Homo sapiens gene C2orf49, encoding chromosome 2 open reading frame 49.
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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 3 spliced variants.

AceView synopsis, each blue text links to tables and details
Expression: According to AceView, this gene is expressed at high level, 1.6 times the average gene in this release. The sequence of this gene is defined by 188 GenBank accessions from 168 cDNA clones, some from brain (seen 14 times), kidney (9), pooled germ cell tumors (8), eye (5), germinal center B cell (5), hippocampus (5), hypothalamus (5) and 75 other tissues. We annotate structural defects or features in 6 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 4 distinct introns (3 gt-ag, 1 gc-ag). Transcription produces 4 different mRNAs, 3 alternatively spliced variants and 1 unspliced form. There are 2 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, splicing versus retention of one intron. 257 bp of this gene are antisense to spliced gene ronu, raising the possibility of regulated alternate expression.
Function: There are 2 articles specifically referring to this gene in PubMed. Proteins are expected to localize in various compartments (mitochondrion, nucleus). No phenotype has yet been reported to our knowledge: this gene's in vivo function is yet unknown.
Protein coding potential: 2 spliced mRNAs putatively encode good proteins, altogether 2 different isoforms (2 complete), apparently vertebrate specific. The remaining 2 mRNA variants (1 spliced, 1 unspliced; 1 partial) appear not to encode good proteins. Finally proteins from this gene may be modulated by phosphorylation, as detailed at PhosphoSite.

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 C2orf49 maps on chromosome 2, at 2q12.1 according to Entrez Gene. In AceView, it covers 12.09 kb, from 105953709 to 105965802 (NCBI 37, August 2010), on the direct strand.
Links to: manual annotations from PhosphoSite, the SNP view, gene overviews from Entrez Gene 79074, 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 C2orf49, asw, MGC5509 or FLJ45759, LOC79074. It has been described as ashwin, OTTHUMP00000203145.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene AI597479 (e=2 10-73)
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
C2orf49 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 6.21 12.4 5.40 2.70 5.40 6.21 7.64 5.40 10.1 8.78 10.1 11.6 8.19 9.41 10.1 4.71 6.21 14.3 8.19 11.6 12.4 7.13 9.41 5.40 11.6 10.8 6.65 6.21 8.19 7.64 12.4 8.19 9.41 15.3 8.78 9.41 6.21 7.13 5.79 5.40 13.3 8.78 7.13 7.64 7.13 4.39 9.41 9.41 10.1 9.41 10.1 4.39 8.78 8.78 8.78 4.71 9.41 8.19 11.6 9.41 8.19 4.71 12.4 8.19 5.79 8.78 11.6 7.13 10.8 10.8 5.79 9.41 6.65 8.78 8.78 6.65 6.65 8.19 8.19 8.19 7.13 8.19 10.1 9.41 8.78 9.41 7.64 8.78 16.4 10.8 9.41 8.19 8.19 8.78 5.40 8.19 10.8 7.13 10.8 11.6 5.79 11.6 8.78 8.78 8.19 10.8 9.41 13.3 7.13 11.6 10.1 8.19 8.19 10.8 8.78 5.04 7.64 8.19 10.1 8.78 15.3 11.6 8.78 11.6 5.04 7.64 5.40 9.41 7.13 7.13 10.8 8.78 10.1 9.41 9.41 6.21 9.41 5.79 8.78 8.19 11.6 8.78 7.64 5.40 7.64 6.65 9.41 10.1 12.4 7.64 5.79 15.3 8.19 9.41 7.64 8.78 10.8 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 C2orf49 5' 3' encoded on plus strand of chromosome 2 from 105,953,709 to 105,965,802 37626 32655 35773 a [NM] 37626 32655 35773 b c-u 37626 d 1kb 0 146 bp exon 146 bp exon 1896 bp [gt-ag] intron 46 GenBank accessions 37580 RNA-seq supporting reads 6701 UHR pooled cells 4399 Brain 3398 Blood 22736 