Homo sapiens complex locus C1QTNF5andMFRP, encoding membrane frizzled-related protein and C1q and tumor necrosis factor related protein 5.
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SUMMARY back to top
RefSeq summary
[MFRP] This gene encodes a member of the frizzled-related proteins. The encoded protein may play a role in eye development, as mutations in this gene have been associated with nanophthalmos, posterior microphthalmia, retinitis pigmentosa, foveoschisis, and optic disc drusen. The protein is encoded by a bicistronic mRNA, which also encodes C1q and tumor necrosis factor related protein 5.
[C1QTNF5] This gene encodes a member of the a member of the C1q/tumor necrosis factor superfamily. The encoded protein may be a component of basement membranes and may play a role in cell adhesion. This gene is contained entirely within the 3' UTR of the membrane frizzled-related protein gene on chromosome 11q23 and both genes are expressed from a bicistronic transcript. Mutations in this gene have been associated with late-onset retinal degeneration.

RefSeq annotates 2 representative transcripts from 2 genes that we see as a complex (NM included in AceView variant.b), 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 8 spliced variants.

AceView synopsis, each blue text links to tables and details
Note that this locus merges 2 different NCBI genes, because some GenBank cDNA has significant sequence overlap or common intron boundaries with both gene models.
Expression: According to AceView, this gene is well expressed, 1.1 times the average gene in this release. The sequence of this gene is defined by 124 GenBank accessions from 111 cDNA clones, some from eye (seen 12 times), brain (10), pancreas (10), islets of langerhans (7), pooled brain, lung, testis (6), rpe/choroid (6), hippocampus (4) and 45 other tissues. We annotate structural defects or features in 5 cDNA clones.
Alternative mRNA variants and regulation: The gene contains 20 distinct introns (19 gt-ag, 1 gc-ag). Transcription produces 9 different mRNAs, 8 alternatively spliced variants and 1 unspliced form. There are 2 non overlapping alternative last exons and 3 validated alternative polyadenylation sites (see the diagram). The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 6 cassette exons, overlapping exons with different boundaries, splicing versus retention of one intron.
Note that mRNA .bAug10 was found in vivo, although it is a predicted target of nonsense mediated mRNA decay (NMD).
Function: There are 24 articles specifically referring to this gene in PubMed. Functionally, the gene has been tested for association to diseases (OMIM: late-onset retinal degeneration; microphthalmia, isolated 5; nanophthalmos 2; Other sources: Eye Diseases; Hyperopia; Microphthalmia, posterior, with retinitis pigmentosa, foveoschisis, and optic disc drusen; Optic Disk Drusen; Retinal degeneration, late-onset, autosomal dominant) and proposed to participate in processes (response to stimulus, visual perception). Proteins are expected to localize in various compartments (membrane, extracellular region). Putative protein interactors have been described (C1QTNF5ANDMFRP, SLC2A4).
Protein coding potential: 7 spliced and the unspliced mRNAs putatively encode good proteins, altogether 7 different isoforms (2 complete, 2 COOH complete, 3 partial), some containing domains C1q domain, Collagen triple helix repeat (20 copies), CUB domain, Fz domain, Low-density lipoprotein receptor domain class A [Pfam], some transmembrane domains [Psort2]. The remaining mRNA variant (spliced; partial) 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 11, links to other databases and other names
Map: This gene C1QTNF5andMFRP maps on chromosome 11, at 11q23.3 according to Entrez Gene. In AceView, it covers 7.74 kb, from 119217383 to 119209646 (NCBI 37, August 2010), on the reverse strand.
Links to: manual annotations from OMIM_605670, OMIM_609549, OMIM_611040, the SNP view, SNP view, gene overviews from Entrez Gene 114902, 83552, 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 C1QTNF5andMFRP, RD6, NNO2, FLJ30570, MGC32938, DKFZP586B0621, UNQ303/PRO344, LORD, CTRP5, MFRP, C1QTNF5 or LOC114902, LOC83552. It has been described as membrane frizzled-related protein, membrane-type frizzled-related protein, complement C1q tumor necrosis factor-related protein 5.
