Homo sapiens complex locus RSAD2, encoding radical S-adenosyl methionine domain containing 2.
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SUMMARY back to top
RefSeq annotates one representative transcript (NM included in AceView variant.a), but Homo sapiens cDNA sequences in GenBank, dbEST, Trace and SRA, filtered against clone rearrangements, coaligned on the genome and clustered in a minimal non-redundant way by the manually supervised AceView program, support at least 5 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus is complex: it appears to produce several proteins with no sequence overlap.
Expression: According to AceView, this gene is expressed at high level, 1.5 times the average gene in this release. The sequence of this gene is defined by 176 GenBank accessions from 157 cDNA clones, some from lung (seen 33 times), trachea (8), uterus (8), placenta (6), adenocarcinoma (5), pancreas (5), stomach (5) and 51 other tissues. We annotate structural defects or features in 6 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 8 distinct gt-ag introns. Transcription produces 6 different mRNAs, 5 alternatively spliced variants and 1 unspliced form. There are 3 probable alternative promotors, 3 non overlapping alternative last exons and 5 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 3' end, overlapping exons with different boundaries. 100 bp of this gene are antisense to spliced gene CMPK2, raising the possibility of regulated alternate expression.
Efficacy of translation may be reduced by the presence of a shorter translated product (uORF) initiating at an AUG upstream of the main open reading frame (in variant aAug10, bAug10).
Function: There are 14 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to a disease (Hepatitis C, Chronic) and proposed to participate in processes (defense response to virus, regulation of ossification). Proteins are expected to have molecular functions (catalytic activity, iron-sulfur cluster binding, metal ion binding) and to localize in various compartments (endoplasmic reticulum, cytoplasm, mitochondrion, endoplasmic reticulum membrane, Golgi apparatus).
Protein coding potential: 5 spliced mRNAs putatively encode good proteins, altogether 5 different isoforms (3 complete, 1 COOH complete, 1 partial), some containing Radical SAM superfamily domain [Pfam]. The remaining mRNA variant (unspliced) appears not to encode a good protein.

Please quote: AceView: a comprehensive cDNA-supported gene and transcripts annotation, Genome Biology 2006, 7(Suppl 1):S12.
Map on chromosome 2, links to other databases and other names
Map: This gene RSAD2 maps on chromosome 2, at 2p25.2 according to Entrez Gene. In AceView, it covers 33.00 kb, from 7005938 to 7038937 (NCBI 37, August 2010), on the direct strand.
Links to: the SNP view, gene overviews from Entrez Gene 91543, GeneCards, expression data from ECgene, UniGene, molecular and other annotations from UCSC, or our GOLD analysis.
The previous AceView annotation is here.
Other names: The gene is also known as RSAD2, cig5, vig1, cig33 or 2510004L01Rik, LOC91543. It has been described as radical S-adenosyl methionine domain-containing protein 2, viperin, cytomegalovirus-induced gene 5 protein, virus inhibitory protein, endoplasmic reticulum-associated, interferon-inducible.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Rsad2 (e= 10-131).
The closest C.elegans gene, according to BlastP, is the AceView/WormGene XO712 (e=0.26)
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
RSAD2 Gene expression in 15 primates, 16 tissues, from the NHPRTR project in sFPKM BAB SkeletalMuscle WholeBlood CHP Kidney Liver Lung Spleen CMC CMM Cerebellum HUM Brain Colon Heart LymphNode Ovary Testis JMI BoneMarrow MLM OWL PTM RMC RMI Pituitary SQM Thymus MST SMY RTL 0.36 11.6 3.10 2.90 6.65 1.91 6.21 7.64 0.78 0.39 4.71 3.10 2.19 6.65 1.45 0.72 6.21 3.33 1.91 5.04 4.71 18.8 6.65 21.6 0.36 26.6 4.39 43.2 16.4 0.89 1.45 9.41 2.35 1.10 1.91 14.3 0.32 0.78 5.79 1.35 0.78 1.66 3.82 3.33 3.10 0.19 0.22 0.63 1.45 0.36 0.72 0.42 2.35 1.45 30.6 1.78 2.05 10.1 6.21 3.33 3.57 21.6 0.68 0.72 0.45 2.70 0.48 1.18 0.39 1.66 0.72 0.72 13.3 1.78 0.83 4.10 1.35 0.45 2.05 2.19 1.55 2.70 28.5 1.45 0.55 0.89 0.68 12.4 0.83 0.55 0.68 3.10 1.26 0.21 1.26 2.52 0.27 0.96 0.39 0.21 0.13 1.10 0.78 1.02 1.02 1.26 0.16 3.57 1.18 1.10 1.45 2.19 0.34 17.6 1.78 7.13 0.48 2.35 1.35 1.66 8.19 3.33 7.64 7.13 23.2 10.8 5.79 1.18 5.04 10.8 5.04 17.6 17.6 0.08 0.21 2.19 3.33 1.91 3.33 10.8 1.26 6.65 6.21 0.63 0.48 1.02 4.39 20.2 12.4 2.05 35.1 Expression quantiles None Weak 1 2 3 4 5 6 7 8 10 20 This gene All genes log2 distributions RNA-seq gene expression profile across 16 selected tissues from the Non-Human Primates Reference Transcriptome Resource (link to NHPRTR project).
