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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAGAAACTCAACAGTACCACAAGAAGGCTATGGAACAGCAAGTGTCATACCTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAGgtgacctgtctcatggttgtctgttgcacacgcataccacagcatatttaccaagttattcatggagatatctatgtactttctgcag

Basic information

species Oryza sativa
transcript LOC_Os08g22864.1
intron # 13
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g22864.1 (Oryza sativa), 5'ss of exon 13
lower sequence: GRMZM2G327394_T01 (Zea mays), 5'ss of exon 13
AAGAAACTCAACAGTACCACAAGAAGGCTATGGAACAGCAAGTGTCATACCTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAGgtgacctgtctcatggttgtctgttgcacacgcataccacagcatatttaccaagttattcatggagatatctatgtactttctgcag
|||||| || |  || || |||||||| |||||||||||||||||||||||||||||||| |||||||| || || || |||||||||||||| |||||||||||||||||  | ||||||||||  | | |  |  ||||  |   |||  | ||| ||||||| ||| |        ||| |||||
AAGAAATTCCAATGTGCCTCAAGAAGGGTATGGAACAGCAAGTGTCATACCTGACCAAGGAATTTTCCTAGCCGCGTCTGTTTACCGTCCTGTTTTTGAGgtgacctgtcttgtagttgtctgttttatatgtgtctcacactaccattattatgttgttcatggggattt--------tttttgcag
















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|58669478|gb|CK058164.1|CK058164
EST:     CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAG                         TTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG
genomic: CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAGgtgacctgtc ... ctttctgcagTTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG
EST: gi|58691060|gb|CK079747.1|CK079747
EST:     CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAG                         TTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG
genomic: CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAGgtgacctgtc ... ctttctgcagTTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG
EST: gi|58677228|gb|CK065915.1|CK065915
EST:     CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAG                         TTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG
genomic: CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAGgtgacctgtc ... ctttctgcagTTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG
EST: gi|58654931|gb|CK043611.1|CK043611
EST:     CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAG                         TTTATGAATAAAATTGGACTGATGCTTCCGCGAGAAATATTGGCAACTTGG
genomic: CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAGgtgacctgtc ... ctttctgcagTTTATGAATAAAATTGGACTGATGCTTCCGC-AGAAATATTGGCAACTTGG
EST: gi|29665535|gb|CB661810.1|CB661810
EST:     CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAG                         TTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG
genomic: CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAGgtgacctgtc ... ctttctgcagTTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG
EST: gi|218502076|gb|FG960994.1|FG960994
EST:     CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAG                         TTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG
genomic: CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAGgtgacctgtc ... ctttctgcagTTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG
EST: gi|33678899|gb|CF307138.1|CF307138
EST:     CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAG                         TTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAAC
genomic: CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAGgtgacctgtc ... ctttctgcagTTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAAC
EST: gi|58610277|gb|CK038129.1|CK038129
EST:     CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAG                         TTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG
genomic: CTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAGgtgacctgtc ... ctttctgcagTTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG
EST: gi|58672488|gb|CK061174.1|CK061174
EST:     CAGTTTACCGTCCTGTATTTGAG                         TTTATGAATAAAA-TGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG
genomic: CAGTTTACCGTCCTGTATTTGAGgtgacctgtc ... ctttctgcagTTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG

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: 50 (upstream exon), 73 (downstream exon)
Score: 55

AAGAAACTCAACAGTACCACAAGAAGGCTATGGAACAGCAAGTGTCATACCTGACCAAGGGATTTTCCTTGCAGCATCAGTTTACCGTCCTGTATTTGAGgtgacctgtc ... ctttctgcagTTTATGAATAAAATTGGACTGATGCTTCCGCAGAAATATTGGCAACTTGG




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