In molecular biology , reading frames are defined as spans of DNA sequence between the start and stop codons . Usually, this is considered within a studied region of a prokaryotic DNA sequence, where only one of the six possible reading frames will be "open" (the "reading", however, refers to the RNA produced by transcription of the DNA and its subsequent interaction with the ribosome in translation ). Such an ORF may contain a start codon (usually AUG in terms of RNA ) and by definition cannot extend beyond a stop codon (usually UAA, UAG or UGA in RNA). That start codon (not necessarily the first) indicates where translation may start. The transcription termination site is located after the ORF, beyond the translation stop codon. If transcription were to cease before the stop codon, an incomplete protein would be made during translation.
23-1211: 128989 27883 ENSG00000183597 ENSMUSG00000013539 Q6ICL3 P54797 NM_001283179 NM_001283186 NM_001283199 NM_001283215 NM_001283235 NM_001283248 NM_152906 NM_001322141 NM_001322142 NM_001322143 NM_001322144 NM_001322145 NM_001322146 NM_001322147 NM_001322148 NM_001322149 NM_001322150 NM_001322153 NM_001322155 NM_001322160 NM_001322163 NM_001322166 NM_001322167 NM_001322169 NM_001322171 NM_001322172 NM_001322173 NM_001322174 NM_001322175 NM_138583 NP_001270108 NP_001270115 NP_001270128 NP_001270144 NP_001270164 NP_001270177 NP_001309070 NP_001309071 NP_001309072 NP_001309073 NP_001309074 NP_001309075 NP_001309076 NP_001309077 NP_001309078 NP_001309079 NP_001309082 NP_001309084 NP_001309089 NP_001309092 NP_001309095 NP_001309096 NP_001309098 NP_001309100 NP_001309101 NP_001309102 NP_001309103 NP_001309104 NP_690870 n/a Transport and golgi organization 2 homolog (TANGO2) also known as chromosome 22 open reading frame 25 (C22orf25)
46-410: A DNA sequence. The presence of an ORF does not necessarily mean that the region is always translated . For example, in a randomly generated DNA sequence with an equal percentage of each nucleotide , a stop-codon would be expected once every 21 codons . A simple gene prediction algorithm for prokaryotes might look for a start codon followed by an open reading frame that is long enough to encode
69-402: A DNA strand has three distinct reading frames. The double helix of a DNA molecule has two anti-parallel strands; with the two strands having three reading frames each, there are six possible frame translations. The ORF Finder (Open Reading Frame Finder) is a graphical analysis tool which finds all open reading frames of a selectable minimum size in a user's sequence or in a sequence already in
92-518: A hit in BLASTX, the program predicts the coding regions based on the translation reading frames identified in BLASTX alignments, otherwise, it predicts the most probable coding region based on the intrinsic signals of the query sequences. The output is the predicted peptide sequences in the FASTA format, and a definition line that includes the query ID, the translation reading frame and the nucleotide positions where
115-452: A typical protein, where the codon usage of that region matches the frequency characteristic for the given organism's coding regions. Therefore, some authors say that an ORF should have a minimal length, e.g. 100 codons or 150 codons. By itself even a long open reading frame is not conclusive evidence for the presence of a gene . Some short ORFs (sORFs), also named Small open reading frames , usually < 100 codons in length, that lack
138-623: A vast array of phenotypes and is not attributed to the loss of a single gene. The vast phenotypes arise from deletions of not only DiGeorge Syndrome Critical Region (DGCR) genes and disease genes but other unidentified genes as well. C22orf25 is in close proximity to DGCR8 as well as other genes known to play a part in DiGeorge Syndrome such as armadillo repeat gene deleted in Velocardiofacial syndrome ( ARVCF ), Cathechol-O-methyltransferase ( COMT ) and T-box 1 ( TBX1 ). The promoter for
161-571: Is a protein that in humans is encoded by the TANGO2 gene. The function of C22orf25 is not currently known. It is characterized by the NRDE superfamily domain (DUF883), which is strictly known for the conserved amino acid sequence of (N)- Asparagine (R)- Arginine (D)- Aspartic Acid (E)- Glutamic Acid . This domain is found among distantly related species from the six kingdoms: Eubacteria , Archaebacteria , Protista , Fungi , Plantae , and Animalia and
184-504: Is a R-package in Bioconductor for finding open reading frames and using Next generation sequencing technologies for justification of ORFs. orfipy is a tool written in Python / Cython to extract ORFs in an extremely and fast and flexible manner. orfipy can work with plain or gzipped FASTA and FASTQ sequences, and provides several options to fine-tune ORF searches; these include specifying
207-595: Is a domain of unknown function spanning majority of the C22orf25 gene and is found among distantly related species, including viruses. Post translational modifications of the C22orf25 gene that are evolutionarily conserved in the Animalia and Plantae kingdoms as well as the Canarypox Virus include glycosylation (C-mannosylation), glycation , phosphorylation (kinase specific), and palmitoylation . C22orf25 localizes to
230-485: Is a program which not only gives information about the coding and non coding sequences but also can perform pairwise global alignment of different gene/DNA regions sequences. The tool efficiently finds the ORFs for corresponding amino acid sequences and converts them into their single letter amino acid code, and provides their locations in the sequence. The pairwise global alignment between the sequences makes it convenient to detect
253-585: Is a sequence that has a length divisible by three and is bounded by stop codons. This more general definition can be useful in the context of transcriptomics and metagenomics , where a start or stop codon may not be present in the obtained sequences. Such an ORF corresponds to parts of a gene rather than the complete gene. One common use of open reading frames (ORFs) is as one piece of evidence to assist in gene prediction . Long ORFs are often used, along with other evidence, to initially identify candidate protein-coding regions or functional RNA -coding regions in
