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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

GGATTCCTCCAAGGAATCCTTTGGTTGTGTACAGATTAATCCTATGGTGGTTGATTGCTATTCCAACCATCCGTGAGTACAACTCCTACTTGCAAAACAGgttatcccaatttccctgcacgcccaatagcattgcacattttttacaattttacttaatggcttgctaatatatattttttcatggtcacaccag

Basic information

species Oryza sativa
transcript LOC_Os05g48060.1
intron # 11
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os05g48060.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G085491_T01 (Zea mays), 5'ss of exon 1
GGATTCCTCCAAGGAATCCTTTGGTTGTGTACAGATTAATCCTATGGTGGTTGATTGCTATTCCAACCATCCGTGAGTACAACTCCTACTTGCAAAACAGgttatcccaatttccctgcacgcccaatagcatt-gcacatttt-------ttacaattttacttaatggcttgctaatatatattttt--tcatggtcacaccag
                                                         | || ||||||||||| ||||||||||||||||||||| ||||||||  ||||   |      |      |||||   ||||   |        ||| ||  ||  | ||| | || ||||||| |  |  |     ||||||   |||
--------------------------------------------------------TCCATCCCAACCATCCGCGAGTACAACTCCTACTTGCAAGACAGgttagtccaagagcgtcattcatttgttagcaacagcacgcatgaccagcattagaaaatt-ttaaattggttactaatatttggtgctggcgttggtcatcacag

upper sequence: LOC_Os05g48060.1 (Oryza sativa), 5'ss of exon 11
lower sequence: GRMZM2G477340_T01 (Zea mays), 5'ss of exon 11
GGATTCCTCCAAGGAATCCTTTGGTTGTGTACAGATTAATCCTATGGTGGTTGATTGCTATTCCAACCATCCGTGAGTACAACTCCTACTTGCAAAACAGgttatcccaatttccctgcacgcc------caatagcattgca-----cat-----tttttacaatt--ttacttaatggcttgctaatatatattttt--tcatggtcacaccag
|||| |||||||||||||| || || ||||||||||| ||||| |||||| ||||||| || ||||||||||| ||||||||||||||||| ||| ||||||||  ||||     |    |         ||| |||| | ||     |||     |   || || |  |   || ||   || ||||| | |  |  |  |  ||||||   |||
GGATCCCTCCAAGGAATCCCTTAGTCGTGTACAGATTGATCCTCTGGTGGCTGATTGCCATCCCAACCATCCGCGAGTACAACTCCTACTTACAAGACAGgttagtccaagagtgccattcatttgttagcaacagcagtacagctcgcatgaccatcactataactagtctttttattcattcctaatgtttggtgctggttttggtcatcacag
















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|86505674|gb|CI148307.1|CI148307
EST:     TTGATTGCTATTCCAACCATCCGTGAGTACAACTCCTACTTGCAAAACAG                         CAAACCGGTGAAGAAGGTTGGGGCTTTTTGCTGGCTCTCTCTAGCTATATG
genomic: TTGATTGCTATTCCAACCATCCGTGAGTACAACTCCTACTTGCAAAACAGgttatcccaa ... gtcacaccagCAAACCGGTGAAGAAGGTTGGGGCTTTTTGCTGGCTCTCTCTAGCTATATG
EST: gi|86497839|gb|CI140472.1|CI140472
EST:     TTGATTGCTATTCCAACCATCCGTGAGTACAACTCCTACTTGCAAAACAG                         CAAACCGGTGAAGAAGGTTGGGGCTTTTTGCTGGCTCTCTCTAGCTATATG
genomic: TTGATTGCTATTCCAACCATCCGTGAGTACAACTCCTACTTGCAAAACAGgttatcccaa ... gtcacaccagCAAACCGGTGAAGAAGGTTGGGGCTTTTTGCTGGCTCTCTCTAGCTATATG
EST: gi|27547688|gb|CA767380.2|CA767380
EST:     TTGATTGCTATTCCAACCATCCGTGAGTACAACTCCTACTTGCAAAACAG                         CAAACCGGTGAAGAAGGTTGGGGCTTTTTGCTGGCTCTCTCTAGCTATATG
genomic: TTGATTGCTATTCCAACCATCCGTGAGTACAACTCCTACTTGCAAAACAGgttatcccaa ... gtcacaccagCAAACCGGTGAAGAAGGTTGGGGCTTTTTGCTGGCTCTCTCTAGCTATATG
EST: gi|32948073|gb|BP184645.1|BP184645
EST:     TTGATTGCTATTCCAACCATCCGTGAGTACAACTCCTACTTGCAAAACAG                         CAAACCGGTGAAGAAGGTTGGGGCTTTTTGCTGGCTCTCTCTAGCTATATG
genomic: TTGATTGCTATTCCAACCATCCGTGAGTACAACTCCTACTTGCAAAACAGgttatcccaa ... gtcacaccagCAAACCGGTGAAGAAGGTTGGGGCTTTTTGCTGGCTCTCTCTAGCTATATG
EST: gi|86413288|gb|CI067693.1|CI067693
EST:     TTGATTGCTATTCCAACCATCCGTGAGTACAACTCCTACTTGCAAAACAG                         CAAACCGGTGAAGAAGGTTGGGGCTTTTTGCTGGCTCTCTCNAGCTATATG
genomic: TTGATTGCTATTCCAACCATCCGTGAGTACAACTCCTACTTGCAAAACAGgttatcccaa ... gtcacaccagCAAACCGGTGAAGAAGGTTGGGGCTTTTTGCTGGCTCTCTCTAGCTATATG

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: 66 (upstream exon), 67 (downstream exon)
Score: 11

GGATTCCTCCAAGGAATCCTTTGGTTGTGTACAGATTAATCCTATGGTGGTTGATTGCTATTCCAACCATCCGTGAGTACAACTCCTACTTGCAAAACAGgttatcccaa ... gtcacaccagCAAACCGGTGAAGAAGGTTGGGGCTTTTTGCTGGCTCTCTCTAGCTATATGCATTGTAGAGCTTCTTATATGTATGAAGTTTGGACATG




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