FAM13B

Last updated
Human Chromosome 5 Ideogram human chromosome 5.svg
Human Chromosome 5
FAM13B
Identifiers
Aliases FAM13B , ARHGAP49, C5orf5, FAM13B1, KHCHP, N61, family with sequence similarity 13 member B
External IDs OMIM: 609371 MGI: 2447834 HomoloGene: 9585 GeneCards: FAM13B
Orthologs
SpeciesHumanMouse
Entrez

51306

225358

Ensembl

ENSG00000031003

ENSMUSG00000036501

UniProt

Q9NYF5

Q8K2H3

RefSeq (mRNA)

NM_001101800
NM_001101801
NM_016603

NM_146084

RefSeq (protein)

NP_001095270
NP_001095271
NP_057687

NP_666196

Location (UCSC) Chr 5: 137.94 – 138.05 Mb Chr 18: 34.58 – 34.64 Mb
PubMed search [3] [4]
Wikidata
View/Edit Human View/Edit Mouse
Tertiary Structure of the human FAM13B protein from AlphaFold Tertiary Structure FAM13B.png
Tertiary Structure of the human FAM13B protein from AlphaFold

Family with sequence similarity 13 member B is a protein which in humans is encoded by the FAM13B gene, [5] also known as C5ORF5. The FAM13B gene is found in vertebrates and jawed fish. FAM13B is expressed ubiquitously in human tissues [6] and has been linked to maglinant myelomas [7] susceptibility to atrial fibrillation, a cardiac arrhythmia. [8]

Contents

Molecular Features

Gene

The FAM13B gene is located on human chromosome 5q31, spanning 5610 base pairs and containing 23 exons. [6]

mRNA

There are 18 transcript variants, the longest mRNA contains 5610 base pairs. [6]

Expression

The FAM13B gene is expressed at high levels ubiquitously among human cell tissues with some variability, with the highest expression in the brain and the lowest expression in the liver. [6]

Protein

The longest protein product of FAM13B consists of 915 amino acids [9] with a molecular mass of 105kD. [10] FAM13B variants have the potential to encode several swapped proteins, including proteins with internal deletions, with different C termini, and with a deletion of the N terminus. [10] The protein has an isoelectric point of 4.9. [11] The human FAM13B protein is localized in the nucleoplasm and contains multiple peroxisomal targeting signals and nuclear localization signals. [12] The FAM13B protein has a lower amount of threonine and a higher amount of glutamate compared to other human proteins. [11]

The FAM13B contains 2 disordered region and 2 conserved domains: [6]

The RHOGAP domain is also found in the orthologs.

Annotated FAM13B protein, made from The CUCKOO Workgroup Nucleotide fam13b.png
Annotated FAM13B protein, made from The CUCKOO Workgroup

Post-translation modifications

The human FAM13B protein can undergo post-translational modifications including phosphorylation, acetylation, and methylation. [12]

Annotated post-translational modification sites on human FAM13B protein, made from The CUCKOO Workgroup Post mods fam13b.png
Annotated post-translational modification sites on human FAM13B protein, made from The CUCKOO Workgroup

Interacting proteins

The human FAM13B protein interacts with several proteins that are localized in the nucleoplasm, including RAC1, NME5, SPATA24, HIGD1A, PPP2CA, SAMHD1, UNK, YWHAZ. [15]

Evolution

Multiple sequence alignment of a conserved area of the FAM13B protein Fam13b strict orthologs msa.png
Multiple sequence alignment of a conserved area of the FAM13B protein

Orthologs

Orthologs of the FAM13B gene can be found in vertebrates including mammals, aves, reptiles, amphibians, and jawed fish. [6] There are no FAM13B orthologs found in invertebrates. FAM13B is more conserved in mammals, aves, and reptiles. FAM13B has a moderate mutation rate that is slower than Fibrinogen Alpha Chain but faster than Cytochrome C.