Neuroblastoma 346 Other (also 5163 Primates bodymap) 167 bp exon 3098 bp [gt-ag] intron 47 GenBank accessions 32608 RNA-seq supporting reads 6267 UHR pooled cells 3928 Brain 4023 Blood 18175 Neuroblastoma 215 Other (also 7003 Primates bodymap) 376 bp exon 2091 bp [gt-ag] intron 51 GenBank accessions 35722 RNA-seq supporting reads 7052 UHR pooled cells 4722 Brain 3866 Blood 19906 Neuroblastoma 176 Other (also 8448 Primates bodymap) 4031 bp exon 147 accessions, NM_024093.1 some from brain (seen 13 times) kidney (8), pooled germ cell tumors (6) eye (5), germinal center B cell (5) capped 5' end, 10 accessions Validated 3' end, 9 accessions Validated 3' end, 10 accessions Validated 3' end, 2 accessions Validated 3' end, 1 accession 4031 bp exon 435 bp exon 435 bp exon 1896 bp [gt-ag] intron 46 GenBank accessions 37580 RNA-seq supporting reads 6701 UHR pooled cells 4399 Brain 3398 Blood 22736 Neuroblastoma 346 Other (also 5163 Primates bodymap) 167 bp exon 3098 bp [gt-ag] intron 47 GenBank accessions 32608 RNA-seq supporting reads 6267 UHR pooled cells 3928 Brain 4023 Blood 18175 Neuroblastoma 215 Other (also 7003 Primates bodymap) 127 bp exon 126 bp [gc-ag] intron 10 GenBank accessions 9791 RNA-seq supporting reads 2293 UHR pooled cells 1547 Brain 1192 Blood 4712 Neuroblastoma 47 Other (also 1681 Primates bodymap) 123 bp exon 2091 bp [gt-ag] intron 51 GenBank accessions 35722 RNA-seq supporting reads 7052 UHR pooled cells 4722 Brain 3866 Blood 19906 Neuroblastoma 176 Other (also 8448 Primates bodymap) 282 bp exon 13 accessions, some from hippocampus (seen 2 times) leukopheresis (2), placenta (2) pre-eclamptic placenta (2) trachea (2) Validated 3' end, 2 accessions 282 bp exon 588 bp exon 588 bp exon 1 accession from substantia nigra capped 5' end, 1 accession 588 bp exon 115 bp exon 1896 bp [gt-ag] intron 46 GenBank accessions 37580 RNA-seq supporting reads 6701 UHR pooled cells 4399 Brain 3398 Blood 22736 Neuroblastoma 346 Other (also 5163 Primates bodymap) 163 bp exon 8 accessions, some from pooled germ cell tumors (seen 2 times) breast carcinoma (once) placenta normal (once) 163 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 Upstream sequence Transcription
unit
pre-mRNA
Downstream sequence
aAug10 4720 bp 232 aa 47 bp 3974 bp 2kb including Promoter 11805 bp 1kb
bAug10 1134 bp 228 aa 222 bp 225 bp 2kb possibly including promoter 8345 bp 1kb
cAug10-unspliced 588 bp 90 aa 76 bp 239 bp 2kb including Promoter 588 bp 1kb
dAug10 278 bp 43 aa 146 bp 2kb probably including promoter 2174 bp 1kb

Gene neighbors and Navigator on chromosome 2q12.1 back to top
MRPS9 D C I R P R GPR45 D C P R C2orf49 C R P R NCK2 C I R P R R R D C I R P TGFBRAP1 R D C I R P FHL2 R 100kb 0 POU3F3, 54 accessions 2 variants MRPS9, 200 accessions 8 variants spoydey, 5 accessions 3 variants GPR45, 32 accessions stydey, 1 accession C2orf49, 175 accessions 4 variants mogabo, 12 accessions 2 variants NCK2, 344 accessions, 10 variants kunomo, 2 accessions shorjubu, 2 accessions stawjobo, 13 accessions blajubu, 2 accessions blyjubu, 1 accession blujubu, 1 accession doybubu, 1 accession blojubu, 1 accession blarjubu, 1 accession bapabo, 2 accessions blawjubu, 1 accession speydey, 1 accession bleejubu, 2 accessions blerjubu, 1 accession bleyjubu, 1 accession feebubu, 1 accession barpabo, 2 accessions flyjubu, 1 accession flujubu, 1 accession flojubu, 1 accession gybubu, 1 accession storjobo, 1 accession bawpabo, 1 accession flawjubu, 1 accession gububu, 1 accession fleejubu, 2 accessions