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C12orf29

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C12orf29
Identifiers
AliasesC12orf29, chromosome 12 open reading frame 29, LOC91298, FLJ38158, MGC102978, DKFZp313K0436, DKFZp434N2030, DKFZp686L04169
External IDsMGI: 1921197; HomoloGene: 18409; GeneCards: C12orf29; OMA:C12orf29 - orthologs
Orthologs
SpeciesHumanMouse
Entrez

91298

68281

Ensembl

ENSG00000133641

ENSMUSG00000046567

UniProt

Q8N999

Q8BHN7

RefSeq (mRNA)

NM_001009894

NM_175128

RefSeq (protein)

NP_001009894

NP_780337

Location (UCSC)Chr 12: 88.03 – 88.05 MbChr 10: 100.41 – 100.43 Mb
PubMed search[3][4]
Wikidata
View/Edit HumanView/Edit Mouse

C12orf29 is a protein that in humans is encoded by chromosome 12 open reading frame 29. The gene is ubiquitously expressed in various tissues.[5] The protein has 325 amino acids. The biological process of C12orf29 has been annotated as hematopoietic progenitor cell differentiation.[6] The molecular and cellular functions of C12orf29 gene have not yet well understood by the scientific community.

Research suggested that C12orf29 is a potential structural protein in skeletal tissue with a role in the extracellular matrix of articular and growth cartilage. It has increased expression in osteosarcoma (OS) tumor cells and other tumor cells, and it could be a potential biomarker for detecting osteosarcoma.

Gene

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C12orf29 gene in human is located on the positive strand at 12q21.32 (p = short arm, q = long arm). It has 7 exons and 6 introns. The gene spans from 88,035,536 to 88,050,160 with 14,645 base pairs. There is only one isoform of the transcript, which is the transcript of this gene itself.[5]

An overview of human C12orf29 gene transcript from NCBI Gene.

Neighbor genes around human C12orf29 are: C12orf50 (-), RNA5SP364 (+), LOC107984542 (-), LOC100420011 (+), CEP290 (-).

Neighbor genes of human C12orf29 from NCBI Gene.

Expression

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C12orf29 gene is ubiquitously expressed in 27 tissues.[5] It is expressed a little bit higher in esophagus, skin, brain and bone marrow.[5] It showed increased expression in several tumor cells and tissues such as in colorectal tumor tissue,[7] in ovarian cancer epithelial cells,[8] and in hyperplastic enlarged lobular units epithelial cells.[9]

Protein

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C12orf29 protein has 325 amino acids.[10] The molecular weight is 37.5 kD, and the isoelectric point is 6.6 pH.[11] It is not a membrane protein, and it stays in the cytosol.[12] For the content of the amino acids, compared with other human proteins, C12orf29 is high in asparagine and histidine, but it is low in alanine.[11] There are no validated domains or motifs.[10] It has a short repetitive structures of "INGNP", but it is not conserved in orthologs.[11] However, there are two highly conserved predicted motifs. They are the protease caspase 3 and 7 cleavage motif, and the mitogen-activated protein kinase (MAPK) docking motif.[13][14] There are several predicted protein kinase c phosphorylation sites and casein kinase II phosphorylation sites, but they are not conserved in orthologs.[13][14] 

         1  MKRLGSVQRK MPCVFVTEVK EEPSSKREHQ PFKVLATETV SHKALDADIY SAIPTEKVDG
        61  TCCYVTTYKD QPYLWARLDR KPNKQAEKRF KNFLHSKENP KEFFWNVEED FKPAPECWIP
       121  AKETEQINGN PVPDENGHIP GWVPVEKNNK QYCWHSSVVN YEFEIALVLK HHPDDSGLLE
       181  ISAVPLSDLL EQTLELIGTN INGNPYGLGS KKHPLHLLIP HGAFQIRNLP SLKHNDLVSW
       241  FEDCKEGKIE GIVWHCSDGC LIKVHRHHLG LCWPIPDTYM NSRPVIINMN LNKCDSAFDI
       301  KCLFNHFLKI DNQKFVRLKD IIFDV
Some SNP and predicted post-translational modification of C12orf29 protein. (Green double underline represent beta-sheet. Pink squiggly underline represents alpha-helix. Bolded letters represent the conserved amino acids in distant orthologs)[11][15][16][13][14][17][18]

Protein interaction

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NCL and LRRK2 was experimentally determined to interacted with C12orf29.[19] NCL physically interacted with C12orf29, and LRRK2 was associated with C12orf29.[19] There are several predicted protein interactions for C12orf29. C12orf50, C1orf186/RHEX, TOR4A, FAM171A1 are associated with C12orf29 by text-mining, and the specific type of interaction was not studied yet.[20] The interactions with PNN, OTUD68, and ACTR6 were predicted by co-expression.[20]