Closest AceView homologs in other species ?
The closest mouse gene, according to BlastP, is the AceView gene Mfrp (e=3 10-64).
The closest C.elegans genes, according to BlastP, are the AceView/WormGenes 5N107 (e=2 10-06), nas-39 (e=2 10-05), mom-5 (e=4 10-05), which may contain interesting functional annotation
RNA_seq discoveries back to top
Expression/conservation in primates tissues evaluated by cross-mapping to human. back to top
C1QTNF5andMFRP 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 0.83 1.66 0.59 5.79 0.59 8.78 1.18 3.57 7.64 3.10 10.8 1.26 8.19 12.4 1.55 7.13 6.21 2.90 0.51 0.45 3.10 0.59 0.83 2.19 0.59 0.96 1.10 1.91 1.55 1.10 0.36 0.55 1.78 2.70 3.33 1.10 1.91 1.45 6.21 0.34 0.39 0.78 2.90 2.70 1.78 1.10 1.78 1.45 0.39 2.90 0.48 2.52 0.45 0.36 2.70 0.59 1.35 2.52 0.51 2.90 2.90 2.52 1.45 0.68 1.35 1.02 2.19 2.70 1.26 3.57 2.70 1.26 0.14 1.55 1.55 1.66 1.45 2.35 2.70 2.52 1.02 2.52 1.91 3.10 0.83 3.57 0.89 0.32 1.35 0.21 1.26 6.65 4.39 5.04 2.70 7.13 5.79 4.39 7.64 1.18 0.83 3.10 2.90 1.78 1.18 0.83 0.59 0.89 1.91 1.91 0.59 0.63 2.90 1.26 2.19 4.39 0.24 1.66 1.66 1.91 0.45 1.91 1.91 2.35 1.78 3.33 0.39 0.27 1.91 1.78 0.51 1.91 1.55 0.51 3.82 0.78 0.96 0.17 1.18 0.21 0.42 0.34 1.35 1.66 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 C1QTNF5andMFRP 5' 3' encoded on minus strand of chromosome 11 from 119,217,383 to 119,209,646 159 147 182 216 136 190 296 173 121 135 167 a 159 147 182 216 136 190 296 173 121 135 167 16945 20607 b [NM] 159 147 182 216 136 2 121 1 c g-u 20607 d 6 147 182 216 e 16945 24 h 4 147 i 78 f 1 2kb 0 201 bp exon 201 bp exon 85 bp [gt-ag] intron 12 GenBank accessions 147 RNA-seq supporting reads 146 Brain 1 Other (also 38 Primates bodymap) 103 bp exon 112 bp [gt-ag] intron 12 GenBank accessions 107 RNA-seq supporting reads 106 Brain 1 Neuroblastoma (also 12 Primates bodymap) 114 bp exon 117 bp [gt-ag] intron 15 GenBank accessions 132 RNA-seq supporting reads 132 Brain (also 6 Primates bodymap) 156 bp exon 139 bp [gt-ag] intron 10 GenBank accessions 172 RNA-seq supporting reads 172 Brain (also 16 Primates bodymap) 214 bp exon 415 bp [gt-ag] intron 8 GenBank accessions 208 RNA-seq supporting reads 199 Brain 7 Neuroblastoma 2 Other (also 26 Primates bodymap) 131 bp exon 116 bp [gt-ag] intron 7 GenBank accessions 129 RNA-seq supporting reads 2 UHR pooled cells 124 Brain 2 Neuroblastoma 1 Other (also 16 Primates bodymap) 126 bp exon 240 bp [gt-ag] intron 6 GenBank accessions 184 RNA-seq supporting reads 181 Brain 3 Other (also 51 Primates bodymap) 77 bp exon 350 bp [gt-ag] intron 6 GenBank accessions 290 RNA-seq supporting reads 1 UHR pooled cells 281 Brain 7 Neuroblastoma 1 Other (also 37 Primates bodymap) 149 bp exon 812 bp [gt-ag] intron 7 GenBank accessions 166 RNA-seq supporting reads 164 Brain 2 Other (also 8 Primates bodymap) 131 bp exon 145 bp [gt-ag] intron 8 GenBank accessions 113 RNA-seq supporting reads 113 Brain (also 10 Primates bodymap) 132 bp exon 611 bp [gt-ag] intron 6 GenBank accessions 129 RNA-seq supporting reads 127 Brain 2 Neuroblastoma (also 15 Primates bodymap) 128 bp exon 84 bp [gt-ag] intron 10 GenBank