Sequence
atgc intronic sequence ATGC exonic sequenceTTTTATTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGATCCTGTACCTGTCAGCATGCCTGGTATTCTCATCACAGATGTCAGCAGAACAAAGgtactacctccgtcccaaaatgtagctatttctagcacagtactttgtcccaaaatgaagctatttttctacctaccttctcctctcaaccaatcacaac...
Basic information
species | Oryza sativa |
transcript | LOC_Os06g48650.2 |
intron # | 7 |
splice site | 5' |
intron type | U2 |
Orthologous splice sites
atgc intronic sequence ATGC exonic sequence
upper sequence: LOC_Os06g48650.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G099452_T02 (Zea mays), 5'ss of exon 8
TTTTATTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGATCCTGTACCTGTCAGCATGCCTGGTATTCTCATCACAGATGTCAGCAGAACAAAGgtactacctccgtcccaaaatgtagctatttctagcacagtactttgtcccaaaatgaagctatttttctacctaccttctcctctcaaccaatcacaac----
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CTTTGTTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGACCCTGTACCAGTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACCGAGgtattatacgtctagcagaaccttattgcatat----ttgcttatgattgccatgcgtaggcaacatcatacatagaagtatgaaaaaatgagactgtatattc
upper sequence: LOC_Os06g48650.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GRMZM2G114394_T02 (Zea mays), 5'ss of exon 8
TTTTATTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGATCCTGTACCTGTCAGCATGCCTGGTATTCTCATCACAGATGTCAGCAGAACAAAGgtactac----ctccgtcccaaa-----atgtagctatttctagcacagtactttgtcccaaaatgaagctatttttctacctaccttctcctctcaaccaatcacaac
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CTTTGTTGTTGCTGTGGAGAATAATTACCCAGGAACAAAATTTGACCCTGTACCATTCAGCATCCCTGGAATTCTCATCACAGATGTCAGCAAAACGGAGgtattgcagagccttatttcatatttgcatatggttgccacttgtagacaacatcatacatagacatatggaaaaatgagactgtatattcatg--aataga-------
upper sequence: LOC_Os06g48650.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA09G06640.1 (Glycine max), 5'ss of exon 8
TTTTATTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGATCCTGTACCTGTCAGCATGCCTGGTATTCTCATCACAGATGTCAGCAGAACAAAGgtactacctccgtcccaaaatgtagctatttctagcacagtact--ttgtcccaaaatgaagctatttttctacctaccttctcctctcaaccaatcacaac-
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ATTTGTTCTTTGTGTTGAAAATGTTTCCCCTGGAACAAAATTTGATCCCGTCCCTGTTGGCATTCCTGGGATTCTTATCACAGATGCCAGCAAATCAAAGgtacttgaatcacatctag--gtagatatcgatgatg-aatgctgactgtttccatctgttttcttgtagccgattatttactccacagcctaatattcagtt
upper sequence: LOC_Os06g48650.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA15G17830.1 (Glycine max), 5'ss of exon 7
TTTTATTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGATCCTGTACCTGTCAGCATGCCTGGTATTCTCATCACAGATGTCAGCAGAACAAAGgtact--acctccgtcccaaaatgtagctatttctagcacagtactttgtcccaaaatgaagctatttttctacctaccttctcct-ctcaaccaatcacaac---
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GTTTGTTCTTTGTGTTGAAAATGTTTCTCCTGGAACAAAATTTGATCCAGTCCCTGTTGGCATTCCTGGGATTCTTATCACAGATGCCAGCAAATCAAAGgtacttgaatcacatctaggtagataacgatgatgaatgcta---actgtttccatct---gttttcttgtagccgatgatttactacacagcctaattcagctgc
upper sequence: LOC_Os06g48650.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA13G00580.1 (Glycine max), 5'ss of exon 7
TTTTATTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGATCCTGTACCTGTCAGCATGCCTGGTATTCTCATCACAGATGTCAGCAGAACAAAGgtactacctc-cgtcccaaaatgtagctatttctagcacagtactttgtcccaaaatgaagctatttttctacctaccttctcctctcaaccaatcacaac
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ATTTGTTCTTTGTGTTGAAAACAATTCCCCAGGAACAAAATTTGATCCAGTCCCTGTTGGTCTTCCTGGGATTCTCATCACAGATGTCAGCAATTCTAAGgtaatccgacacatctgtactggtgtatatatgcagaggtagattgagtttgatgctaaatccattttctcttggcccttaatttattccacagtcaagt-
upper sequence: LOC_Os06g48650.3 (Oryza sativa), 5'ss of exon 7
lower sequence: GLYMA17G06740.1 (Glycine max), 5'ss of exon 7
TTTTATTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGATCCTGTACCTGTCAGCATGCCTGGTATTCTCATCACAGATGTCAGCAGAACAAAGgtactacctccgtcccaaaatgtagctatttctagcacagtactttgtcccaaaatgaagctatttttctacctaccttctcctctcaacc-aatcacaac-
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ATTTGTTCTTTGTGTTGAAAACATTTCCCTAGGAACAAAATTTAATCCAGTTCCTGTTGGCCTTCCTGGGATTCTCATCATAGATGTCAGCAATTCAAAGgtaatcagactcatctgtactggtg-tatctat-gtagaggtagatgtttgaagctaaatccattttctcttggcccttaattttttggctgaattgcagtt
upper sequence: LOC_Os06g48650.3 (Oryza sativa), 5'ss of exon 7
lower sequence: Vv11s0103g00550.t01 (Vitis vinifera), 5'ss of exon 8
TTTTATTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGATCCTGTACCTGTCAGCATGCCTGGTATTCTCATCACAGATGTCAGCAGAACAAAGgta------cta--cctccgtcccaaaatgtagctatttctagcacagtactttgtcccaaaatgaagctatttttctacctaccttctc-ctctcaaccaatcacaac
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GTTTGTTCTTGCTGTGGAAAATGTTTCTCCAGGAACAAAGTTTGATCCTGTTCCTGTCAGTATTCCTGGGATTCTCATCACAGAAGTCAGCAAATCAATGgtaaatatcttaattcttcttctttaatgatatatatttccagta-ggtagatagtggtccagtgtgactggcaccatctggaacatcccgctatcagttg--------Mapped 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|66913003|gb|CX099851.1|CX099851EST: TACCTGTCAGCATGCCTGGTATTCTCATCACAGATGTCAGCAGAACAAAA GATCTTATAGACTACTACAACTCTTCTACAATAAGAGATTGGGCAGGA
genomic: TACCTGTCAGCATGCCTGGTATTCTCATCACAGATGTCAGCAGAACAAAGgtactacctc ... ggttctgtagGATCTTATAGACTACTACAACTCTTCTACAATAAGAGATTGGGCAGGA
Putative cis-regulatory sequences
atgc | intron | ATGC | exonic elements by Pertea et al. |
ATGC | exon | atgc | putative intronic elements |
| | ATGC | putative exonic elements identified for retained introns |
10 20 30 40 50 60 70 80 90 100 110 120 130 140 150 160 170 180 190 200 210 220
---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|---------|
TTTTATTGTTGCTGTGGAGAATAGTTACCCAGGAACAAAATTTGATCCTGTACCTGTCAGCATGCCTGGTATTCTCATCACAGATGTCAGCAGAACAAAGgtactacctccgtcccaaaatgtagctatttctagcacagtactttgtcccaaaatgaagctatttttctacctaccttctcctctcaaccaatcacaac
- - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - - CAGATG