Sequence
atgc intronic sequence ATGC exonic sequencegtaatttccttaactttataattggtattgtacttttatgccataccaaatatagggactaaattttataattggaattgtacttttaactgtggcagCTAGGAATTGGCCTACTTGTACTGCAACAGCTAAGTGGAATCAATGGAATATTGTTTTATGCAGGTAGCATCTTCAAAGCAGCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os05g49270.1 |
intron # | 9 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G160430_T04 (Zea mays), 3'ss of exon 9
gtaatttccttaactttataattggtattgtacttttatgccataccaaatatagggactaaattttataattggaattgta-----------cttttaactgtggcagCTAGGAATTGGCCTACTTGTACTGCAACAGCTAAGTGGAATCAATGGAATATTGTTTTATGCAGGTAGCATCTTCAAAGCAGCAG
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---------gtaagtttataacttatatc-tgcttatctg--gtaccaaat-tagcaatcacattccataactgtcagcttatggtggcaatgctacaacttcccgcagctaggaattggcctacttgtgttgcaacagctaagtggaataaattgtataatcttttattcagGTAGCATCTTCAAAGCTGCAG
upper sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G160460_T02 (Zea mays), 3'ss of exon 9
gtaatttccttaactttataat-tggtattgtacttttatgccataccaaatatagggactaaattttataattggaattgtac-------ttttaactgtg--gcagCTAGGAATTGGCCTACTTGTACTGCAACAGCTAAGTGGAATCAATGGAATATTGTTTTATGCAGGTAGCATCTTCAAAGCAGCAG
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-----------------gtaacataatcttatctgcttatctcatacccaat-tagaattcacattttataattgtcagtttgtgacagtgccacaactttttcgcagATAGGAATTGGTCTACTTGTGCTGCAACAGCTAAGTGGAATAAATGGTATACTATTTTATGCAAGTAGCATCTTCAAAGCTGCCG
upper sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G160504_T01 (Zea mays), 3'ss of exon 9
gtaatttccttaactttataattggtattgtacttttatgccataccaaatatagggactaaattttataattggaattgtacttttaactgtggcagCTAGGAATTGGCCTACTTGTACTGCAACAGCTAAGTGGAATCAATGGAATATTGTTTTATGCAGGTAGCATCTTCAAAGCAGCAG
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gtaatttccttaacttcgtcacc------------ttagtccatgccaagatcaacaactatagtttgtaattgtgattatttattaaatt--ggcagCTAGGGATTGGCCTACTTGTACTGCAAAATCTTAGTGGAATCAACGGTGTACTGTTTTATGCAAGTAGCATCTTCAAAGCTGCAG
upper sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G098679_T01 (Zea mays), 3'ss of exon 9
gtaatttccttaactttata-attggtattgtacttttatgccataccaaatatagggactaaattttataattggaattgtacttttaactgtggcagCTAGGAATTGGCCTACTTGTACTGCAACAGCTAAGTGGAATCAATGGAATATTGTTTTATGCAGGTAGCATCTTCAAAGCAGCAG
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gtaggtttgc-aactttatctgcttatatgggaccaaattagtg-atcgcatttcg----taaactgtctgctcatgacaatgctgcaacctctcgcagCTAGGAATGGGCCTACTTGTGTTGCAGCAGCTGAGTGGAATAAACGGTATAATCTTTTATGCAGGTAGCATCTTCAAAGCTGCAG
upper sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G077546_T02 (Zea mays), 3'ss of exon 9
gtaatttccttaactttata-attggtattgtacttttatgccataccaaatatagggactaa-attttataattggaattgtacttttaactgtggcagCTAGGAATTGGCCTACTTGTACTGCAACAGCTAAGTGGAATCAATGGAATATTGTTTTATGCAGGTAGCATCTTCAAAGCAGCAG
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gtaagtttgt-aactttatgtgcttatctggtacgaa-attagttattgcatttcgtaactcttagtttatgacaaatgctacaatttt-----tcacagCTAGGAATTGGCCTACTTGTGTTGCAACAGCTAAGTGGAATAAACTGTATAGTATTTTATTCAGGTAGCATCTTCAAAGCTGCAG
upper sequence: LOC_Os05g49270.1 (Oryza sativa), 3'ss of exon 9
lower sequence: GRMZM2G098679_T03 (Zea mays), 3'ss of exon 9
gtaatttccttaactttata-attggtattgtacttttatgccataccaaatatagggactaaattttataattggaattgtacttttaactgtggcagCTAGGAATTGGCCTACTTGTACTGCAACAGCTAAGTGGAATCAATGGAATATTGTTTTATGCAGGTAGCATCTTCAAAGCAGCAG---------------
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gtaggtttgc-aactttatctgcttatatgggaccaaattagtg-atcgcatttcg----taaactgtctgctcatgacaatgctgcaacctctcgcagCTAGGAATGGGCCTACTTGTGTTGCAGCAGCTGAGTGGAATAAACGGTATAATCTTTTATGCAGGTAGCATCTTCAAAGCTGCAGGTAAGCTGTGCACTTMapped 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|44678080|gb|CR291514.1|CR291514EST: CGATCCGTTTTCAAGAATTAAACCAGAAGAAATACCGCACACCCCTAATA CTAGGAATTGGCCTACTTGTACTGCAACAGGTAAGTGGAATCACCGGAATA
genomic: CGATCCGTTTTCAAGAATTAAACCAGAAGAAATACCGCACACCCCTAATAgtaatttcct ... actgtggcagCTAGGAATTGGCCTACTTGTACTGCAACAGCTAAGTGGAATCAATGGAATA
EST:
gi|29687040|gb|CB683315.1|CB683315EST: GATCCGCCTTTC-AGAATTAAACCAGAAGAAATACCGCACACCCCTAATA CTAGGAATTGGCCTACTTGTACTGCAACAGCTAAGTGGAATCAATGGAATA
genomic: GATCCG-TTTTCAAGAATTAAACCAGAAGAAATACCGCACACCCCTAATAgtaatttcct ... actgtggcagCTAGGAATTGGCCTACTTGTACTGCAACAGCTAAGTGGAATCAATGGAATA
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:
67 (upstream exon),
60 (downstream exon)
Score:
15AGAGCAGTAGCGTCAGCAAACAAAAGGACAACGATCCGTTTTCAAGAATTAAACCAGAAGAAATACCGCACACCCCTAATAgtaatttcct ... actgtggcagCTAGGAATTGGCCTACTTGTACTGCAACAGCTAAGTGGAATCAATGGAATATTGTTTTATGCAGGTAGCATCTTCAAAGCAGCAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.taccaaatatagggactaaattttataattggaattgtacttttaactgtggcagCTAGGAATTGGCCTACTTGTACTGCAACAGCTAAGTGGAATCAATGGAATATTGTTTTATGCAGGTAGCATCTTCAAAGCAGCAG
ttttaac putative branch site (score: 15)
taaattttataattgg TA-rich tract