Table of selected orthologs from all animal groups
Genus and SpeciesCommon NameEstimated Divergence (MYA)Accession NumberAmino Acid LengthSequence Similarity (%)
Homo sapiens Humans0NP_001372850915100
Macaca mulatta Rhesus monkey28.8NP_00124787791699.2
Mus musculus House mouse87NP_66619685187.3
Alligator sinesis Chinese alligator319XP_00602691893087.0
Gallus gallus Chicken319NP_00126467490585.9
Xenopus tropicalis Tropical clawed frog352XP_00293367983172.0
Amblyraja radiata Thorny skate462XP_03288527782558.4

Paralogs

The human FAM13B gene has two paralogs, FAM13A [16] and FAM13C. [17] Similar to FAM13B, the FAM13A and FAM13C are found in vertebrates including mammals, aves, reptiles, amphibians, and jawed fish. The paralogs are not found in invertebrates.

Clinical significance

FAM13B is frequently deleted in malignant myelomas, suggesting its potential role in cancer development. [7] Altered expression of FAM13B has been linked to susceptibility to atrial fibrillation, [7] a cardiac arrhythmia. [8]

Related Research Articles

<span class="mw-page-title-main">METTL26</span> Protein-coding gene in the species Homo sapiens

METTL26, previously designated C16orf13, is a protein-coding gene for Methyltransferase Like 26, also known as JFP2. Though the function of this gene is unknown, various data have revealed that it is expressed at high levels in various cancerous tissues. Underexpression of this gene has also been linked to disease consequences in humans.

<span class="mw-page-title-main">Proline-rich 12</span> Protein-coding gene in the species Homo sapiens

Proline-rich 12 (PRR12) is a protein of unknown function encoded by the gene PRR12.

<span class="mw-page-title-main">FAM203B</span> Protein-coding gene in the species Homo sapiens

Family with Sequence Similarity 203, Member B (FAM203B) is a protein encoded by the FAM203B gene (8q24.3) in humans. While FAM203B is only found in humans and possibly non-human primates, its paralog, FAM203A, is highly conserved. The FAM203B protein contains two conserved domains of unknown function, DUF383 and DUF384, and no transmembrane domains. This protein has no known function yet, although the homolog of FAM203A in Caenorhabditis elegans (Y54H5A.2) is thought to help regulate the actin cytoskeleton.

<span class="mw-page-title-main">CCDC94</span> Protein found in humans

Coiled-coil domain containing 94 (CCDC94) is a protein that in humans is encoded by the CCDC94 gene. The CCDC94 protein contains a coiled-coil domain, a domain of unknown function (DUF572), an uncharacterized conserved protein (COG5134), and lacks a transmembrane domain.

<span class="mw-page-title-main">C8orf48</span> Protein-coding gene in the species Homo sapiens

C8orf48 is a protein that in humans is encoded by the C8orf48 gene. C8orf48 is a nuclear protein specifically predicted to be located in the nuclear lamina. C8orf48 has been found to interact with proteins that are involved in the regulation of various cellular responses like gene expression, protein secretion, cell proliferation, and inflammatory responses. This protein has been linked to breast cancer and papillary thyroid carcinoma.

<span class="mw-page-title-main">Zinc finger protein 684</span> Protein found in humans

Zinc finger protein 684 is a protein that in humans is encoded by the ZNF684 gene.

<span class="mw-page-title-main">TMEM176B</span> Protein-coding gene in the species Homo sapiens

Transmembrane Protein 176B, or TMEM176B is a transmembrane protein that in humans is encoded by the TMEM176B gene. It is thought to play a role in the process of maturation of dendritic cells.

<span class="mw-page-title-main">C10orf67</span> Protein-coding gene in the species Homo sapiens

Chromosome 10 open reading frame 67 (C10orf67), also known as C10orf115, LINC01552, and BA215C7.4, is an un-characterized human protein-coding gene. Several studies indicate a possible link between genetic polymorphisms of this and several other genes to chronic inflammatory barrier diseases such as Crohn's Disease and sarcoidosis.