- Primates: Apes (HUM: Human (Illumina BodyMap 2), CHP: Chimpanzee), Old World monkeys (PTM: Pig-Tailed Macaque, JMI Japanese Macaque, RMI Rhesus Macaque Indian, RMC Rhesus Macaque Chinese, CMM Cynomolgus Macaque Mauritian, CMC Cynomolgus Macaque Chinese, BAB Olive Baboon, SMY Sooty Mangabey); New World monkeys (MST common Marmoset, SQM Squirrel Monkey, OWL Owl Monkey); and Lemurs (MLM Mouse Lemur, RTL Ring-Tailed Lemur).
- The level for significantly expressed genes is color coded in 8 equal sized bins (light to dark green). Light gray is for weak not-accurately measured expression (2 to 8 reads above intergenic background); dark gray for no expression or no sequence conservation (0 read in gene). The plot to the right shows the distribution of measured expression values in all tissues for all genes (blue) and for this gene (green), in Magic index = log2(1000 sFPKM).
You may also examine the strand-specific genome coverage plots on the experimental AceView/Magic hub at UCSC, by tissue or by species. Tracks may be slow to load; please reload if some tracks come up yellow-greenish, and thanks to UCSC for the great work!.
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          Complete gene on genome diagram: back to top
Please choose between the zoomable GIF version., and the HTML5/SVG version.
This diagram shows in true scale the gene on the genome, the mRNAs and the cDNA clones.
Compact gene diagram back to top
Gene RSAD2 5' 3' encoded on plus strand of chromosome 2 from 7,005,938 to 7,038,937 244 e 15175 16467 14770 15784 11627 a [NM] 172 16467 14770 15784 11627 b 15175 c 549 16467 d f-u 1 2kb 0 239 bp exon 239 bp exon 10670 bp [gt-ag] intron 3 GenBank accessions 241 RNA-seq supporting reads 6 UHR pooled cells 11 Brain 64 Blood 157 Neuroblastoma 3 Other (also 2 Primates bodymap) 461 bp exon 2 accessions, some from leiomyosarcoma (seen once) thymus (once), uterus (once) capped 5' end, 1 accession 461 bp exon 502 bp exon 502 bp exon 135 bp uORF 502 bp exon 502 bp exon 5224 bp [gt-ag] intron 98 GenBank accessions 15077 RNA-seq supporting reads 221 UHR pooled cells 458 Brain 9275 Blood 4614 Neuroblastoma 509 Other (also 2616 Primates bodymap) 162 bp exon 162 bp exon 3402 bp [gt-ag] intron 77 GenBank accessions 16390 RNA-seq supporting reads 207 UHR pooled cells 658 Brain 9612 Blood 5345 Neuroblastoma 568 Other (also 2437 Primates bodymap) 230 bp exon 230 bp exon 3011 bp [gt-ag] intron 19 GenBank accessions 14751 RNA-seq supporting reads 168 UHR pooled cells 565 Brain 8651 Blood 4817 Neuroblastoma 550 Other (also 3692 Primates bodymap) 150 bp exon 150 bp exon 3345 bp [gt-ag] intron 18 GenBank accessions 15766 RNA-seq supporting reads 132 UHR pooled cells 609 Brain 10480 Blood 4174 Neuroblastoma 371 Other (also 2607 Primates bodymap) 33 bp exon 33 bp exon 2074 bp [gt-ag] intron 18 GenBank accessions 11609 RNA-seq supporting reads 118 UHR pooled cells 505 Brain 6548 