stoyjobo, 1 accession beepabo, 1 accession floyjubu, 3 accessions glajubu, 1 accession borpabo, 1 accession bawvorbo, 1 accession glujubu, 1 accession glojubu, 2 accessions sherpobo, 2 accessions lerbubu, 1 accession klawjubu, 2 accessions dypabo, 4 accessions kleejubu, 1 accession meebubu, 1 accession puklar, 1 accession plyjubu, 1 accession ferpabo, 1 accession gapabo, 1 accession gawpabo, 1 accession nawbubu, 1 accession swerjobo, 1 accession koylo, 3 accessions rawbubu, 2 accessions skyjubu, 2 accessions skujubu, 2 accessions tobubu, 1 accession tarbubu, 1 accession gorpabo, 1 accession skeejubu, 1 accession skerjubu, 1 accession skeyjubu, 1 accession shoypobo, 1 accession wububu, 1 accession slorjubu, 1 accession sloyjubu, 1 accession warbubu, 1 accession smarjubu, 3 accessions smawjubu, 1 accession kuwaro, 6 accessions smerjubu, 1 accession jupabo, 2 accessions smeyjubu, 1 accession jopabo, 1 accession weebubu, 1 accession worbubu, 1 accession jawpabo, 1 accession zububu, 1 accession smoyjubu, 5 accessions snajubu, 1 accession jerpabo, 1 accession snojubu, 2 accessions snarjubu, 1 accession snawjubu, 1 accession spoynoybo, 1 accession shoyjubu, 3 accessions steejobo, 4 accessions stanoybo, 1 accession stunoybo, 8 accessions swarnoybo, 1 accession bupabo, 1 accession pyklar, 1 accession blorjubu, 2 accessions bloyjubu, 1 accession flajubu, 1 accession keylo, 5 accessions ferbubu, 1 accession garbubu, 1 accession sharpobo, 1 accession fleyjubu, 1 accession florjubu, 1 accession gerbubu, 2 accessions glarjubu, 1 accession boypabo, 1 accession sheypobo, 4 accessions gleyjubu, 1 accession stadey, 1 accession gloyjubu, 1 accession klajubu, 3 accessions klyjubu, 1 accession lawbubu, 1 accession klujubu, 1 accession klojubu, 2 accessions klarjubu, 1 accession klerjubu, 1 accession kleyjubu, 2 accessions korlo, 6 accessions klorjubu, 1 accession dupabo, 1 accession shorpobo, 1 accession kloyjubu, 2 accessions blaneebo, 4 accessions plajubu, 2 accessions moybubu, 1 accession plarjubu, 1 accession derpabo, 2 accessions fawpabo, 1 accession feepabo, 1 accession nineyo, 1 accession swawjobo, 1 accession nuneyo, 1 accession sweejobo, 1 accession pleyjubu, 1 accession noybubu, 1 accession geypabo, 2 accessions sweyjobo, 1 accession ployjubu, 3 accessions skajubu, 2 accessions neneyo, 1 accession skojubu, 3 accessions sworjobo, 1 accession skarjubu, 1 accession swoyjobo, 1 accession bajarbo, 1 accession byjarbo, 1 accession skoyjubu, 1 accession bujarbo, 1 accession slajubu, 1 accession pawklar, 2 accessions mumomo, 1 accession slyjubu, 1 accession slujubu, 2 accessions slojubu, 1 accession slarjubu, 1 accession peeklar, 1 accession perklar, 1 accession sleejubu, 1 accession slerjubu, 1 accession sleyjubu, 1 accession peyklar, 4 accessions smyjubu, 1 accession smujubu, 1 accession smojubu, 1 accession smorjubu, 1 accession jarpabo, 1 accession kenomo, 2 accessions stordey, 1 accession snyjubu, 1 accession snujubu, 1 accession zawbubu, 1 accession spodey, 43 accessions 6 variants paklar, 13 accessions 4 variants sweykoy, 9 accessions 3 variants spordey, 11 accessions 3 variants TGFBRAP1, 232 accessions 4 variants ronu, 38 accessions, 4 variants FHL2, 405 accessions, 20 variants sterdey, 18 accessions 6 variants ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               2 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c-u, .d Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes C

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 !