi|88376757|gb|CI605379.1|CI605379
EST:     GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAAC                         GGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGNGAG
genomic: GCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAACgtaactacgc ... gtgtgtgcagGGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGGGAG

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: 75 (upstream exon), 75 (downstream exon)
Score: 29

GGTGTCCATCGTGCGCCGCGGCATGGCGCAGGCAGTGCAGAAGGAGTCGCGCATGGGCGCCTCCATCCTCCGCCTCTTCTTCCACGACTGCTTCGTCAACgtaactacgc ... gtgtgtgcagGGGTGCGACGCCTCCATCTTGCTCGACGACACGGCGAACTTCACCGGGGAGAAGAACGCCGGGCCGAACGCCAACTCGGTGCGCGGGTACGAGGTCATCG




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