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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGGGGTTCAAGGCGGCGGGTATCTACGGCGGTCTGCGCGCCAAGGGCGAGAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggctatcaccaacactttctattcagttcactcgtagtagcagaagtttcttcagagttcagacttcagtttcacttctcgttaccatttctcag...

Basic information

species Oryza sativa
transcript LOC_Os03g17120.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g17120.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G044237_T01 (Zea mays), 5'ss of exon 2
AAGGGGTTCAAGGCGGCGGGTATCTACGGCGGTCTGCGCGCCAAGGGCGAGAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggctatcaccaacactttctattcagttcactcgtagtagcagaagtttcttcagagttcagacttcagtttcacttctcgttaccatttctcag
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AAGGGGTTCAAGGCGGCGGGTATCTACAGTGGGTTGCGTGCCAAAGGCGAGAAGCCTGACTTGGCACTGGTCGCCTGCGACGTCGACGCCACTGTAGCAGgtactccctccggtttcctattagttgtcgttttggataaggttcgagtcaaacttataaaattttggctacaaataactattttgttatttaattttag
















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|88412169|gb|CI573445.1|CI573445
EST:     GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGG                         GAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGTTTTGTA
genomic: GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggcta ... ttcttttcagGAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGTTTTGTA
EST: gi|86901578|gb|CI308559.1|CI308559
EST:     GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGG                         GAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGT
genomic: GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggcta ... ttcttttcagGAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGT
EST: gi|88433054|gb|CI569723.1|CI569723
EST:     GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGG                         GAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGTTTTGTACTGTAAGC
genomic: GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggcta ... ttcttttcagGAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGTTTTGTACTGTAAGC
EST: gi|88358225|gb|CI605150.1|CI605150
EST:     GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGG                         GAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGTTTTGTACTGTAAGC
genomic: GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggcta ... ttcttttcagGAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGTTTTGTACTGTAAGC
EST: gi|88720332|gb|CI743631.1|CI743631
EST:     AAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGCTCGCGG                         GAGCTTTTACTACGAATGTTGTTGNTGCTGCACCAGTTTTGTACTGTAAG
genomic: AAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTG-TCGCGGgtaaaggcta ... ttcttttcagGAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGTTTTGTACTGTAAG
EST: gi|88443537|gb|CI597004.1|CI597004
EST:     GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGG                         GAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGTTTTGTACTGTAAGC
genomic: GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggcta ... ttcttttcagGAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGTTTTGTACTGTAAGC
EST: gi|58662721|gb|CK051407.1|CK051407
EST:     GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGG                         GAGCTTTTACTACGAATGTTGTTGCTGCTGCACC
genomic: GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggcta ... ttcttttcagGAGCTTTTACTACGAATGTTGTTGCTGCTGCACC
EST: gi|88358912|gb|CI619416.1|CI619416
EST:     GAAGCCCGACCTTGCGCTGGTCGCCTGAGACGTCGACGCCACTGTCGCGG                         GAGCTTTTACTACGAATGTTGTTGCTG
genomic: GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggcta ... ttcttttcagGAGCTTTTACTACGAATGTTGTTGCTG
EST: gi|29613226|gb|CB618239.1|CB618239
EST:     GAAGCCCGACCTTGCGCTGGTCGCCTGCAACGTCGACGCCACTGTCGCGG                         GAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGTTTTGTACTGTAAGC
genomic: GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggcta ... ttcttttcagGAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGTTTTGTACTGTAAGC
EST: gi|88389112|gb|CI595346.1|CI595346
EST:     GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGG                         GAGCTTTTACTACGAATG
genomic: GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggcta ... ttcttttcagGAGCTTTTACTACGAATG
EST: gi|88392288|gb|CI612762.1|CI612762
EST:     GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGG                         GAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGTTTTGTACTGTAAGC
genomic: GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggcta ... ttcttttcagGAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGTTTTGTACTGTAAGC
EST: gi|88741107|gb|CI764615.1|CI764615
EST:     GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGG                         GAGCTTTNACTACGAAT
genomic: GAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggcta ... ttcttttcagGAGCTTTTACTACGAAT

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: 71 (upstream exon), 71 (downstream exon)
Score: 20

AAGGGGTTCAAGGCGGCGGGTATCTACGGCGGTCTGCGCGCCAAGGGCGAGAAGCCCGACCTTGCGCTGGTCGCCTGCGACGTCGACGCCACTGTCGCGGgtaaaggcta ... ttcttttcagGAGCTTTTACTACGAATGTTGTTGCTGCTGCACCAGTTTTGTACTGTAAGCGTGTCCTTAATTCATCAAAAACA




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