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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttctatagcattctgcgatccaataactccatgactacatgagatgaaattctttctctgatacacgattttttaagttattgttttattgtcgcaatggtttctctgatacacgattttaagttgttgttttattgtcgcaatggttttttttttaccattttttttatttttcag

Basic information

species Oryza sativa
transcript LOC_Os02g53060.1
intron # 4
splice site 5'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os02g53060.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G374881_T02 (Zea mays), 5'ss of exon 4
AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttctatagcattctgcgatccaataactccatgactacatga--gatgaaattctttctctgatacacgattttttaagttattgttttattgtcgcaatggtttctc--tgatacacgattttaagttgttgttttattgtcgcaatggttttttttttaccattttttttatttttcag
||| |||||||| || |||||||| || ||||||||||| ||||| ||||||||| | ||||||||||| ||||||| ||  |  ||||||||   | ||||  |    | |   | | | |  ||| |    ||      |  |   ||| ||  ||  | |||||  | |     ||| || | |   | |||  |                                                               
AATCCAGCTTGGACAACCAGCTACTGTTAAAGTTGCAGCTAACTTGATTAGGTTGCTAGCTTATCAGAATAAGgtatgtt--ccgtagcattccaggttccagcacaaacttactttcctcattgataagtacctggtgtcgtaatttgatgtt--aaactcttgttgaactaaaaaaattgtgtgttattaatatccag-------------------------------------------------------------

upper sequence: LOC_Os02g53060.1 (Oryza sativa), 5'ss of exon 4
lower sequence: GRMZM2G152775_T04 (Zea mays), 5'ss of exon 4
AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttctatagcattctgcgatccaataactccatgactacatgagatgaaattctttctctgatacacgattttttaagttattgttttattgtcgcaatggtttctctgatacacgattttaagttgttgttttattgtcgcaatggttttttttttaccattttttttatttttcag
||| |||||||| || ||||||||||| ||||||||||||||||| ||||||||| | ||||||||||||||||||| ||  | |||||||||    |   |      |  | |  ||| |   |  | || | || ||||||  |      |   ||     |||||| || | ||   ||  |  | ||    | |  | ||| | || ||| | |  ||                                   
AATCCAGCTTGGACAACCAGCTACCGTTAAAGTTGCAGCCAACTTGATTAGGTTGCTAGCTTATCAGAACAAGgtatgtt--ccatagcattccagcacgta------ctgttaaaacacgc--ttcacttttctcactgataagca---cctggtgtcggaattttat-gttg-aactcttgtttagctatgaaaatgaatgtt-tggtattaatatt-cag----------------------------------
















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|86496862|gb|CI139495.1|CI139495
EST:     CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG                         AACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
genomic: CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttc ... tatttttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
EST: gi|8527814|gb|AU092629.1|AU092629
EST:     CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG                         AACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
genomic: CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttc ... tatttttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
EST: gi|58588610|gb|CF986918.1|CF986918
EST:     CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG                         AACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
genomic: CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttc ... tatttttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
EST: gi|58692319|gb|CK081006.1|CK081006
EST:     CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG                         AACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
genomic: CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttc ... tatttttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
EST: gi|25799545|gb|CA755506.1|CA755506
EST:     CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG                         AACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
genomic: CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttc ... tatttttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
EST: gi|38477245|gb|CF961378.1|CF961378
EST:     CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG                         AACATGTTGCAAGCTGGCATG
genomic: CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttc ... tatttttcagAACATGTTGCAAGCTGGCATG
EST: gi|218498714|gb|FG963991.1|FG963991
EST:     CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG                         AACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
genomic: CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttc ... tatttttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
EST: gi|218498950|gb|FG948071.1|FG948071
EST:     CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG                         AAGATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
genomic: CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttc ... tatttttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
EST: gi|38472737|gb|CF956869.1|CF956869
EST:     CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG                         AACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
genomic: CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttc ... tatttttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
EST: gi|33803228|gb|CF327486.1|CF327486
EST:     CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG                         AACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATG
genomic: CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttc ... tatttttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATG
EST: gi|218504275|gb|FG947024.1|FG947024
EST:     CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG                         AACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
genomic: CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttc ... tatttttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
EST: gi|218486985|gb|FG965418.1|FG965418
EST:     CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAG                         AACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA
genomic: CCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttc ... tatttttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGA

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), 64 (downstream exon)
Score: 92

AATTCAGCTTGGGCAGCCAGCTACCGTGAAAGTTGCAGCCAACTTAATTAGGTTGTTGGCTTATCAGAACAAGgtatattttc ... tatttttcagAACATGTTGCAAGCTGGCATGATTGTTGGTGGATGGGATAAATATGAGGGAGGCCAAATTTTCTCAGTCCCCCTTGGTGGAACAATTCTGAGGCAACCAT




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