Sequence
atgc intronic sequence ATGC exonic sequenceTTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactgttttgagtctcttagtttcagttgataatgttattcttcaccttagatgcatgattcttactttcagaagttcgattgttttaaacttatttcctcaaataatttcag
Basic information
species | Oryza sativa |
transcript | LOC_Os03g05740.1 |
intron # | 3 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GRMZM2G362088_T02 (Zea mays), 5'ss of exon 4
TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgatt-actgttttgagtctcttagtttcagttgataatgttattcttcaccttagatgcatgattcttactttcagaagttcgattgttttaaacttatttcctcaaataatttcag
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TTGGTATTGCTGGGAGACTCAGGTGTTGGGAAAAGTTGCATTGTTCTTCGTTTTGTTCGTGGTCAGTTTGATCCTACTTCCAAGgtgatttactgttttga-----tcagatcgacccatgaatgaaacttt----------------actttcggttgcagcatttccatt--ccccaacttatcttctcaaatggttacag
upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA20G32320.1 (Glycine max), 5'ss of exon 3
TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattac-tgtt--ttgagtctcttagtttcagttgataatgttattcttcacctta--------gatgcatgattcttactttcagaagttcgattgttttaaacttatttcctcaaataatttcag--------------
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CTTGTTCTCTTAGGTGATTCTGGTGTTGGCAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatatgttgcttcggtacttttattttattttttaatataatttttcttaatatggtttatgatataaattttttgtctttttatgtt-aattattccatggaaattttcttatatgttttagactctgtaatgtaag
upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 3
lower sequence: GLYMA10G35230.3 (Glycine max), 5'ss of exon 3
TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattac-tgtt-ttgagt-ctcttagtttcagttgataatgttattcttcaccttaga-tgcatgattcttactttcagaagttcgattgttttaaacttatttcctcaaataatttcag-------------------------
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CTTGTTCTCTTAGGTGATTCTGGTGTTGGTAAAAGCTGTATTGTTCTACGATTTGTTCGTGGTCAGTTTGATCCAACATCTAAGgtaaatatatgttatttagtacttttatttttattttttaatgtaattttttttaatatagtttatgacaaaaaaatattgtcgtcttgatatgttaa--ttattccatggaattgttcttatatgttttagactttgtaatgtaag
upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 3
lower sequence: AT3G54840.2 (Arabidopsis thaliana), 5'ss of exon 3
TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactgttttga-gtctcttagtttcagttgataatgttattcttcaccttagatgcatgattct-tactttcagaagttcgattgttt---taaacttatttcctcaaataatttcag--------------------
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TTAGTTCTATTAGGAGACTCTGGTGTTGGTAAAAGTTGTATTGTCCTTCGATTTGTACGTGGTCAGTTTGACGCTACATCTAAGgtaagtaaagccttgttatctaattgtctttattgaccatctgacacctttttagaacaccatgctctgatgtgagtgaatattagactattagagtatacttatctgc-cactagatctcaagactactagctatgtatcag
upper sequence: LOC_Os03g05740.1 (Oryza sativa), 5'ss of exon 3
lower sequence: Vv13s0019g04680.t01 (Vitis vinifera), 5'ss of exon 3
TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactgttttgagtctcttagtttcagttgataatgttattcttcaccttagatgcatgattcttactttcagaagttcgattgttttaa-acttatttcctcaaataatttcag----------------------------------------------------------------
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CTGGTTTTGTTGGGGGATTCTGGTGTTGGAAAAAGCTGTATTGTTCTTCGTTTTGTTCGTGGCCAGTTTGACCCTACATCCAAGgtaagaaatatacatagctatatattatgtgatgcacattttttttttcccttttattatattaaatt--ctgttcaaccttgttttgtgccaatggatgttagcatcaatcctctcatgcaaaatacatggatgttatttcatgatagatttacttagattggttgatcttaataacttcagMapped 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|11565095|gb|AU165731.1|AU165731EST: GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAG GTAACTG-CGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
genomic: GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactg ... ataatttcagGTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
EST:
gi|3760086|gb|C97344.1|C97344EST: GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAG GTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
genomic: GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactg ... ataatttcagGTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
EST:
gi|6782805|gb|C99985.1|C99985EST: GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAG GTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
genomic: GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactg ... ataatttcagGTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
EST:
gi|300216317|gb|HO088102.1|HO088102EST: GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAG GTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
genomic: GTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactg ... ataatttcagGTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCA
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:
74 (upstream exon),
64 (downstream exon)
Score:
20TTGGTATTGCTTGGTGACTCTGGTGTAGGGAAAAGTTGCATTGTTCTTCGCTTTGTTCGTGGTCAGTTTGATCCCACTTCCAAGgtgattactg ... ataatttcagGTAACTGTCGGTGCATCATTTTTATCACAAACATTGGCTTTGGAGGACTCAACAATAGTGAAATTTGAAATATGGGATACCGCTGGACAAGAGAG
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