Sequence
atgc intronic sequence ATGC exonic sequencegtaaatttatgcttgcggggaaggaatagtctagccttgttactgtagtgggatgtaagatgtgttgtttggatgcttttggttaactgatagatggcttaattgtgatgctttgcatgattatctgatttacctgtggaattcgccaattccatgcagATCAAGAAAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAATGTGAGGCGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATG
Basic information
species | Oryza sativa |
transcript | LOC_Os06g39640.1 |
intron # | 5 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 5
lower sequence: AC189879.3_FGT003 (Zea mays), 3'ss of exon 4
gtaaatttatgcttgcggggaaggaatagtctagccttgttactgtagtgggatgtaagatgtgttgtttggatgcttttggttaactgatagatggcttaattgtgatgctttgcatgattatctgatttacctgtggaattcgccaattccatgcagATCAAGAAAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAATGTGAGGCGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATG
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-------------------------------------------------------------------gtaacattactgtggtcgggcgggcatggaatctagcatatagtagtgcagcgatatctaac--acttatt----------atgccaagcagATCAAGAAGGCATTACGGGGCGTAAAAGTTGAGGTCACGCACCGGGGGAATGTAAGGCGCAAGTATCGCATATCTGGGCTCACAACACAGCCAACTCATG
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 5
lower sequence: GRMZM2G079080_T01 (Zea mays), 3'ss of exon 5
gtaaatttatgcttgcggggaaggaatagtctagccttgttactgtagtgggatgtaagatgtgttgtttggatgcttttggttaactgatagatggcttaattgtgatgctttgcatgattatctgatttacctgtggaattcgccaattccatgcagATCAAGAAAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAATGTGAGGCGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATG
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-------------------------------------------taaaaagaaacggagggagtatataacagctgccattgggcg-ctagta--ttgctta--tggattaatatttatc-ttgtgtaattcgcttat----tttgccaat------cagATCAAGAAGGCATTGCGGGGTGTAAAAGTTGAGGTCACTCACCGGGGGAATGTACGGCGCAAGTATCGCATTTCAGGCCTCACAACACAGCCAACTCATG
upper sequence: LOC_Os06g39640.1 (Oryza sativa), 3'ss of exon 5
lower sequence: PP1S173_134V6.1 (Physcomitrella patens), 3'ss of exon 5
gtaaatttatgcttgcggggaaggaatagtctagccttgttactgtagtgggatgtaagatgtgttgtttggatgcttttggttaactgatagatggcttaattgtgatgctttgcatgattatctgatttacctgtggaattcgccaattccat-gcagATCAAGAAAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAATGTGAGGCGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATG
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------gtatgctt-cgtttacacttgtatctgttggcatcgctctttcgaactgtataat------tttagccgtgtcttgt--gtccatctgcgtcgaaacgatatacctttgtggaggg---tgatttg--tgcggaacaacacggttcttttgcagATCAAGAAAGCCCTCCGTGGGGTGAAGGTGGAAGTCACTCATCGCGGAAGTATGCGGCGCAAGTATCGCATATCTGGGCTCACTAATCAGGCCACCAGTGMapped 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|58664728|gb|CK053414.1|CK053414EST: TAGGGAAGGATGTCATATCGAGGCCATTGTCGGATGCAAACAGAATCAAG ATCAAGAAAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAAT
genomic: TAGGGAAGGATGTCATATCGAGGCCATTGTCGGATGCAAACAGAATCAAGgtaaatttat ... ttccatgcagATCAAGAAAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAAT
EST:
gi|29636940|gb|CB641949.1|CB641949EST: TAGGGAAGGATGTCATATCGAGGCCATTGTCGGATGCAAACAGAATCAAG ATCAAGAAAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAAT
genomic: TAGGGAAGGATGTCATATCGAGGCCATTGTCGGATGCAAACAGAATCAAGgtaaatttat ... ttccatgcagATCAAGAAAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAAT
EST:
gi|29636971|gb|CB641980.1|CB641980EST: TAGGGAAGGATGTCATATCGAGGCCATTGTCGGATGCAAACAGAATCAAG ATCAAGAAAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAAT
genomic: TAGGGAAGGATGTCATATCGAGGCCATTGTCGGATGCAAACAGAATCAAGgtaaatttat ... ttccatgcagATCAAGAAAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAAT
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:
45 (upstream exon),
61 (downstream exon)
Score:
7TACCGCGTTCATCGAGCCGCTACCAGTGATCGAATTCGTGGCCCAAATACTAGGGAAGGATGTCATATCGAGGCCATTGTCGGATGCAAACAGAATCAAGgtaaatttat ... ttccatgcagATCAAGAAAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAATGTGAGGCGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.gtgatgctttgcatgattatctgatttacctgtggaattcgccaattccatgcagATCAAGAAAGCCTTGCGGGGCGTGAAAGTTGAAGTCACTCACCGGGGAAATGTGAGGCGGAAGTATCGCATTTCAGGGCTGACAACACAACCAACTCATG
atctgat putative branch site (score: 7)
atgattat TA-rich tract