<span class="mw-page-title-main">C17orf98</span> Protein-coding gene in the species Homo sapiens

C17orf98 is a protein which in humans is coded by the gene c17orf98. The protein is derived from Homo sapiens chromosome 17. The C17orf98 gene consists of a 6,302 base sequence. Its mRNA has three exons and no alternative splice sites. The protein has 154 amino acids, with no abnormal amino acid levels. C17orf98 has a domain of unknown function (DUF4542) and is 17.6kDa in weight. C17orf98 does not belong to any other families nor does it have any isoforms. The protein has orthologs with high percent similarity in mammals and reptiles. The protein has additional distantly related orthologs across the metazoan kingdom, culminating with the sponge family.

<span class="mw-page-title-main">PROB1</span> Protein-coding gene in the species Homo sapiens

Proline-rich basic protein 1(PROB1) is a protein encoded by the PROB1 gene located on human chromosome 5, open reading frame 65. PROB1 is also known as C5orf65 and weakly similar to basic proline-rich protein.

<span class="mw-page-title-main">FAM178B</span> Protein coding

FAM178B is a protein coding that is located on the plus strand of chromosome 2. The locus for the gene is 2q11.2. It is also known by the aliases Family with Sequence Similarity 178, Member B, and HSPC234. In total there are 24 exons in the gene. FAM178B spans 110,720 base pairs, and contains 827 amino acids.

<span class="mw-page-title-main">C17orf78</span> Mammalian protein found in Homo sapiens

Uncharacterized protein C17orf78 is a protein encoded by the C17orf78 gene in humans. The name denotes the location of the parent gene, being at the 78th open reading frame, on the 17th human chromosome. The protein is highly expressed in the small intestine, especially the duodenum. The function of C17orf78 is not well defined.

<span class="mw-page-title-main">C1orf94</span> Protein-coding gene in the species Homo sapiens

Chromosome 1 Opening Reading Frame 94 or C1orf94 is a protein in human coded by the C1orf94 gene. The function of this protein is still poorly understood.

<span class="mw-page-title-main">TMEM169</span> Gene

Transmembrane protein 169 (TMEM169) in humans is encoded by TMEM169 gene. The aliases of TMEM169 include FLJ34263, DKFZp781L2456, and LOC92691. TMEM169 has the highest expression in the brain, particularly the fetal brain. TMEM169 has homologs mammals, reptiles, amphibians, birds, fish, chordates and invertebrates. The most distantly related homolog of TMEM169 is Anopheles albimanus.

<span class="mw-page-title-main">FAM166C</span>

Family with Sequence Similarity 166, member C (FAM166C), is a protein encoded by the FAM166C gene. The protein FAM166C is localized in the nucleus. It has a calculated molecular weight of 23.29 kDa. It also contains DUF2475, a protein of unknown function from amino acid 19–85. The FAM166C protein is nominally expressed in the testis, stomach, and thyroid.

<span class="mw-page-title-main">C22orf15</span> Protein-coding gene in the species Homo sapiens

C22orf15 is a protein which, in humans, is encoded by the C22orf15 gene.

<span class="mw-page-title-main">ZNF548</span> Protein-coding gene in the species Homo sapiens

Zinc Finger Protein 548 (ZNF548) is a human protein encoded by the ZNF548 gene which is located on chromosome 19. It is found in the nucleus and is hypothesized to play a role in the regulation of transcription by RNA Polymerase II. It belongs to the Krüppel C2H2-type zinc-finger protein family as it contains many zinc-finger repeats.

<span class="mw-page-title-main">C5orf22</span> Protein-coding gene in the species Homo sapiens

Chromosome 5 open reading frame 22 (c5orf22) is a protein-coding gene of poorly characterized function in Homo sapiens. The primary alias is unknown protein family 0489 (UPF0489).

<span class="mw-page-title-main">FAM131A</span> Information on the FAM131A gene and the protein it encodes

FAM131A is a protein that is encoded by the FAM131A gene in humans. Aliases for FAM131A include C3orf40, FLAT715, and PRO1378.