accessions 157 RNA-seq supporting reads 154 Brain 1 Neuroblastoma 2 Other (also 15 Primates bodymap) 857 bp exon 3 accessions, some from eye (seen 2 times) fetal eyes, lens, eye anterior segment optic nerve, retina, retina foveal and macular RPE andchoroid (once) rpe/choroid (once) Validated 3' end, 1 accession 857 bp exon 214 bp exon 214 bp exon 85 bp [gt-ag] intron 12 GenBank accessions 147 RNA-seq supporting reads 146 Brain 1 Other (also 38 Primates bodymap) 103 bp exon 112 bp [gt-ag] intron 12 GenBank accessions 107 RNA-seq supporting reads 106 Brain 1 Neuroblastoma (also 12 Primates bodymap) 114 bp exon 117 bp [gt-ag] intron 15 GenBank accessions 132 RNA-seq supporting reads 132 Brain (also 6 Primates bodymap) 156 bp exon 139 bp [gt-ag] intron 10 GenBank accessions 172 RNA-seq supporting reads 172 Brain (also 16 Primates bodymap) 214 bp exon 415 bp [gt-ag] intron 8 GenBank accessions 208 RNA-seq supporting reads 199 Brain 7 Neuroblastoma 2 Other (also 26 Primates bodymap) 131 bp exon 116 bp [gt-ag] intron 7 GenBank accessions 129 RNA-seq supporting reads 2 UHR pooled cells 124 Brain 2 Neuroblastoma 1 Other (also 16 Primates bodymap) 126 bp exon 240 bp [gt-ag] intron 6 GenBank accessions 184 RNA-seq supporting reads 181 Brain 3 Other (also 51 Primates bodymap) 77 bp exon 350 bp [gt-ag] intron 6 GenBank accessions 290 RNA-seq supporting reads 1 UHR pooled cells 281 Brain 7 Neuroblastoma 1 Other (also 37 Primates bodymap) 149 bp exon 812 bp [gt-ag] intron 7 GenBank accessions 166 RNA-seq supporting reads 164 Brain 2 Other (also 8 Primates bodymap) 131 bp exon 145 bp [gt-ag] intron 8 GenBank accessions 113 RNA-seq supporting reads 113 Brain (also 10 Primates bodymap) 132 bp exon 611 bp [gt-ag] intron 6 GenBank accessions 129 RNA-seq supporting reads 127 Brain 2 Neuroblastoma (also 15 Primates bodymap) 128 bp exon 84 bp [gt-ag] intron 10 GenBank accessions 157 RNA-seq supporting reads 154 Brain 1 Neuroblastoma 2 Other (also 15 Primates bodymap) 1078 bp exon 1078 bp exon 254 bp [gt-ag] intron 23 GenBank accessions 16922 RNA-seq supporting reads 262 UHR pooled cells 899 Brain 15657 Neuroblastoma 104 Other (also 605 Primates bodymap) 257 bp exon 335 bp [gt-ag] intron 30 GenBank accessions 20577 RNA-seq supporting reads 162 UHR pooled cells 534 Brain 19872 Neuroblastoma 9 Other (also 107 Primates bodymap) 92 accessions, NM_015645.3 NM_031433.2, some from brain (seen 8 times) pancreas (8), eye (7) islets of langerhans (5) rpe/choroid (4) Validated 3' end, 18 accessions 910 bp exon 206 bp exon 206 bp exon 85 bp [gt-ag] intron 12 GenBank accessions 147 RNA-seq supporting reads 146 Brain 1 Other (also 38 Primates bodymap) 103 bp exon 112 bp [gt-ag] intron 12 GenBank accessions 107 RNA-seq supporting reads 106 Brain 1 Neuroblastoma (also 12 Primates bodymap) 114 bp exon 117 bp [gt-ag] intron 15 GenBank accessions 132 RNA-seq supporting reads 132 Brain (also 6 Primates bodymap) 156 bp exon 139 bp [gt-ag] intron 10 GenBank accessions 172 RNA-seq supporting reads 172 Brain (also 16 Primates bodymap) 214 bp exon 415 bp [gt-ag] intron 8 GenBank accessions 208 RNA-seq supporting