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Data associated with selected splice site

Sequence

 atgc   intronic sequence     ATGC   exonic sequence

gtaattcggtcactgccattctaatcatcctttatcatgcttgttgaatcaataccaaaattatggatgaaaacttgtaccaatgaactagattgatctgatgaacctctccgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGAGTCTGCTTCTCACTCTTCTCCCCGGCATTCAACCTCGCCACCAATGACC

Basic information

species Oryza sativa
transcript LOC_Os12g31850.4
intron # 6
splice site 3'
intron type U2

Orthologous splice sites


 atgc   intronic sequence     ATGC   exonic sequence


upper sequence: LOC_Os12g31850.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G025528_T02 (Zea mays), 3'ss of exon 5
gtaattcggtcactgccattctaatcatcctttatcatgcttgttgaatcaataccaaaattatggatgaaaacttgtaccaatgaactagat--tgatc-tgatgaacctctccgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGAGTCTGCTTCTCACTCTTCTCCCCGGCATTCAACCTCGCCACCAATGACC
                                              || ||  |     ||||||||| || |   |  |    |   | |||  |||    | | |   | |    ||| ||||| ||||| |||| ||||||||| ||||| ||||| || |||||| | || || |||||||| |||||||||||||| |||||||| ||||| || ||||
--------------------------------------------gtaaccaccatactcattatggatcaatagcagccctggggtttttgatcttgacgacggtaattgtatttcctgc-cagGTATTCGGTTCAAACACCTTCATCGGGCTGGGGATCGTCTTCTTCGCGGGCGTGTGCTTCTCGCTCTTCTCCCCGGCGTTCAACCTGGCCACTAACGACC

upper sequence: LOC_Os12g31850.1 (Oryza sativa), 3'ss of exon 6
lower sequence: GRMZM2G091891_T01 (Zea mays), 3'ss of exon 4
----------------------gtaattcggtcactgccattctaatcatcctttatcatgcttgttgaatcaataccaaaattatggatgaaaa-----------cttgtaccaatgaactagattgatctgatgaacctctccgttgcgc-------agGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGAGTCTGCTTCTCACTCTTCTCCCCGGCATTCAACCTCGCCACCAATGACC
                         | ||   ||    |||    || | |    |  |      || | | || ||  |  || || | |||||            ||    |    |||| ||  |     |||     | |     |||       |||| ||||| |||| ||| ||||| || || ||||| ||||||||| | || |  |||||||| |||||||||||||| |||||||| || ||||| ||||
gtatccgtccgtccatccatccaatactcatccatactcatggggataaacacagacgacctcatttaatttaacacttag-ttctgaaagaaaaaaaaacattttttttcttctcaaaactggaacgtaaaaatggcttgcacacccacgcgggcaccagGTATTCGGTTCAAACACGTTCATCGGTCTGGGGATCGTGTTCTTCGCGGGGGCGTGCTTCTCGCTCTTCTCCCCGGCGTTCAACCTGGCAACCAACGACC
















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|11025713|gb|AU162314.1|AU162314
EST:     AGGAACTNG-GNAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAG                         GTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
genomic: AGGAACT-GCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAGgtaattcggt ... cgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
EST: gi|218501335|gb|FG958585.1|FG958585
EST:     CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAG                         GTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
genomic: CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAGgtaattcggt ... cgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
EST: gi|29644126|gb|CB649133.1|CB649133
EST:     CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAG                         GTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
genomic: CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAGgtaattcggt ... cgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
EST: gi|29614658|gb|CB619671.1|CB619671
EST:     CAGGAACTGCGGAATACTTGATCGAGCTCGAAGAACGGCGTTCGATCAAG                         GTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCANGA
genomic: CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAGgtaattcggt ... cgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
EST: gi|29665274|gb|CB661549.1|CB661549
EST:     CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAG                         GTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
genomic: CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAGgtaattcggt ... cgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
EST: gi|218483875|gb|FG965316.1|FG965316
EST:     CAGGAACTGCGGAATACTTGATCGAGCTCGAAGAACGGCGTTCGATCAAG                         GTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA
genomic: CAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAGgtaattcggt ... cgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGA

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: 45

GGACTTGGAGAATGGAGCTTCTGCAACCAAATATGTTGCCAAAGCTGAAGCAGGAACTGCGGAATACTTGATTGAGCTCGAAGAACGGCGTTCGATCAAGgtaattcggt ... cgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGAGTCTGCTTCTCACTCTTCTCCCCGGCATTCAACCTCGCCACCAATGACC




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 atgc   intronic sequence     ATGC   exonic sequence

Intronic sequence truncated to 55 bases.

atgaaaacttgtaccaatgaactagattgatctgatgaacctctccgttgcgcagGTGTTCGGATCAAGCACCTTCATAGGGCTTGGGATAGTGTTCTTCTCAGGAGTCTGCTTCTCACTCTTCTCCCCGGCATTCAACCTCGCCACCAATGACC
                             atctgat  putative branch site (score: 45)
                                       cctctccgtt  putative PPT