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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AAAAGAGGTGAGGAAAATAGCCTCAGATTTGCTGTCCAATCCAGTCCAAGTTAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAGgtaatgaaaatggtgctttctttttgttgatcagactttgtttcgttattttgaagcagattgttatatgttgcag

Basic information

species Oryza sativa
transcript LOC_Os01g07740.3
intron # 8
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os01g07740.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G481227_T01 (Zea mays), 5'ss of exon 4
AAAAGAGGTGAGGAAAATAGCCTCAGATTTGCTGTCCAATCCAGTCCAAGTTAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAGgtaa-tgaaaatggtgctttctttttgttgatcagac--tttgtttcgttattttgaagcagattgttatatgttgcag
|| |||||| || |||||||| || ||||| ||| | || ||||| |||||||||||||| ||||||||||| |||||  | ||||||||||| |||||||| | | ||||||  | |||||||||    | |||||  ||||||||  || |||||||  | |||||| |   |||||
AAGAGAGGTTAGAAAAATAGCGTCTGATTTACTGGCTAACCCAGTTCAAGTTAACATTGGAAACACTGATCAGCTGGTCACAAATAAGTCAATTACTCAGgtgagtaaaaatgtcgttttcttttttcaaaccagacactttgtttctgtaatttgaagtggtttgttacacactgcag

upper sequence: LOC_Os01g07740.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G462134_T01 (Zea mays), 5'ss of exon 4
AAAAGAGGTGAGGAAAATAGCCTCAGATTTGCTGTCCAATCCAGTCCAAGTTAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAGgtaa-tgaaaatggtgctttctttttgttgatcagac--tttgtttcgttattttgaagcagattgttatatgttgcag
|| |||||| || |||||||| || ||||| ||| | || ||||| |||||||||||||| ||||||||||| ||||| || ||||||||||| |||||||| | | ||||||  | |||||||||    | |||||  ||| ||||  || |||||||  | |||||| |   |||||
AAGAGAGGTTAGAAAAATAGCGTCTGATTTACTGGCTAACCCAGTTCAAGTTAACATTGGAAACACTGATCAGCTGGTCGCAAATAAGTCAATTACTCAGgtgagtaaaaatgtcgttttcttttttcaaaccagacactttatttctgtaatttgaagtggtttgttacacactgcag

upper sequence: LOC_Os01g07740.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G066440_T01 (Zea mays), 5'ss of exon 7
AAAAGAGGTGAGGAAAATAGCCTCAGATTTGCTGTCCAATCCAGTCCAAGTTAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAGgtaa-tgaaaatggtgctttctttttgttgatcagactttgtttcgttattttgaagcagattgttatatgttgcag
||||||||| || |||||||| || ||||| |||   || ||||| |||||||||||||| ||||||||||| |||||||| ||||| ||||| |||||||| | |  |||||    ||| ||||        | ||||||||||  || |||||||  | |||||  |   |||||
AAAAGAGGTTAGAAAAATAGCGTCGGATTTACTGAATAACCCAGTTCAAGTTAACATTGGAAACACTGATCAGCTGGTTGCAAATAAATCAATTACTCAGgtgagtagaaatg----tttattttcaaacccgatactttgtttctgtactttgaagtggtttgttgcacactgcag

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|218485434|gb|FG946451.1|FG946451
EST:     TTAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAG                         TATGTGGATGTTATCACACCTCCGGGAGAAATCGAGGCGGCTTGATCAAAT
genomic: TTAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAGgtaatgaaaa ... tatgttgcagTATGTGGATGTTATCACACCTCC-GGAGAAATCGAGGCGGCTTGATCAAAT
EST: gi|58594039|gb|CF992347.1|CF992347
EST:     TTAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAG                         TATGTGGATGTTATCACACCTCCGGAGAAATCGAGGC
genomic: TTAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAGgtaatgaaaa ... tatgttgcagTATGTGGATGTTATCACACCTCCGGAGAAATCGAGGC
EST: gi|58667068|gb|CK055754.1|CK055754
EST:     AAGTCAATCACTCAG                         TATGTGGATGTTATCACACCTCCGGAGAAATCGAGGCGGCTTGATCAAATC
genomic: AAGTCAATCACTCAGgtaatgaaaa ... tatgttgcagTATGTGGATGTTATCACACCTCCGGAGAAATCGAGGCGGCTTGATCAAATC
EST: gi|56550141|gb|CX056245.1|CX056245
EST:     TAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAG                         TATGTGGATGTTATCACACCTCCGGAGAAATCGAGGCGGCTTGATCAAATC
genomic: TAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAGgtaatgaaaa ... tatgttgcagTATGTGGATGTTATCACACCTCCGGAGAAATCGAGGCGGCTTGATCAAATC
EST: gi|218485214|gb|FG951281.1|FG951281
EST:     TTAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAG                         TATGTGGATGTTATCACACCTCCGGAGAAATCGAGGCGGCTTGATCAAATC
genomic: TTAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAGgtaatgaaaa ... tatgttgcagTATGTGGATGTTATCACACCTCCGGAGAAATCGAGGCGGCTTGATCAAATC
EST: gi|58660094|gb|CK048774.1|CK048774
EST:     TTAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAG                         TATGTGGATGTTATCACACCTCCGGAGAAATCGAGGCGGCTTGATCAAATC
genomic: TTAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAGgtaatgaaaa ... tatgttgcagTATGTGGATGTTATCACACCTCCGGAGAAATCGAGGCGGCTTGATCAAATC

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), 69 (downstream exon)
Score: 29

AAAAGAGGTGAGGAAAATAGCCTCAGATTTGCTGTCCAATCCAGTCCAAGTTAACATTGGGAACACTGATCAACTGGTTGCCAATAAGTCAATCACTCAGgtaatgaaaa ... tatgttgcagTATGTGGATGTTATCACACCTCCGGAGAAATCGAGGCGGCTTGATCAAATCCTAAGGTCACAGGAACCTGGATCGAAAATCATAATATTTTGCTCCACAA




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