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#1732869356956276-553: Is known to be involved in Golgi organization and protein secretion. It is likely that it localizes in the cytoplasm but is anchored in the cell membrane by the second amino acid. C22orf25 is also xenologous to T10 like proteins in the Fowlpox Virus and Canarypox Virus . The gene coding for C22orf25 is located on chromosome 22 and the location q11.21, so it is often associated with 22q11.2 deletion syndrome . The C22orf25 gene
299-460: Is located on the long arm (q) of chromosome 22 in region 1, band 1, and sub-band 2 (22q11.21) starting at 20,008,631 base pairs and ending at 20,053,447 base pairs. There is a 1.5-3.0 Mb deletion containing around 30-40 genes , spanning this region that causes the most survivable genetic deletion disorder known as 22q11.2 deletion syndrome , which is most commonly known as DiGeorge syndrome or Velocaridofacial syndrome. 22q11.2 deletion syndrome has
322-419: The C22orf25 gene spans 687 base pairs from 20,008,092 to 20,008,878 with a predicted transcriptional start site that is 104 base pairs and spans from 20,008,591 to 20,008,694. The promoter region and beginning of the C22orf25 gene (20,008,263 to 20,009,250) is not conserved past primates. This region was used to determine transcription factor interactions. Some of the main transcription factors that bind to
345-435: The TANGO2 gene may cause defects in mitochondrial β-oxidation and increased endoplasmic reticulum stress and a reduction in Golgi volume density. These mutations results in early onset hypoglycemia , hyperammonemia , rhabdomyolysis , cardiac arrhythmias , and encephalopathy that later develops into cognitive impairment. Abnormal autophagy and mitophagy have been associated with TANGO2-related disease and may explain
368-526: The classical hallmarks of protein-coding genes (both from ncRNAs and mRNAs) can produce functional peptides. 5’-UTR of about 50% of mammal mRNAs are known to contain one or several sORFs, also called upstream ORFs or uORFs . However, less than 10% of the vertebrate mRNAs surveyed in an older study contained AUG codons in front of the major ORF. Interestingly, uORFs were found in two thirds of proto-oncogenes and related proteins. 64–75% of experimentally found translation initiation sites of sORFs are conserved in
391-447: The coding region begins and ends. OrfPredictor facilitates the annotation of EST-derived sequences, particularly, for large-scale EST projects. ORF Predictor uses a combination of the two different ORF definitions mentioned above. It searches stretches starting with a start codon and ending at a stop codon. As an additional criterion, it searches for a stop codon in the 5' untranslated region (UTR or NTR, nontranslated region ). ORFik
414-611: The cytoplasm and is anchored to the cell membrane by the second amino acid. As mentioned previously, the second amino acid is modified by palmitoylation. Palmitoylation is known to contribute to membrane association because it contributes to enhanced hydrophobicity. Palmitoylation is known to play a role in the modulation of proteins' trafficking, stability and sorting. Palmitoylation is also involved in cellular signaling and neuronal transmission. C22orf25 has been shown to interact with NFKB1 , RELA , RELB , BTRC , RPS27A , BCL3 , MAP3K8 , NFKBIA , SIN3A , SUMO1 , Tat . Mutations in
437-520: The database. This tool identifies all open reading frames using the standard or alternative genetic codes. The deduced amino acid sequence can be saved in various formats and searched against the sequence database using the basic local alignment search tool (BLAST) server. The ORF Finder should be helpful in preparing complete and accurate sequence submissions. It is also packaged with the Sequin sequence submission software (sequence analyser). ORF Investigator
460-435: The different mutations, including single nucleotide polymorphism . Needleman–Wunsch algorithms are used for the gene alignment. The ORF Investigator is written in the portable Perl programming language , and is therefore available to users of all common operating systems. OrfPredictor is a web server designed for identifying protein-coding regions in expressed sequence tag (EST)-derived sequences. For query sequences with
483-413: The genomes of human and mouse and may indicate that these elements have function. However, sORFs can often be found only in the minor forms of mRNAs and avoid selection; the high conservation of initiation sites may be connected with their location inside promoters of the relevant genes. This is characteristic of SLAMF1 gene, for example. Since DNA is interpreted in groups of three nucleotides (codons),
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#1732869356956506-522: The promoter are listed below. Expression data from Expressed Sequence Tag mapping, microarray and in situ hybridization show high expression for Homo sapiens in the blood , bone marrow and nerves . Expression is not restricted to these areas and low expression is seen elsewhere in the body. In Caenorhabditis elegans , the snt-1 gene (C22orf25 homologue) was expressed in the nerve ring, ventral and dorsal cord processes, sites of neuromuscular junctions, and in neurons. The NRDE (DUF883) domain,
529-578: The varying presentation in muscle biopsies, including secondary abnormal fatty acid and mitochondrial metabolism. Open reading frame In eukaryotic genes with multiple exons , introns are removed and exons are then joined together after transcription to yield the final mRNA for protein translation. In the context of gene finding , the start-stop definition of an ORF therefore only applies to spliced mRNAs , not genomic DNA, since introns may contain stop codons and/or cause shifts between reading frames. An alternative definition says that an ORF
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