Sequence
atgc intronic sequence ATGC exonic sequencegtatgtctgctttccaatggtttaatctaccattcatttttggcaatcacaccccatttgtatacgaaatttatcattgaatgaaagatgcagctaggtttgaaatattttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG
Basic information
species | Oryza sativa |
transcript | LOC_Os12g13590.1 |
intron # | 16 |
splice site | 3' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GRMZM5G823484_T01 (Zea mays), 3'ss of exon 2
gtatgtctgctttccaatggtttaatctaccattcatttttggcaatcacaccccatttgtatacgaaatttatcattgaatgaaagatgcagctaggtttgaaatattttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG
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------------tagaaaagcaagaacgact-tacaatttagatggaaggagtacatctatataaggagtt-atcattttatgtgaaatttatttgaatttcaaatatttg--cagCAAGAGGTGGCAGCTTCAGCTGGTGAGAGCAGCTTTAGATCCTTTATGATTGCTGTGCAGCGTTGTACCAGTAGCGTAGCTATTCTTCAGCAG
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA16G01660.1 (Glycine max), 3'ss of exon 16
gtatgtctgctttccaatggtttaatctaccattcatttttggcaatcacaccccatttgtatacgaaatttatcattga-atgaaagatgcagctaggtttgaaatattttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG
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--------gtaattacatgattt--ttttgcatgctcttgtta-aagtatatagtacatatgagcacatttcaccatacatattcaagatttatttg---ttgatatg------cagGCAGAGGCGGCGGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTCATGATTGCTGTGCAACGTTCTGGAAGCAGTGTAGCTATTATTCAACAA
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 16
lower sequence: GLYMA07G05160.1 (Glycine max), 3'ss of exon 16
gtatgtctgctttccaatggtttaatctaccattcatttttggcaatcacaccccatttgtatacgaaatttatcattga-atgaaagatgcagctaggtttgaaatattttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG
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--------gtaattacataattt--ttttgcatactcttgtta-aagtatatagtatatatgagcacatttcaccagacatattcaagatttatttg---ttgatatg------cagGCAGAGGCGGCAGCAGCTGCTGGTGAAAGTAGTTTCAGATCTTTTATGATTGCTGTACAACGTTCTGGAAGCAGTGTAGCTATTATTCAACAA
upper sequence: LOC_Os12g13590.1 (Oryza sativa), 3'ss of exon 16
lower sequence: Vv15s0046g02200.t01 (Vitis vinifera), 3'ss of exon 16
---------------------gtatgtctgctttccaatggtttaatctaccattcatttttgg-caat-cacaccccattt-----gtatacga-aatttatcattgaatgaa-agatgcagctaggtttgaaatattttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG
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gtaattacttgatcacatggccattttctgcattttaa-aatttactctactacatacctcaattcaatgtatatgcttcttagaaagtattgaataatttatctagaaattatcgggcataagagaatttgttactgatgtgtagGCAGAAGCTGCTGCTGCTGCTGGTGAAAGCAGTTTCAGATCTTTCATGGTGGCTGTACAGCGTTGTGCTAGCAGTGTGGCTATTGTTCAGCAAMapped 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|33822211|gb|CF336920.1|CF336920EST: TCATTGGAACAAGTG-TAGTAGAAGGGTTGCTACTGCTGCTGCTAATGCT GCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGANT
genomic: TCATTGGAACAAGTGTTAGTAGAAGGGTTGCTACTGCTGCTGCTAATGCTgtatgtctgc ... attttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGA-T
EST:
gi|29669745|gb|CB666020.1|CB666020EST: TCATTGGAACAAGTGTTAGTAGAAGGGTTGCTACTGCTGCTGCTAATGCT GCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATT
genomic: TCATTGGAACAAGTGTTAGTAGAAGGGTTGCTACTGCTGCTGCTAATGCTgtatgtctgc ... attttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATT
EST:
gi|33822202|gb|CF336916.1|CF336916EST: TCATTGGAACAAGTGTTAGTAGAAGGGTTGCTACTGCTGCTGCTAATGCT GCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATT
genomic: TCATTGGAACAAGTGTTAGTAGAAGGGTTGCTACTGCTGCTGCTAATGCTgtatgtctgc ... attttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATT
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:
65 (upstream exon),
66 (downstream exon)
Score:
21CCATGCTAGAGAGAGTTTAAATCATGCAGCAACTCAACGGGATAGATATGTCATTGGAACAAGTGTTAGTAGAAGGGTTGCTACTGCTGCTGCTAATGCTgtatgtctgc ... attttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG
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atgc intronic sequence ATGC exonic sequenceIntronic sequence truncated to 55 bases.atacgaaatttatcattgaatgaaagatgcagctaggtttgaaatattttttcagGCAGAGGCGGCAGCTGCTGCAGGTGAGAGTAGCTTTAGATCCTTCATGATTGCTGTGCAGCGTTGTGCTAGCAGTGTGGCTATTCTTCAGCAG
tattttttc CT-rich tract
tttgaaatattttttc TA-rich tract