reads 199 Brain 7 Neuroblastoma 2 Other (also 26 Primates bodymap) 131 bp exon 116 bp [gt-ag] intron 7 GenBank accessions 129 RNA-seq supporting reads 2 UHR pooled cells 124 Brain 2 Neuroblastoma 1 Other (also 16 Primates bodymap) 126 bp exon 1628 bp [gt-ag] intron 1 GenBank accession 1 RNA-seq supporting reads 1 Brain 131 bp exon 145 bp [gt-ag] intron 8 GenBank accessions 113 RNA-seq supporting reads 113 Brain (also 10 Primates bodymap) 132 bp exon 823 bp [gt-ag] intron 1 GenBank accession 350 bp exon 1 accession from caudate nucleus 350 bp exon 544 bp exon 1 accession from placenta from pre-eclamptic placenta 544 bp exon 385 bp exon 335 bp [gt-ag] intron 30 GenBank accessions 20577 RNA-seq supporting reads 162 UHR pooled cells 534 Brain 19872 Neuroblastoma 9 Other (also 107 Primates bodymap) 907 bp exon 7 accessions, some from pooled brain lung, testis (seen 3 times) human placenta (once) placenta (once), uterus (once) Validated 3' end, 1 accession 907 bp exon 158 bp exon 158 bp exon 300 bp [gt-ag] intron 2 GenBank accessions 4 RNA-seq supporting reads 3 Brain 1 Neuroblastoma 114 bp exon 117 bp [gt-ag] intron 15 GenBank accessions 132 RNA-seq supporting reads 132 Brain (also 6 Primates bodymap) 156 bp exon 139 bp [gt-ag] intron 10 GenBank accessions 172 RNA-seq supporting reads 172 Brain (also 16 Primates bodymap) 214 bp exon 415 bp [gt-ag] intron 8 GenBank accessions 208 RNA-seq supporting reads 199 Brain 7 Neuroblastoma 2 Other (also 26 Primates bodymap) 81 bp exon 2 accessions, some from eye (seen once) hippocampus (once), rpe/choroid (once) 81 bp exon 129 bp exon 254 bp [gt-ag] intron 23 GenBank accessions 16922 RNA-seq supporting reads 262 UHR pooled cells 899 Brain 15657 Neuroblastoma 104 Other (also 605 Primates bodymap) 132 bp exon 460 bp [gc-ag] fuzzy intron 2 GenBank accessions 22 RNA-seq supporting reads 2 UHR pooled cells 19 Neuroblastoma 1 Other (also 14 Primates bodymap) 621 bp exon 2 accessions, some from pooled brain lung, testis (seen once) 621 bp exon 158 bp exon 143 bp [gt-ag] intron 1 GenBank accession 3 RNA-seq supporting reads 3 Brain 271 bp exon 271 bp exon 117 bp [gt-ag] intron 15 GenBank accessions 132 RNA-seq supporting reads 132 Brain (also 6 Primates bodymap) 1 accession from hippocampus 152 bp exon 104 bp exon 104 bp exon 846 bp [gt-ag] intron 2 GenBank accessions 76 RNA-seq supporting reads 13 Brain 63 Neuroblastoma (also 22 Primates bodymap) 2 accessions, some from islets of langerhans (seen 2 times) pancreas (2) 479 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 2519 bp 579 aa 147 bp 632 bp 2kb probably including promoter 5745 bp 1kb
bAug10 3920 bp 579 aa 160 bp 2020 bp 2kb probably including promoter 7735 bp 1kb
cAug10 1663 bp 461 aa 152 bp 125 bp 2kb probably including promoter 5243 bp 1kb
dAug10 1292 bp 300 aa 389 bp 2kb 1627 bp 1kb
eAug10 723 bp 240 aa 2kb 1694 bp 1kb
fAug10 583 bp 194 aa 2kb 1429 bp 1kb
gAug10-unspliced 544 bp 181 aa 2kb 544 bp 1kb
hAug10 882 bp 145 aa 444 bp 2kb 1596 bp 1kb
iAug10 581 bp 100 aa 281 bp 2kb 841 bp 1kb

Gene neighbors and Navigator on chromosome 11q23.3 back to top
