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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAATCATTGGGCTTGTATAAATTTCTCAAGGAGTGTGCAAGAAACTACTGCTCGGGGATTCTGCCAGGAGTTGGCACAAATGTGTCAGATATCCGGCATGgtatataactcttaacttcatctaatggttttgcataatattggtgcttttataatgttatttgttggctgcatcttttcagttttatctctgctcttcttgcag

Basic information

species Oryza sativa
transcript LOC_Os06g39640.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 11
lower sequence: AC189879.3_FGT003 (Zea mays), 5'ss of exon 10
GAATCATTGGGCTTGTATAAATTTCTCAAGGAGTGTGCAAGAAACTACTGCTCGGGGATTCTGCCAGGAGTTGGCACAAATGTGTCAGATATCCGGCATGgtatataactcttaacttcatctaatggttttgcataatattggtgctt-ttataatgttatttgttggctgcatcttttcagttttatctctgctcttcttgcag
||  || ||||| |||||||| |||||||||||||| | |||| | || ||||||||||| |||||||| ||||||||||||||||| || || |||||||||  || | ||   | ||  || ||| || |||| || |    | ||| ||  |||   |  |||  ||| |    ||| | ||| | |||      | || |||
GAGCCACTGGGCATGTATAAACTTCTCAAGGAGTGTTCCAGAAGCCACAGCTCGGGGATTTTGCCAGGAATTGGCACAAATGTGTCAAATTTCGGGCATGgtacgtacccct---cctctgctcatgtttgtgcacaagacaaatacttgtttcaattgaaactgtaagcttc----ttttaatttgacctcc-tgaatattacag

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G079080_T02 (Zea mays), 5'ss of exon 11
GAATCATTGGGCTTGTATAAATTTCTCAAGGAGTGTGCAAGAAACTACTGCTCGGGGATTCTGCCAGGAGTTGGCACAAATGTGTCAGATATCCGGCATGgtatataactcttaacttcatctaatggttttgcataatattggtgcttttataatgttatttgttggctgcatcttttcagttttatctctgctcttcttgcag
||  |||||||| |||||||| |||||||||||||| | |||||| || ||||||||||| |||||||| ||||||||||||||||| || || ||||||||||   ||   | |  |   || ||| || |||| || |      ||| | |||  | |     ||   ||||||||| |  |||  ||       | || |||
GAGCCATTGGGCATGTATAAACTTCTCAAGGAGTGTTCCAGAAACCACAGCTCGGGGATTTTGCCAGGAATTGGCACAAATGTGTCAAATTTCGGGCATGgtatgatacctctcatctgtgctcatgtttgtgcacaagacaaaaacttgtttaaattga--aactgtaagcatcttttaa--tttgacttcctaagtattacag

upper sequence: LOC_Os06g39640.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GLYMA17G12850.1 (Glycine max), 5'ss of exon 11
GAATCATTGGGCTTGTATAAATTTCTCAAGGAGTGTGCAAGAAACTACTGCTCGGGGATTCTGCCAGGAGTTGGCACAAATGTGTCAGATATCCGGCATGgtatataactcttaacttcatctaatggttttgcataatattggtgcttttataatgttatttgttggctgcatcttttcagtttt-atctctgctcttcttgcag
 |   ||||||||||||| ||||||||| | ||| | ||||||| ||||||||| || || |||||  |||| |  ||||| || || || || |||||||||   || | | || ||    | ||   |||    |  | |  |   ||    |     | | |   | |||      |||||   ||| ||  |||  |     
AAGATATTGGGCTTGTATTAATTTCTCACGAAGTATCCAAGAAAGTACTGCTCGCGGGTTTTGCCAACAGTTAGTTCAAATATGCCAAATCTCAGGCATGgta---aagtttcaaattttggttatacctttattaagaagttatatattagagacagcttgtttgaacagcactagcacagttcagatcacttttctaatca---

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|66920341|gb|CX107189.1|CX107189
EST:     CTCGGGGATTCTGCCAGGAGTTGGCACAAATGTGTCAGATATCCGGCATG                         GAATTCAACAGTGAGCCTGTGATACCAATATACTCAGCTAGACCAGATCAA
genomic: CTCGGGGATTCTGCCAGGAGTTGGCACAAATGTGTCAGATATCCGGCATGgtatataact ... cttcttgcagGAATTCAACAGTGAGCCTGTGATACCAATATACTCAGCTAGACCAGATCAA
EST: gi|58680597|gb|CK069284.1|CK069284
EST:     CTCGGGGATTCTGCCAGGAGTTGGCACAAATGTGTCAGATATCCGGCATG                         GAATTCAACAGTGAGCCTGTGATACCAATATACTCAGCTAGACCAGATCAA
genomic: CTCGGGGATTCTGCCAGGAGTTGGCACAAATGTGTCAGATATCCGGCATGgtatataact ... cttcttgcagGAATTCAACAGTGAGCCTGTGATACCAATATACTCAGCTAGACCAGATCAA

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: 61 (upstream exon), 57 (downstream exon)
Score: 14

GAATCATTGGGCTTGTATAAATTTCTCAAGGAGTGTGCAAGAAACTACTGCTCGGGGATTCTGCCAGGAGTTGGCACAAATGTGTCAGATATCCGGCATGgtatataact ... cttcttgcagGAATTCAACAGTGAGCCTGTGATACCAATATACTCAGCTAGACCAGATCAAGTAGAGAAGGCGCTTAAGCATGTGTATAATATGTCATTAAACAAGCTCA




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