Predicted protein interaction of C12orf29 by STRING. (Green line represent predicted relation by text-mining, black line represents predicted relation by co-expression)

Homology and evolution

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Orthologs of C12orf29 protein are found within the mammals, birds, reptiles, amphibians, fishes, and invertebrates.[21] The length and contents of the protein sequence was highly conserved in the selected orthologs (table below).[18] It is important to notice that the C12orf29 protein was only found in mollusks, tunicate, and cephalochordata in invertebrates, but it was not found in insects, arachnids, crustaceans, corals, worms, jellyfishes, sponges within the other groups in invertebrates.[17][22] C12orf29 protein was not found in bacteria, fungi, and viruses.[17] There is no paralog for C12orf29 protein.[17] The mutation rate of C12orf29 was close to that of fibrinogen alpha chain. The human's C12orf29 protein was more closely related to the sheep's ortholog than to the mouse's ortholog. The invertebrates C12orf29 orthologs were mostly distantly related to the human protein.

Ortholog table

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Selected Orthologs Table of C12orf29 Protein[18][21][17][22][23]
Sequence Number Ortholog Group Genius and Species Taxonomic Group Common Name Time Since Divergence (Estimated MYA) Accession Number Sequence Length (aa) Sequence Identity Sequence Similarity
1 Mammals Homo sapiens Primates Human 0 NP_001009894.2 325 100% 100%
2 Mammals Mus musculus Rodentia House Mouse 90 NP_780337.2 327 84% 90%
3 Mammals Ovis aries Artiodactyla Sheep 96 NP_001186723.1 325 91% 96%
4 Mammals Phascolarctos cinereus Diprotodontia Koala 159 XP_020849155.1 325 86% 92%
5 Mammals Ornithorhynchus anatinus Monotremata Platypus 177 XP_028934667.1 326 78% 89%
6 Aves Gallus gallus Galliformes Chicken 312 XP_040518235.1 324 75% 86%
7 Aves Cygnus atratus Anseriformes Black Swan 312 XP_035407728.1 324 75% 86%
8 Aves Calypte anna Apodiformes Anna's Hummingbird 312 XP_030312194.1 324 75% 87%
9 Reptiles Crocodylus porosus Crocodylia Australian Saltwater Crocodile 312 XP_019400824.1 323 76% 88%
10 Reptiles Zootoca vivipara Squamata Common Lizard 312 XP_034983157.1 325 71% 85%
11 Reptiles Python bivittatus Squamata Burmese Python 312 XP_007429130.1 323 70% 84%
12 Reptiles Dermochelys coriacea Testudines Leatherback Sea Turtle 312 XP_038257651.1 325 78% 90%
13 Amphibians Bufo bufo Anura Common Toad 351.8 XP_040264560.1 324 63% 77%
14 Amphibians Rhinatrema bivittatum Gymnophiona Two-lined Caecilian 351.8 XP_029457527.1 335 66% 82%
15 Fishes Danio rerio Cypriniformes Zebrafish 435 NP_001008606.1 325 60% 79%
16 Fishes Rhincodon typus Orectolobiformes Whale Shark 473 XP_020369226.1 330 56% 73%
17 Invertebrates Styela clava Stolidobranchia Asian Tunicate 676 XP_039256956.1 351 44% 59%
18 Invertebrates Branchiostoma floridae Amphioxiformes Florida Lancelet 684 XP_035678444.1 341 43% 62%
19 Invertebrates Pecten maximus Pectinida King Scallop 797 XP_033752428.1 347 44% 62%
20 Invertebrates Crassostrea gigas Ostreida Pacific Oyster 797 XP_034327602.1 357 41% 59%
Estimated date of divergence and the corrected divergence of orthologous protein sequence. The average mutation rate of C12orf29 protein, cytochrome c protein (slow-evolving), and fibrinogen alpha chain protein (fast-evolving) are estimated by the linear regression.
Unrooted phylogenetic tree of C12orf 29 orthologs in 20 vertebrates and invertebrates.

In research

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In bone

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In sheep (Ovis aries) bone, C12orf29 protein has a high expression in mandible osteoblasts cells (mOB cells) and periodontal ligament cells (PDLCs). It has a relatively low but still noticeable amount of expression in prostate cancer cell line (PC3). It is observed to be expressed in the extracellular matrix (ECM) around the mOB cells, and it is suggested that C12orf29 protein is imported and embedded into ECM from mOB cells. C12orf29 are also discovered in the area around mineralization zone of the growth plate and calcified cartilage of trabecular bone in rats. C12orf29 is a potential structural protein in skeletal tissue with a role in the extracellular matrix of articular and growth cartilage. It might be decorated with glycosaminoglycans, thus a potential proteoglycan.[24]

