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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaatacaagaataagaaatcgagcctactttagcgcgtctggcatgttgtactttcaacagtataacatgatactacactgcatgttgccttcttttaatttcctttgtctgcatttgtagTTACAAGCTTGTCGTGTCTACGCCGGAACCTAGAAAAGTGGCATCTCCGACCATTTCAAATATCCAG

Basic information

species Oryza sativa
transcript LOC_Os08g01180.1
intron # 3
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g01180.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G021784_T02 (Zea mays), 3'ss of exon 3
gtaatacaagaataagaaatcgagcctactttagcgcgtctggcatgtt-gtactttcaac---------agtataacatg------atactacactgc-------atgttgccttcttttaatttcctttgtctgcatttgtagTTACAAGCTTGTCGTGTCTACGCCGGAACCTAGAAAAGTGGCATCTCCGACCATTTCAAATATCCAG---------------------------------
|||||||    || |||||| | || || ||||    | |  || | || | ||||  | |         | || ||  ||       |   | |||||       ||| |   || || | || |  ||| | |  | | |||||||||| |||||||| ||  |  | || |||||||||||| ||||||| |||||||| |||||||||                                 
gtaatactc--atgagaaattgtgcatattttaaactggccagcctttttgcacttcgagccctaacccaactacaatgtgtggaaagtttgaaactgccagtctcatggttttttgttctgatattttttatttcaactcgtagTTACAAACTTGTCGTATCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCAACCATTTCTAATATCCAGGTAGCCTTTATTCTAAAATCAATTTACTGTCAA

upper sequence: LOC_Os08g01180.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G021784_T01 (Zea mays), 3'ss of exon 3
gtaatacaagaataagaaatcgagcctactttagcgcgtctggcatgtt-gtactttcaac---------agtataacatg------atactacactgc-------atgttgccttcttttaatttcctttgtctgcatttgtagTTACAAGCTTGTCGTGTCTACGCCGGAACCTAGAAAAGTGGCATCTCCGACCATTTCAAATATCCAG
|||||||    || |||||| | || || ||||    | |  || | || | ||||  | |         | || ||  ||       |   | |||||       ||| |   || || | || |  ||| | |  | | |||||||||| |||||||| ||  |  | || |||||||||||| ||||||| |||||||| |||||||||
gtaatactc--atgagaaattgtgcatattttaaactggccagcctttttgcacttcgagccctaacccaactacaatgtgtggaaagtttgaaactgccagtctcatggttttttgttctgatattttttatttcaactcgtagTTACAAACTTGTCGTATCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCAACCATTTCTAATATCCAG

upper sequence: LOC_Os08g01180.1 (Oryza sativa), 3'ss of exon 3
lower sequence: GRMZM2G451366_T02 (Zea mays), 3'ss of exon 3
gtaatacaagaataagaaatcgagcctactttagcgcgtctggcatgtt-gtactttcaac---------agtataacatg----atactacactgcatgt-----tgccttcttttaat-ttcctttgtctgcatttgtagTTACAAGCTTGTCGTGTCTACGCCGGAACCTAGAAAAGTGGCATCTCCGACCATTTCAAATATCCAG
|||||||    || |||||  | || || ||||    | |  || | || | ||||  | |         | || ||  ||    ||     ||||   ||     |   ||||| | || ||  ||||| |  | |||||||||||| ||||| |||||  |  | || |||||||||||| |||||||||||||||| |||||||||
gtaatactc--atgagaaaatgtgcatattttaaactggccagcctttttgcacttagagctctaacccaactacaatgtggaaaatttggaactgtcagtctcagtattttcttctgatatttttttgtttcaacttgtagTTACAAACTTGTGGTGTCCTCAGCAGAGCCTAGAAAAGTGTCATCTCCGACCATTTCTAATATCCAG

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|58603712|gb|CK014240.1|CK014240
EST:     ATACGTAAAATTGCCTCTTCAGGTCAGCCAGCCTCAGCAACAACAGGAGG                         TTACAAGCTTGTCGTGTCTACGCCGGAACCTAGAAAAGTGGCATCTCCGAC
genomic: ATACGTAAAATTGCCTCTTCAGGTCAGCCAGCCTCAGCAACAACAGGAGGgtaatacaag ... gcatttgtagTTACAAGCTTGTCGTGTCTACGCCGGAACCTAGAAAAGTGGCATCTCCGAC




















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: 68 (upstream exon), 74 (downstream exon)
Score: 47

CGGTCTACTTCGCTTTCCAGGATGACCACTTTGATAACCTGCTGGCGGATATACGTAAAATTGCCTCTTCAGGTCAGCCAGCCTCAGCAACAACAGGAGGgtaatacaag ... gcatttgtagTTACAAGCTTGTCGTGTCTACGCCGGAACCTAGAAAAGTGGCATCTCCGACCATTTCAAATATCCAG




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

catgatactacactgcatgttgccttcttttaatttcctttgtctgcatttgtagTTACAAGCTTGTCGTGTCTACGCCGGAACCTAGAAAAGTGGCATCTCCGACCATTTCAAATATCCAG
                           ttttaat  putative branch site (score: 47)
                                 tttcctttgtctgc  CT-rich tract
                           ttttaatttccttt  TA-rich tract