Blood 4072 Neuroblastoma 366 Other (also 2050 Primates bodymap) 3029 bp exon 3029 bp exon 147 accessions, NM_080657.4 some from lung (seen 32 times) trachea (7), uterus (7) adenocarcinoma (5), pancreas (5) capped 5' end, 38 accessions Validated 3' end, 1 accession Validated 3' end, 4 accessions Validated 3' end, 1 accession Validated 3' end, 2 accessions 3029 bp exon 247 bp exon 247 bp exon 69 bp uORF 247 bp exon 247 bp exon 4329 bp [gt-ag] intron 2 GenBank accessions 170 RNA-seq supporting reads 3 UHR pooled cells 9 Brain 75 Blood 81 Neuroblastoma 2 Other 162 bp exon 162 bp exon 3402 bp [gt-ag] intron 77 GenBank accessions 16390 RNA-seq supporting reads 207 UHR pooled cells 658 Brain 9612 Blood 5345 Neuroblastoma 568 Other (also 2437 Primates bodymap) 230 bp exon 230 bp exon 3011 bp [gt-ag] intron 19 GenBank accessions 14751 RNA-seq supporting reads 168 UHR pooled cells 565 Brain 8651 Blood 4817 Neuroblastoma 550 Other (also 3692 Primates bodymap) 150 bp exon 150 bp exon 3345 bp [gt-ag] intron 18 GenBank accessions 15766 RNA-seq supporting reads 132 UHR pooled cells 609 Brain 10480 Blood 4174 Neuroblastoma 371 Other (also 2607 Primates bodymap) 33 bp exon 33 bp exon 2074 bp [gt-ag] intron 18 GenBank accessions 11609 RNA-seq supporting reads 118 UHR pooled cells 505 Brain 6548 Blood 4072 Neuroblastoma 366 Other (also 2050 Primates bodymap) 532 bp exon 532 bp exon 2 accessions, some from pericardium (seen 2 times) capped 5' end, 1 accession 532 bp exon 210 bp exon 210 bp exon 5224 bp [gt-ag] intron 98 GenBank accessions 15077 RNA-seq supporting reads 221 UHR pooled cells 458 Brain 9275 Blood 4614 Neuroblastoma 509 Other (also 2616 Primates bodymap) 518 bp exon 4 accessions, some from blood (seen once) breast normal (once) lymphocyte (once), testis normal (once) Validated 3' end, 1 accession 518 bp exon 218 bp exon 218 bp exon 17325 bp [gt-ag] intron 2 GenBank accessions 547 RNA-seq supporting reads 6 UHR pooled cells 59 Brain 40 Blood 432 Neuroblastoma 10 Other (also 230 Primates bodymap) 162 bp exon 3402 bp [gt-ag] intron 77 GenBank accessions 16390 RNA-seq supporting reads 207 UHR pooled cells 658 Brain 9612 Blood 5345 Neuroblastoma 568 Other (also 2437 Primates bodymap) 187 bp exon 2 accessions, some from lymph (seen once) 187 bp exon 2721 bp exon 2721 bp exon 1 accession from thalamus capped 5' end, 1 accession 2721 bp exon Alternative mRNAs are shown aligned from 5' to 3' on a virtual genome where introns have been shrunk to a minimal length. Exon size is proportional to length, intron height reflects the number of cDNAs supporting each intron, the small numbers show the support of the introns in deep sequencing (with details in mouse-over) . Introns of the same color are identical, of different colors are different. 'Good proteins' are pink, partial or not-good proteins are yellow, uORFs are green. 5' cap or3' poly A flags show completeness of the transcript.
