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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgtttccaatgtgcacatagcatggttattttttctaccaacttgtgactgtgacacgtataattataactatacctattctccgaaatctattg...

Basic information

species Oryza sativa
transcript LOC_Os02g52420.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g52420.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G101438_T02 (Zea mays), 5'ss of exon 9
GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgtttccaatg--tgcacatagcatggttattttttctaccaacttgtgactgtgacacgtataattataactatacct--attctccgaaatctattg
|||||||||||||||| |||||||  ||||| |||||||||||||||||||||  ||||||  |  ||| | |    |  | |  | |  |   || |  ||    |      |  |  | | | || |  |  |  ||  | || ||    
GAAACAATGAATGGGGACGTATGATGTTGAATCAAACATTTACTATAGgtacacctttccacagcttgcccgtgttctattaacctgtgattaaaattgctgctctttttctattgacctgtgattaaaatttcacactgtggaacct----

upper sequence: LOC_Os02g52420.2 (Oryza sativa), 5'ss of exon 9
lower sequence: GRMZM2G101438_T03 (Zea mays), 5'ss of exon 8
----------------------------------------------------GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgtttccaatg--tgcacatagcatggttattttttctaccaacttgtgactgtgacacgtataattataactatacct--attctccgaaatctattg
                                                    |||||||||||||||| |||||||  ||||| |||||||||||||||||||||  ||||||  |  ||| | |    |  | |  | |  |   || |  ||    |      |  |  | | | || |  |  |  ||  | || ||    
TCTGCACCATATTAGGATGTGATATCTGTGCCAATGACTTCGAAATTTGCAGGAAACAATGAATGGGGACGTATGATGTTGAATCAAACATTTACTATAGgtacacctttccacagcttgcccgtgttctattaacctgtgattaaaattgctgctctttttctattgacctgtgattaaaatttcacactgtggaacct----
















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|88663432|gb|CI482070.1|CI482070
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG                         AGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttttattagAGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
EST: gi|88662360|gb|CI467473.1|CI467473
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG                         AGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttttattagAGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
EST: gi|88662872|gb|CI474688.1|CI474688
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG                         AGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttttattagAGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
EST: gi|313084050|gb|HO213833.1|HO213833
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG                         AGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttttattagAGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
EST: gi|88661931|gb|CI462321.1|CI462321
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG                         AGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttttattagAGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
EST: gi|86841002|gb|CI335146.1|CI335146
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAG                         AGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttttattagAGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
EST: gi|86492814|gb|CI135447.1|CI135447
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCCAACATTTACTATAG                         AGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttttattagAGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
EST: gi|88662988|gb|CI476281.1|CI476281
EST:     GAAACAATGAATGGGGCCGTATGACATTGAACCANACATTTACTATAG                         AGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT
genomic: GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttttattagAGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACT

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: 49 (upstream exon), 27 (downstream exon)
Score: 1

GAAACAATGAATGGGGCCGTATGACATTGAACCAAACATTTACTATAGgtacatgttt ... tttttattagAGCCCATGCTAACCGTGGGGAGCGTAAATCCAGTTATATGGTCCGATGACTGGACAGCGGTGACTGAAGACGGCAGCTTGTCAGCACAGTTTGAGCACAC




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