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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaattttactgctcaatagtgcatgctgaatcttcaccttctgtaatcagtcaaataattcacttgttatgcaatctgcag

Basic information

species Oryza sativa
transcript LOC_Os03g52840.3
intron # 5
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GRMZM2G135283_T03 (Zea mays), 5'ss of exon 8
ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaattttactgctcaatagtgcatgctgaatcttcaccttctgtaatcagtcaaataattcacttgttatgcaatctgcag-----------------------------------------------------------------
 |||||||||| || |||||||||||||||||||||||| |||| ||||||||||||||||| || || ||||| |||||||| ||||||||||  |  ||| ||   ||  |  | ||  |   ||          |  | | | || || |||   ||     | | | | |||                                                                 
TTGGAGAAAAGCGCTGTTCTTTTTAGGCCAAAGTTGATCATTGCTGGTGCAAGTGCATATGCTCGGCTATATGATTATGACCGTATGCGGAAGgcaaggttt-ctttccacgatagtattttttctccaagatgcaagggagctg-cacattattatattacagagaactatacagaacattgaaccgcgatctttttttttttatcaatcaaataattccataatgttatgtgtcgacag

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA02G38160.2 (Glycine max), 5'ss of exon 8
ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaattttactgctcaatagtgcatgctgaatcttcaccttctgtaa----tcagtca----aataattcacttgttatgc---aatctgcag--
 ||||||||||||| || |||||||||||||| || || ||||| ||||| ||||| ||||| || |||||||| ||||  ||  | || ||||| |||| ||       |||  | |   |   | || |   | |  ||    |||||||     ||| |  |  |  |||||   ||| || |   
TTGGAGAAAAGTGCAGTACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAGgtaaattatat---ctgatacagaaacttaggtatttaatgtttagaacaattcagtcatgatgatattgaatcttatatgcttgaatttgtacag

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 8
lower sequence: GLYMA14G36280.1 (Glycine max), 5'ss of exon 8
ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaattttac----tgctcaatagtgcatgctgaatcttcacc----ttctgtaatcagtcaaataattcacttgttatgcaatctgcag--
 ||||||||||||| |  |||||||||||||| || || ||||| ||||| ||||| ||||| || |||||||| ||||  ||  | || ||||| | || ||     | |  ||   |   |  | ||| || |      ||| || || |    | | | ||  || |  |  ||| || |   
TTGGAGAAAAGTGCAGCACTTTTTAGGCCAAAATTAATAGTTGCTGGTGCTAGTGCTTATGCTCGCCTTTATGATTATGCACGTGTTCGCAAGgtaatttatatctgatacagaaacttaggtatttaatgtttagaacaattcagtcatgatggtattgaatcttttatgcttgaatttgtatag

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 8
lower sequence: AT4G37930.1 (Arabidopsis thaliana), 5'ss of exon 8
ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaattttactgctcaatagtgcatgctgaatcttcaccttctgtaatcagtcaaataattcacttgttatgcaatctgcag
||||||||||||||   |||||| |||||||| ||||| ||||| ||||||||||| |||||  |  | |||||||||| ||||||  | ||||| ||||| | | ||||        | | |||        |  ||||||||||       ||   ||   |  |  |   |||
ATGGAGAAAAGTGCTACTCTTTTCAGGCCAAAATTGATTGTTGCTGGTGCAAGTGCTTATGCTAGATTGTATGACTATGCCCGCATCAGAAAGgt-aatttcagt-ctcatatccaactacagaac---agattattgtaatcagtagtgagttttgattcgaactcttttcccag

upper sequence: LOC_Os03g52840.2 (Oryza sativa), 5'ss of exon 8
lower sequence: AT5G26780.3 (Arabidopsis thaliana), 5'ss of exon 8
ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaattttactgctcaatagtgcatgctgaatcttcaccttctgtaat--cagtcaaataattcacttgttatgcaatctgcag
 | || || |||||||| ||||| || || ||  | || ||||||||||||||||| ||||| ||||| ||||||||||  || || || ||||| || | |  |    | |  ||  ||   | |  | |  | |   | |  ||||     |  | |    | |   ||  |||||
CTAGAAAAGAGTGCCGTGCTTTTCAGACCGAAACTTATTGTTGCGGGTGCAAGTGCTTATGCTCGTCTATATGACTATGCACGTATTCGTAAGgtaaagtattgtctcaactcttgagtgtgaagt--ttagttacaaaagttgcagttttcaaggttatgcataaa--aaattgcag

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|25798315|gb|CA754276.1|CA754276
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|27576793|gb|CA999487.1|CA999487
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|58689542|gb|CK078229.1|CK078229
EST:     GGGTGCAAGTGCATATGCGCGTCTTTATGACCATGACCGCATGCGGCAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAG
genomic: GGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGG-AAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAG
EST: gi|38472528|gb|CF956660.1|CF956660
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|58661735|gb|CK050415.1|CK050415
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|58589569|gb|CF987877.1|CF987877
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGAGTATGACCGCATGCGGAAG                         GTTTGTGCACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAG
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTG-ACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAG
EST: gi|58691585|gb|CK080272.1|CK080272
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|13420583|gb|AU174673.1|AU174673
EST:     CGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|29681406|gb|CB677681.1|CB677681
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|14571290|gb|BI118658.1|BI118658
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|29629705|gb|CB634714.1|CB634714
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|38472219|gb|CF956350.1|CF956350
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|29674038|gb|CB670313.1|CB670313
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|33800499|gb|CF326119.1|CF326119
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|29681405|gb|CB677680.1|CB677680
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|38471655|gb|CF955786.1|CF955786
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|29672938|gb|CB669213.1|CB669213
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|84117692|gb|CD285458.1|CD285458
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|33381615|gb|CF196958.1|CF196958
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|4714773|gb|AU055890.1|AU055890
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|29674139|gb|CB670414.1|CB670414
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|58692794|gb|CK081481.1|CK081481
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|58609394|gb|CK037427.1|CK037427
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|11442623|gb|BF430526.1|BF430526
EST:     CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
genomic: CGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGT
EST: gi|218505280|gb|FG952910.1|FG952910
EST:     TGACTATGACCGCATGCGGAAG                         GTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAAG
genomic: TGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATC-AG

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), 75 (downstream exon)
Score: 250

ATGGAGAAAAGTGCCGTTCTTTTTAGGCCAAAGTTGATCGTTGCGGGTGCAAGTGCATATGCGCGTCTTTATGACTATGACCGCATGCGGAAGgtgaatttta ... caatctgcagGTTTGTGACAAGCAGAAGGCAATACTTCTAGCAGATATGGCACATATCAGTGGGCTTGTCGCAGCTGGTGTTGTTCCATCTCCTTTTGATTATGCAGATG




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