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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CAAGACCATTACAGTATACAGATGTGGTCCTCTAGTTGACCTTTGCCGTGGGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAGgtaattctttggttgtcttaagcttttgcttgccaatatttttatggaactatccaatttgtacttgcatgtaaatatgtag

Basic information

species Oryza sativa
transcript LOC_Os08g19850.1
intron # 6
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os08g19850.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G439885_T01 (Zea mays), 5'ss of exon 4
CAAGACCATTACAGTATACAGATGTGGTCCTCTAGTTGACCTTTGCCGTGGGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAGgtaat---tctttggttgtcttaagcttttgcttgccaatatttttatggaactatccaatttgtacttg-----catgtaaatatgtag
||||| |||||| |||||||| ||||||||| |||||||||| |||||||||||||||||||| |||||||||||||| |||||||| |||||||| ||||||||   |||||| |||||  |   |  | || |      ||||  |||||||  | | ||  ||  |      |||||||||||  ||
CAAGAGCATTACTGTATACAGGTGTGGTCCTTTAGTTGACCTATGCCGTGGGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattctttgattgtcc-actatccttctggttctctttttagtggaactgactatttcatatgtataatacatgtaaatattcag

upper sequence: LOC_Os08g19850.1 (Oryza sativa), 5'ss of exon 6
lower sequence: GRMZM2G553314_T01 (Zea mays), 5'ss of exon 6
CAAGACCATTACAGTATACAGATGTGGTCCTCTAGTTGACCTTTGCCGTGGGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAGgtaat---tctttggttgtcttaagcttttgcttgccaatatttttatggaactatccaatt------tgtacttgcatgtaaatatgtag
|||||||||||| |||||||| ||||||||| |||||||||| |||||||||||||||||||| |||||||||||||| |||||||| |||||||| ||||||||   |||||| |||||  |   || | || |      ||||  |||||||  | | ||      | ||| | |||||||||||  ||
CAAGACCATTACTGTATACAGGTGTGGTCCTTTAGTTGACCTATGCCGTGGGCCACACATCCCAAATACTTCCTTTGTCAAAGCTTTCGCTTGTCTGAAGgtaatgattctttgattgtcc-actattcttctggttctctttttagtggaactggctatttcatatgtatacatacatgtaaatattcag

upper sequence: LOC_Os08g19850.1 (Oryza sativa), 5'ss of exon 6
lower sequence: Vv01s0026g00340.t01 (Vitis vinifera), 5'ss of exon 6
CAAGACCATTACAGTATACAGATGTGGTCCTCTAGTTGACCTTTGCCGTGGGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAGgtaattctttggttgtcttaagcttttgcttgccaatatttttatggaactatccaat-ttgtacttgcatgta---aatatgtag
||| || || ||||||||||||||||| ||  | ||||| || ||||||||||| || || || ||||| || ||||||||||| ||||| ||| | |||||  |  |  |  |||  |  |   ||| || |   | |  ||    | ||||    | || |||||    ||    ||| |  ||
CAAAACTATCACAGTATACAGATGTGGGCCATTGGTTGATCTGTGCCGTGGGCCCCATATACCAAATACATCTTTTGTTAAAGCATTTGCCTGTTTGAAGgtt-tgttgcgtatgtagttgggagttgatttcatttgtgcttgcaaatctattttctgttttacttaggcgtctgtaatttccag

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|29622568|gb|CB627579.1|CB627579
EST:     GGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAG                         GCATCATCGTCGTATTGGAGAGGGAAAGCAGATCGAGAGAGCCTGCAGAGA
genomic: GGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAGgtaattcttt ... aaatatgtagGCATCATCGTCGTATTGGAGAGGGAAAGCAGATCGAGAGAGCCTGCAGAGA
EST: gi|58666316|gb|CK055002.1|CK055002
EST:     GGCCACACATCCCCAATACTTCCTTTGTTAAAGC--TTGCTTGTCTTAAG                         GCATCATCGTCGTATTGGAGAGGGAAAGCAGATCGAGAGAGCCTGCAGAGA
genomic: GGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAGgtaattcttt ... aaatatgtagGCATCATCGTCGTATTGGAGAGGGAAAGCAGATCGAGAGAGCCTGCAGAGA
EST: gi|426182|gb|D22042.1|D22042
EST:     GGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAG                         GCATCATCGTCGTATTGGAGAGGGAAAGCAGATCGAGAGAGCCTGCAGAGA
genomic: GGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAGgtaattcttt ... aaatatgtagGCATCATCGTCGTATTGGAGAGGGAAAGCAGATCGAGAGAGCCTGCAGAGA
EST: gi|58689159|gb|CK077846.1|CK077846
EST:     GGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAG                         GCATCATCGTCGTATTGGAGAGGGAAAGCAGATCGAGAGAGCCTGCAGAGA
genomic: GGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAGgtaattcttt ... aaatatgtagGCATCATCGTCGTATTGGAGAGGGAAAGCAGATCGAGAGAGCCTGCAGAGA
EST: gi|58688358|gb|CK077045.1|CK077045
EST:     GGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAG                         GCATCATCGTCGTATTGGAGAGGGAAAGCAGATCGAGAGAGCCTGCAGAGA
genomic: GGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAGgtaattcttt ... aaatatgtagGCATCATCGTCGTATTGGAGAGGGAAAGCAGATCGAGAGAGCCTGCAGAGA
EST: gi|29686166|gb|CB682441.1|CB682441
EST:     GGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAG                         GCATCATCGTCGTATTGGAGAGGGAAAGCAGATCGAGAGAGCCTGCAGAGA
genomic: GGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAGgtaattcttt ... aaatatgtagGCATCATCGTCGTATTGGAGAGGGAAAGCAGATCGAGAGAGCCTGCAGAGA

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), 74 (downstream exon)
Score: 46

CAAGACCATTACAGTATACAGATGTGGTCCTCTAGTTGACCTTTGCCGTGGGCCACACATCCCCAATACTTCCTTTGTTAAAGCTTTTGCTTGTCTTAAGgtaattcttt ... aaatatgtagGCATCATCGTCGTATTGGAGAGGGAAAGCAGATCGAGAGAGCCTGCAGAGAGTATATGGAATTTCTTTTCCTGATTCTAAACGTCTCAAG




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