Sequence
atgc intronic sequence ATGC exonic sequencegtacactgtcacagtttatggaaagttgaaaaatccaacaatagatgtactaaatggattttggttatgttacacagAGGCGAGGTCGTGCAGGACGTGTTCAGCCTGGTGCTTGCTATAGGCTGTATCCTAAAGTCATTTATGATGCGATGCCACAGTTTCAGTTACCTGAAATTC
Basic information
species | Oryza sativa |
transcript | LOC_Os10g33275.1 |
intron # | 12 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G399212_T01 (Zea mays), 3'ss of exon 13
-----------------gtacactgtcacagtttatggaaagttgaaaaatccaacaatagatgtactaaatggattttggttatgttacacagAGGCGAGGTCGTGCAGGACGTGTTCAGCCTGGTGCTTGCTATAGGCTGTATCCTAAAGTCATTTATGATGCGATGCCACAGTTTCAGTTACCTGAAATTC
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gtatgttactgctgacaatatgtaactaggctctttgcagacatgaaaagtccattaacagatgcagt---tctctctttattttatt-cacagAGGAGAGGTCGTGCAGGCCGCGTTCAGCCAGGTTTTTGCTATCGGCTCTATCCAAAGATCATTCACGATGCAATGCCACAGTTTCAGTTGCCTGAAATTC
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G384369_T01 (Zea mays), 3'ss of exon 1
-----------------gtacactgtcacagtttatggaaagttgaaaaatccaacaatagatgtactaaatggattttggttatgttacacagAGGCGAGGTCGTGCAGGACGTGTTCAGCCTGGTGCTTGCTATAGGCTGTATCCTAAAGTCATTTATGATGCGATGCCACAGTTTCAGTTACCTGAAATTC
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gtatgttactgctgacaatatgtaactaggctctttgcagacatgaaaagtccattaacagatgcagt---tctctctttatttttattcacagAGGAGAGGTCGTGCAGGCCGCGTTCAGCCAGGTTTTTGCTATCGGCTCTATCCAAAGATCATTCACGATGCAATGCCATAGTTTCAGTTACCTGAAATTC
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 12
lower sequence: GRMZM2G381470_T01 (Zea mays), 3'ss of exon 4
-----------------gtacactgtcacagtttatggaaagttgaaaaatccaacaatagatgtactaaatggattttggttatgttacacagAGGCGAGGTCGTGCAGGACGTGTTCAGCCTGGTGCTTGCTATAGGCTGTATCCTAAAGTCATTTATGATGCGATGCCACAGTTTCAGTTACCTGAAATTC
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gtatgttactgctgacaatatgtaactcggctctttgcagacatgaaaagtccattaacagatgttgt---tctctctttattttatt-cacagAGGAGAGGTCGTGCAGACCGCGTTCAGCCAGGTTTTTGCTATCGGCTCTATCCAAAGATCATTCACGATGCAATGCCACAGTTTCAGTTACCTGAAATTC
upper sequence: LOC_Os10g33275.1 (Oryza sativa), 3'ss of exon 12
lower sequence: AT2G35920.1 (Arabidopsis thaliana), 3'ss of exon 11
------------------------------------------------------------gtacactgt-cacagtttatggaaag--ttgaaaaatccaacaatagatgtactaaatggattttggttatgttacacagAGGCGAGGTCGTGCAGGACGTGTTCAGCCTGGTGCTTGCTATAGGCTGTATCCTAAAGTCATTTATGATGCGATGCCACAGTTTCAGTTACCTGAAATTC
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gtattcgactaaccataaaattgtctatcagtaatcaagatccctttcattcaatgatctaagtactgcgcccagatcatagatgtgcttgtaagacttaaaacccgtgcttttctctgtggctttggtacaa-atgcagAGACGAGGTCGTGCTGGACGTGTTCAAGCTGGAGTTTGTTATAGGTTGTATCCAAAAGTTATCTATGATGCTTTTCCACAGTATCAGTTACCAGAAATCAMapped 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|58654512|gb|CK043192.1|CK043192EST: AGCTTGCATGCCTTCTACCATCATGGATATCAAAAGCTTCTGCCCATCAG AGGCGAGGTCGTGCAGGGGGTGTTCAGCCTGGTGCTTGCTATAGGCTGTA
genomic: AGCTTGCATGCCTTCTACCATCATGGATATCAAAAGCTTCTGCCCATCAGgtacactgtc ... tgttacacagAGGCGAGGTCGTGCAGGACGTGTTCAGCCTGGTGCTTGCTATAGGCTGTA
EST:
gi|58600773|gb|CK011301.1|CK011301EST: AGCTTGCATGCCTTCTACCATCATGGATATCAAAAGCTTCTGCCCATCAG AGGCGAGGTCGTGCAGGACGTGTTCAGCCTGGTGCTTGCTATAGGCTGTAT
genomic: AGCTTGCATGCCTTCTACCATCATGGATATCAAAAGCTTCTGCCCATCAGgtacactgtc ... tgttacacagAGGCGAGGTCGTGCAGGACGTGTTCAGCCTGGTGCTTGCTATAGGCTGTAT
EST:
gi|112786422|gb|EE590731.1|EE590731EST: AGCTTGCATGCCTTCTACCATCATGGATATCAAAAGCTTCTGCCCATCAG AGGCGAGGTCGTGCAGGACGTGTTCAGCCTGGTGCTTGCTATAGGCTGTAT
genomic: AGCTTGCATGCCTTCTACCATCATGGATATCAAAAGCTTCTGCCCATCAGgtacactgtc ... tgttacacagAGGCGAGGTCGTGCAGGACGTGTTCAGCCTGGTGCTTGCTATAGGCTGTAT
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:
68 (upstream exon),
59 (downstream exon)
Score:
20TGTAATTGATTGTGGCAAAGCAAAGGAAACAAGTTATGATGCCTTAAATAAGCTTGCATGCCTTCTACCATCATGGATATCAAAAGCTTCTGCCCATCAGgtacactgtc ... tgttacacagAGGCGAGGTCGTGCAGGACGTGTTCAGCCTGGTGCTTGCTATAGGCTGTATCCTAAAGTCATTTATGATGCGATGCCACAGTTTCAGTTACCTGAAATTC
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.aagttgaaaaatccaacaatagatgtactaaatggattttggttatgttacacagAGGCGAGGTCGTGCAGGACGTGTTCAGCCTGGTGCTTGCTATAGGCTGTATCCTAAAGTCATTTATGATGCGATGCCACAGTTTCAGTTACCTGAAATTC
tactaaa putative branch site (score: 20)
tactaaat TA-rich tract