C1QTNF5andMFRP Title complex locus C1QTNF5andMFRP, encoding membrane frizzled-related protein and C1q and tumor necrosis factor related protein 5. Summary [RefSeq Summary MFRP] This gene encodes a member of the frizzled-related proteins. The encoded protein may play a role in eye development, as mutations in this gene have been associated with nanophthalmos, posterior microphthalmia, retinitis pigmentosa, foveoschisis, and optic disc drusen. The protein is encoded by a bicistronic mRNA, which also encodes C1q and tumor necrosis factor related protein 5. [RefSeq Summary C1QTNF5] This gene encodes a member of the a member of the C1q/tumor necrosis factor superfamily. The encoded protein may be a component of basement membranes and may play a role in cell adhesion. This gene is contained entirely within the 3' UTR of the membrane frizzled-related protein gene on chromosome 11q23 and both genes are expressed from a bicistronic transcript. Mutations in this gene have been associated with late-onset retinal degeneration. Transcribed_gene C1QTNF5andMFRP Product -----> 9 NewName 11_119217383 GeneId 114902 83552 Other_geneId 83552 114902 LocusLink MFRP C1QTNF5 Unigene Hs.632102 Type Spliced_gene Molecular Pastille_coding Pastille_conserved pastille_conserved_pfam pastille_conserved_taxblast Properties membrane frizzled-related protein membrane-type frizzled-related protein complement C1q tumor necrosis factor-related protein 5 OMIM_mol OMIM_608752 OMIM_606227 Pfam C1q Collagen CUB Fz Ldl_recept_a Predicted Genefinder _C1QTNF5_1 _MFRP_1 Genetic Locus -----> 8 Pastille_disease Extern -----> 9 Disease Microphthalmia, posterior, with retinitis pigmentosa, foveoschisis, and optic disc drusen nanophthalmos 2 Retinal degeneration, late-onset, autosomal dominant Go_b_iea visual perception IEA response to stimulus IEA Expression GO_c_psort membrane C1QTNF5andMFRP.aAug10 C1QTNF5andMFRP.bAug10 C1QTNF5andMFRP.cAug10 C1QTNF5andMFRP.dAug10 C1QTNF5andMFRP.eAug10 Go_c_iea extracellular region IEA membrane IEA MicroArray UKv4_A_23_P259292 UKv4_A_24_P98783 Regulation Pastille_regulation pastille_regulation_complex_locus pastille_regulation_structure pastille_regulation_NMD Complex_locus Two_geneid Interacts with_gene SLC2A4 6517 pm16396496 C1QTNF5andMFRP 114902 pm12944416 83552 pm12944416 with_geneId 114902 pm12944416 HPRD:10575 HPRD:06941 BioGRID:125392 83552 pm12944416 HPRD:10575 HPRD:06941 6517 pm16396496 HPRD:00688 HPRD:10575 Reference -----> 24 Structure -----> 7 Position Balise Map 11 IntMap 11 119217383 119209646 Cytogenetic 11q23.3 SMAP S_Parent Genomic_sequence t11_NT_033899.8_38 Quit Update Attach... Biblio ZOOM IN                D:disease,C:conserved,I:interactions,R:regulation,P:publications         Read more...
Annotated mRNA diagrams back to top
Bibliography:               24 articles in PubMed back to top
? Gene Summary Gene on genome mRNA:.a, .b, .c, .d, .e, .f, .g-u, .h, .i Alternative mRNAs features, proteins, introns, exons, sequences Expression Tissue Function, regulation, related genes DCI

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'.

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