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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagccccaccgcttgcttcgcctgattgcaagtgccacgattcagacgattgattctgtttagataagagcgctgaaccttattagctgtgtgaacttccggatgcaactcgtgtttgcag

Basic information

species Oryza sativa
transcript LOC_Os03g61950.2
intron # 2
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os03g61950.1 (Oryza sativa), 5'ss of exon 2
lower sequence: GRMZM2G351160_T01 (Zea mays), 5'ss of exon 2
CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagccccaccgct--tgcttcgcctgattgcaagtgccacgattcagacgattgattctgtttagataagagcgctgaaccttattagctgtgtgaacttccggatgcaactcgtgtttgcag
||||||||| ||||| | ||| |||||||||||||||||||||||||| |||||||||||||||||||||||| | ||  |  ||||||||||||| |||||||     |  | |   | || || ||| | ||  ||    | | |  | |     |     |  ||  |   | ||   ||  |   |    | | |                           
CGGGCACACTGCGGTTATCATTGGCAAGTCCAAGGTGGTCGTCTTCGGAGGATTCGCCGACAAGCGCTTCCTCGCTGATGTTTCCGTCTACGACGTCGgtaatataattcctctccaattctccgactgttcgcttgtcgtgccaatttgcctgcccacgtcttcgagcaatttgtgc-acacgctgcaactcatctta---------------------------
















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|88389984|gb|CI590497.1|CI590497
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTAAACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|88423266|gb|CI576391.1|CI576391
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|88468919|gb|CI696927.1|CI696927
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|117250064|gb|CT843884.1|CT843884
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|88593275|gb|CI709438.1|CI709438
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCT
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCT
EST: gi|88355627|gb|CI679350.1|CI679350
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|88321948|gb|CI673096.1|CI673096
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|88443548|gb|CI597015.1|CI597015
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|88396872|gb|CI578021.1|CI578021
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|88423265|gb|CI576390.1|CI576390
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|88406641|gb|CI603835.1|CI603835
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|29686595|gb|CB682870.1|CB682870
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         A-AATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|88361530|gb|CI605311.1|CI605311
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|88587351|gb|CI705089.1|CI705089
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|88352722|gb|CI678743.1|CI678743
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|88397430|gb|CI684346.1|CI684346
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|40486394|gb|BX897943.1|BX897943
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|88581551|gb|CI698547.1|CI698547
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
EST: gi|88585547|gb|CI703189.1|CI703189
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTA
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTA
EST: gi|88316019|gb|CI618895.1|CI618895
EST:     CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTG                         AGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC
genomic: CGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGAC

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: 71 (upstream exon), 64 (downstream exon)
Score: 9

CGGGCACACGGCGGTGAGCATCGGCAAGTCCAAGGTGGTCGTCTTCGGCGGATTCGCCGACAAGCGCTTCCTCTCCGACATCGCCGTCTACGACGTTGgtaataagcc ... gtgtttgcagAGAATAGGATTTGGTACACACCTGAATGCAATGGGAGTGGCTCGGATGGACAGGCAGGCCCCAGTCCAAGGGCCTTTCACGTAGCTATCGTCATTGACTG




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