<span class="mw-page-title-main">LRRC74A</span> Protein-coding gene

Leucine-rich repeat-containing protein 74A (LRRC74A), is a protein encoded by the LRRC74A gene. The protein LRRC74A is localized in the cytoplasm. It has a calculated molecular weight of approximately 55 kDa. The LRRC74A protein is nominally expressed in the testis, salivary gland, and pancreas.

References

  1. 1 2 3 GRCh38: Ensembl release 89: ENSG00000031003 - Ensembl, May 2017
  2. 1 2 3 GRCm38: Ensembl release 89: ENSMUSG00000036501 - 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. ↑ "FAM13B family with sequence similarity 13 member B [Homo sapiens (human)] - Gene". National Center for Biotechnology Information (NCBI). U.S. National Library of Medicine.
  6. 1 2 3 4 5 6 "FAM13B family with sequence similarity 13 member B [Homo sapiens (human)] - Gene". National Center for Biotechnology Information (NCBI). U.S. National Library of Medicine. Retrieved 2023-12-07.
  7. 1 2 3 Lai F, Godley LA, Joslin J, Fernald AA, Liu J, Espinosa R, et al. (January 2001). "Transcript map and comparative analysis of the 1.5-Mb commonly deleted segment of human 5q31 in malignant myeloid diseases with a del(5q)". Genomics. 71 (2): 235–245. doi:10.1006/geno.2000.6414. PMID   11161817.
  8. 1 2 Hsu J, Gore-Panter S, Tchou G, Castel L, Lovano B, Moravec CS, et al. (March 2018). "Genetic Control of Left Atrial Gene Expression Yields Insights into the Genetic Susceptibility for Atrial Fibrillation". Circulation. Genomic and Precision Medicine. 11 (3): e002107. doi:10.1161/CIRCGEN.118.002107. PMC   5858469 . PMID   29545482.
  9. ↑ "protein FAM13B isoform 1 [Homo sapiens] - Protein". National Center for Biotechnology Information (NCBI). U.S. National Library of Medicine. Retrieved 2023-12-15.
  10. 1 2 Lai F, Godley LA, Fernald AA, Orelli BJ, Pamintuan L, Zhao N, Le Beau MM (November 2000). "cDNA cloning and genomic structure of three genes localized to human chromosome band 5q31 encoding potential nuclear proteins". Genomics. 70 (1): 123–130. doi:10.1006/geno.2000.6345. PMID   11087669.
  11. 1 2 "SAPS < Sequence Statistics". Statistical Analysis of Protein Sequences. European Bioinformatics Institute. Retrieved 2023-12-15.
  12. 1 2 "PSORT II Prediction". psort.hgc.jp. Retrieved 2023-12-07.
  13. ↑ Moon SY, Zheng Y (January 2003). "Rho GTPase-activating proteins in cell regulation". Trends in Cell Biology. 13 (1): 13–22. doi:10.1016/S0962-8924(02)00004-1. PMID   12480336.
  14. ↑ Ohlenschläger O, Kuhnert A, Schneider A, Haumann S, Bellstedt P, Keller H, et al. (September 2012). "The N-terminus of the human RecQL4 helicase is a homeodomain-like DNA interaction motif". Nucleic Acids Research. 40 (17): 8309–8324. doi:10.1093/nar/gks591. PMC   3458545 . PMID   22730300.
  15. ↑ "FAM13B Interaction Network". IntAct Portal. European Bioinformatics Institute. Retrieved 2023-12-07.
  16. ↑ "Gene: FAM13A (ENSG00000138640) - Paralogues - Homo_sapiens - Ensembl genome browser 110". useast.ensembl.org. Retrieved 2023-12-15.
  17. ↑ "Gene: FAM13C (ENSG00000148541) - Paralogues - Homo_sapiens - Ensembl genome browser 110". useast.ensembl.org. Retrieved 2023-12-15.
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