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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

ACAAAACCTAAGCCGGAGAAAAAGAAAAGACTGTTTTTCAAGAAAGCAGAAAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcagcttgtctaacaattgtcaaataacataaggtaacataagaaaaacatcacagtaaaactcaaatgtttctttactgcag

Basic information

species Oryza sativa
transcript LOC_Os07g14850.1
intron # 10
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os07g14850.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G082580_T01 (Zea mays), 5'ss of exon 9
ACAAAACCTAAGCCGGAGAAAAAGAAAAGACTGTTTTTCAAGAAAGCAGAAAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcagcttgtctaacaattgtca----aataacataaggtaacataagaaaaacatcaca-gtaaaactcaaatgtttctttactgcag-------------------------------------------------------------------------------------------------
|| ||||| ||| ||||||| ||||||||| | |||||||||||||||||||| |  ||||||||||||||| | ||||||||||||||||| ||||||||| |||||| | | || ||||    | |    |  | | | ||    || | | | |   | | |  |||||  | |       | | |||                                                                                                    
ACGAAACCAAAGACGGAGAAGAAGAAAAGATTATTTTTCAAGAAAGCAGAAAACCCATCTCCTGCATATGCTTTGGGTGAAATTGAGGAAGGCGCTCCAGgtgttgtcaacctttcaaacatagcttacaacagcaccgttagagttcaaaggcatattcttagatataaaaaaccaggacagttcttctgttaatccatttcatgttgacttcactacctgttgtgtaaatggatgaaagcatttctgtttctatttgacacttgtgaataacattgcactgttctccag

upper sequence: LOC_Os07g14850.1 (Oryza sativa), 5'ss of exon 10
lower sequence: GRMZM2G177631_T01 (Zea mays), 5'ss of exon 9
ACAAAACCTAAGCCGGAGAAAAAGAAAAGACTGTTTTTCAAGAAAGCAGAAAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcagcttgtctaacaattgtca----aataacataaggtaacataagaaaaacatcacagt---aaaactcaaatgtttctttactgcag---------------------------------------------------------------------------------------------
|||||||| ||| ||||||| ||||||||| | |||||||||||||||||||| |  ||||||||||||||| | ||||||||||| |||||||||||||||| ||||| | | || ||||    | |    |  | |   ||    || | | | |   | | | |   |||||    |   | || | |  |                                                                                               
ACAAAACCAAAGACGGAGAAGAAGAAAAGATTATTTTTCAAGAAAGCAGAAAACCCATCTCCTGCATATGCTTTGGGTGAAATTGATGAAGGTGCTCCAGgtactgtcaacctttcaaacatagcttacaacagcaccgctagagttcaaaggcatatgcttagatttcaaaaaccaggacaatcctgttcaaccatttcctgtcgacttcactacctgttgtgtaaaagggaggagagcatttctgtctctatttgacacttgtaaataacatttcactgttctccag
















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|427599|gb|D23732.1|D23732
EST:     AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGGATTGTGAATCAACAGA-GCTAGAAA-GA
genomic: AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
EST: gi|396941331|gb|HO188540.1|HO188540
EST:     AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
genomic: AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
EST: gi|58664382|gb|CK053068.1|CK053068
EST:     AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
genomic: AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
EST: gi|58610601|gb|CK038313.1|CK038313
EST:     TGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
genomic: TGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
EST: gi|58673459|gb|CK062145.1|CK062145
EST:     AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
genomic: AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
EST: gi|29685626|gb|CB681901.1|CB681901
EST:     AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
genomic: AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
EST: gi|427628|gb|D23761.1|D23761
EST:     AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
genomic: AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA
EST: gi|38473343|gb|CF957475.1|CF957475
EST:     AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAG                         GAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAANAGA
genomic: AAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGA

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: 70 (upstream exon), 54 (downstream exon)
Score: 32

ACAAAACCTAAGCCGGAGAAAAAGAAAAGACTGTTTTTCAAGAAAGCAGAAAATCAGTCTCCTGCATATGCTCTTGGTGAAATTGAGGAAGGTGCTCCAGgtattgtcag ... tttactgcagGAGCTGAGACAGACAAAGCTGGAATTGTGAATCAACAGAAGCTAGAAAAGAAATTTGGGCAGTCTTCTGTTTTTGTTGCATCAACTTTGCTTGAAAATGG




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