Cancer

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C12orf29 is expressed in the most common subtypes (osteoblastic type, mixed osteoblastic/chondroblastic type, and chondroblastic type) of osteosarcoma (OS) patients and humanized OS model. It has a role in promoting the development of the musculoskeletal system. C12orf29 has a significantly high expression in the tumor cells, but its expression is not associated with the proliferation of the tumors. OS located at the jaw or temporal regions has a statistically significant expression of C12orf29 than OS in the extremity or trunk region. C12orf29 expression has a strong positive correlation with the expression of Ki67 gene (a biomarker for tumor proliferation).[25]

KLF9

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The mRNA expression of C12orf29 protein is increased with Krüppel-like factor 9 (KLF9) suppression.KLF9 is a transcriptional regulator of uterine endometrial cell proliferation, adhesion, and differentiation, which are essential processes for pregnancy success. KLF9 expression is suppressed during tumorigenesis.[26]

References

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  1. ^ a b c GRCh38: Ensembl release 89: ENSG00000133641 – Ensembl, May 2017
  2. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000046567 – Ensembl, May 2017
  3. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ a b c d "C12orf29 chromosome 12 open reading frame 29 [Homo sapiens (human)] - Gene - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2021-09-26.
  6. ^ Consortium, Gene Ontology. "AmiGO 2: Gene Product Details for UniProtKB:Q8N999". amigo.geneontology.org. Retrieved 2021-09-26.
  7. ^ "88351102 - GEO Profiles - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2021-12-16.
  8. ^ "61688502 - GEO Profiles - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2021-12-16.
  9. ^ "39401542 - GEO Profiles - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2021-12-16.
  10. ^ a b "uncharacterized protein C12orf29 [Homo sapiens] - Protein - NCBI". www.ncbi.nlm.nih.gov. Retrieved 2021-09-26.
  11. ^ a b c d "SAPS < Sequence Statistics < EMBL-EBI". www.ebi.ac.uk. Retrieved 2021-12-16.
  12. ^ "PSORT: Protein Subcellular Localization Prediction Tool". www.genscript.com. Retrieved 2021-12-16.
  13. ^ a b c "ELM - Search the ELM resource". elm.eu.org. Retrieved 2021-12-16.
  14. ^ a b c "Motif Scan". myhits.sib.swiss. Retrieved 2021-12-16.
  15. ^ "iCn3D: Web-based 3D Structure Viewer". structure.ncbi.nlm.nih.gov. Retrieved 2021-12-16.
  16. ^ "AlphaFold Protein Structure Database". alphafold.ebi.ac.uk. Retrieved 2021-12-16.
  17. ^ a b c d e "BLAST: Basic Local Alignment Search Tool". blast.ncbi.nlm.nih.gov. Retrieved 2021-12-16.
  18. ^ a b c "Clustal Omega < Multiple Sequence Alignment < EMBL-EBI". www.ebi.ac.uk. Retrieved 2021-12-16.
  19. ^ a b "IntAct Portal". www.ebi.ac.uk. Retrieved 2021-12-16.
  20. ^ a b "C12orf29 protein (human) - STRING interaction network". string-db.org. Retrieved 2021-12-16.
  21. ^ a b "C12orf29 orthologs". NCBI. Retrieved 2021-12-16.
  22. ^ a b "Human BLAT Search". genome.ucsc.edu. Retrieved 2021-12-16.
  23. ^ "TimeTree :: The Timescale of Life". www.timetree.org. Retrieved 2021-12-16.
  24. ^ Friis TE, Stephenson S, Xiao Y, Whitehead J, Hutmacher DW (October 2014). "A polymerase chain reaction-based method for isolating clones from a complimentary [sic] DNA library in sheep". Tissue Engineering. Part C, Methods. 20 (10): 780–789. doi:10.1089/ten.tec.2013.0099. PMC 4186646. PMID 24447069.
  25. ^ Wagner F, Holzapfel BM, McGovern JA, Shafiee A, Baldwin JG, Martine LC, et al. (July 2018). "Humanization of bone and bone marrow in an orthotopic site reveals new potential therapeutic targets in osteosarcoma" (PDF). Biomaterials. 171: 230–246. doi:10.1016/j.biomaterials.2018.04.030. hdl:10072/385762. PMID 29705656. S2CID 19093873.
  26. ^ Simmen FA, Su Y, Xiao R, Zeng Z, Simmen RC (September 2008). "The Krüppel-like factor 9 (KLF9) network in HEC-1-A endometrial carcinoma cells suggests the carcinogenic potential of dys-regulated KLF9 expression". Reproductive Biology and Endocrinology. 6 (1): 41. doi:10.1186/1477-7827-6-41. PMC 2542371. PMID 18783612.
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