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Sequences: click on the numbers to get the DNA back to top
mRNA variant mRNA matching the genome Best predicted protein 5' UTR 3' UTR uORF Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10 4106 bp 361 aa 156 bp 2864 bp 132 bp 2kb including Promoter 21162 bp 1kb
bAug10 1354 bp 254 aa 222 bp 367 bp 66 bp 2kb including Promoter 17515 bp 1kb
cAug10 728 bp 210 aa 93 bp 2kb 5952 bp 1kb
dAug10 567 bp 188 aa 2kb 21294 bp 1kb
eAug10 700 bp 60 aa 97 bp 420 bp 2kb including Promoter 11370 bp 1kb
fAug10-unspliced 2721 bp 74 aa 1874 bp 622 bp 2kb including Promoter 2721 bp 1kb

Gene neighbors and Navigator on chromosome 2p25.2 back to top
RSAD2 D C R P RNF144A C I R P G D P R R FLJ42418 C R P CMPK2 G R R 100kb 0 RSAD2, 164 accessions 6 variants RNF144A, 238 accessions 15 variants hohimo, 2 accessions, 2 variants huyoyo, 1 accession sarfabu, 2 accessions hikere, 2 accessions serfabu, 1 accession blolabo, 1 accession shergubo, 1 accession tafabu, 2 accessions tufabu, 1 accession tofabu, 3 accessions blerlabo, 1 accession blagubo, 2 accessions tawfabu, 5 accessions teefabu, 3 accessions torfabu, 1 accession vafabu, 1 accession gawstawby, 1 accession choydar, 2 accessions vufabu, 2 accessions blogubo, 1 accession vofabu, 3 accessions feeneybo, 1 accession varfabu, 1 accession vawfabu, 2 accessions verfabu, 1 accession feyneybo, 3 accessions forneybo, 9 accessions bleylabo, 1 accession veyfabu, 2 accessions skarkla, 3 accessions ganeybo, 2 accessions vorfabu, 2 accessions voyfabu, 1 accession ramoyo, 2 accessions wufabu, 1 accession wawfabu, 1 accession weefabu, 1 accession flerlabo, 3 accessions skawkla, 1 accession skeekla, 3 accessions gerstawby, 1 accession shudar, 8 accessions weyfabu, 1 accession flugubo, 2 accessions worfabu, 1 accession woyfabu, 1 accession fleylabo, 1 accession zyfabu, 2 accessions zufabu, 1 accession guneybo, 4 accessions nuhimo, 2 accessions, 2 variants sleeverbo, 1 accession zawfabu, 1 accession nehimo, 2 accessions, 2 variants zerfabu, 1 accession glolabo, 1 accession goystawby, 1 accession zoyfabu, 3 accessions chafabu, 1 accession chufabu, 1 accession glerlabo, 1 accession chofabu, 1 accession charfabu, 1 accession flergubo, 2 accessions garneybo, 1 accession rimoyo, 1 accession kleylabo, 5 accessions fleygubo, 1 accession cheefabu, 1 accession jastawby, 1 accession florgubo, 1 accession jeestawby, 1 accession doly, 2 accessions komeyo, 1 accession sufabu, 4 accessions plorkla, 1 accession slawverbo, 1 accession blylabo, 1 accession sawfabu, 1 accession seefabu, 1 accession foystawby, 1 accession nahimo, 1 accession sorfabu, 6 accessions soyfabu, 2 accessions tyfabu, 1 accession wamoyo, 1 accession ploykla, 1 accession shorgubo, 1 accession nihimo, 2 accessions, 2 variants shoygubo, 1 accession tarfabu, 2 accessions gostawby, 1 accession terfabu, 2 accessions blygubo, 3 accessions toyfabu, 1 accession vyfabu, 3 accessions skokla, 1 accession blargubo, 1 accession veefabu, 1 accession flulabo, 1 accession flarlabo, 1 accession shadar, 1 accession wafabu, 1 accession wyfabu, 1 accession wofabu, 1 accession warfabu, 2 accessions flawlabo, 1 accession werfabu, 1 accession geestawby, 1 accession shydar, 12 accessions zafabu, 1 accession zarfabu, 1 accession flargubo, 1 accession zeyfabu, 1 accession zorfabu, 1 accession chyfabu, 1 accession glawlabo, 1 accession gloylabo, 1 accession skerkla, 1 accession cherfabu, 2 accessions jostawby, 1 accession LOC391349, 2 accessions chardar, 19 accessions 8 variants FLJ42418, 15 accessions 3 variants CMPK2, 160 accessions 10 variants LOC386597, 34 accessions 5 variants heyoyo, 3 accessions, 3 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               14 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f-u Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DC

To mine knowledge about the gene, please click the 'Gene Summary' or the 'Function, regulation, related genes ' tab at the top of the page. The 'Gene Summary' page includes all we learnt about the gene, functional annotations of neighboring genes, maps, links to other sites and the bibliography. The 'Function, regulation, related genes ' page includes Diseases (D), Pathways, GO annotations, conserved domains (C), interactions (I) reference into function, and pointers to all genes with the same functional annotation.
To compare alternative variants, their summarized annotations, predicted proteins, introns and exons, or to access any sequence, click the 'Alternative mRNAs features' tab. To see a specific mRNA variant diagram, sequence and annotation, click the variant name in the 'mRNA' tab. To examine expression data from all cDNAs clustered in this gene by AceView, click the 'Expression tissue'.

If you know more about this gene, or found errors, please share your knowledge. Thank you !