| NKAPD1 | |||||||||||||||||||||||||||||||||||||||||||||||||||
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| Identifiers | |||||||||||||||||||||||||||||||||||||||||||||||||||
| Aliases | NKAPD1 , C11orf57, chromosome 11 open reading frame 57, NKAP domain containing 1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
| External IDs | MGI: 2143205 HomoloGene: 41233 GeneCards: NKAPD1 | ||||||||||||||||||||||||||||||||||||||||||||||||||
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| Wikidata | |||||||||||||||||||||||||||||||||||||||||||||||||||
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NKAPD1 (NF-kappa-B-activating protein domain containing 1) is a protein, which in humans, is encoded by the gene NKAPD1. This protein is also commonly referred to as C11ORF57 (Chromosome 11 Open Reading Frame 57). [5]
The NKAPD1 gene is found on human chromosome 11 at locus 11q23.1 with plus strand orientation. The exact location is 112,074,086 to 112,085,150, spanning a total of 11,065 base pairs, including introns. [5] [6]
It can be transcribed into 7 different transcript variants resulting in 4 different isoforms of the protein. The longest mRNA transcript contains a total of 6 exons. [6]
The human NKAPD1 gene is closely surrounded by the following genes on chromosome 11. [7]
The human NKAPD1 gene is ubiquitously expressed at moderate levels in various normal tissues throughout the body, with higher expression in the brain and thyroid. [6] [8]
The longest protein isoform produced by the human NKAPD1 gene is known as isoform a and it is 293 amino acids long. This particular protein isoform has a predicted molecular weight around 34 kDa. [5] [6]
| Transcript Variant | Isoform | mRNA Accession # | mRNA Length | Protein Accession # | Protein Length | Notes |
|---|---|---|---|---|---|---|
| 1 | isoform a | NM_018195.4 | 3686 nt | NP_060665.3 | 293 aa | Longest isoform and mRNA |
| 2 | isoform a | NM_001082969.2 | 3128 nt | NP_001076438.1 | 293 aa | Different in 5’ UTR |
| 3 | isoform b | NM_001082970.2 | 3683 nt | NP_001076439.1 | 292 aa | Alternate splice site in 3’ coding region |
| 4 | N/A | NR_103469.2 | 3727 nt | N/A | N/A | Non-coding RNA |
| 5 | isoform b | NM_001301017.2 | 3125 nt | NP_001287946.1 | 292 aa | Alternate splice site at 5’ end of last exon |
| 6 | isoform c | NM_001301019.2 | 3169 nt | NP_001287948.1 | 264 aa | Alternate exons 1 and 2, uses alternate start codon |
| 7 | isoform d | NM_001301021.2 | 3166 nt | NP_001287950.1 | 263 aa | Alternate exons 1 and 2 |
The human NKAPD1 protein contains one domain called the NKAP (NF-kappa-B-activating protein) domain. It also has a lysine rich region directly following the NKAP domain. [9] [10]
Secondary structure predictions suggest that the NKAPD1 protein consists mainly of alpha helices. [13] Predicted three-dimensional structures showed mostly coils with a few small regions of alpha helices. [11]
The human NKAPD1 protein is predicted to undergo SUMOylation at several different lysines as well as phosphorylation, acetylation, and N-myristoylation at different amino acids. [10]
Orthologs to the human NKAPD1 gene can be found in all vertebrates through sharks, rays, and lampreys, however it is not found in any invertebrates. This gene is shown to be very highly conserved in mammals. [6] [14]
When compared to fibrinogen alpha and cytochrome c, the human NKAPD1 gene seems to be evolving at a fairly moderate rate. [6] [15] [16]
There were 8 proteins found to have potential interactions with the human NKAPD1 protein. The table below shows the possible relationships between these proteins and the human NKAPD1 protein. [17]
| Name | Full Name | Basis | Score | Function | Tissue Expression | Subcellular Localization |
|---|---|---|---|---|---|---|
| CSNK2A1 | casein kinase 2 alpha 1 | Experimental/Biochemical Data | 0.615 | Regulates numerous cellular processes | Ubiquitous | nucleus |
| PNN | pinin | Co-Expression, Experimental/Biochemical Data | 0.570 | Component of multiprotein exon junction complex | Ubiquitous | nucleus |
| DHX8 | DEAH-box helicase 8 | Experimental/Biochemical Data | 0.563 | facilitates nuclear export of spliced mRNA | Ubiquitous | nucleus |
| C9orf78 | Chromosome 9 open reading frame 78 | Co-Expression, Experimental/Biochemical Data | 0.541 | regulation of telomere assembly and telomere length | Ubiquitous | nucleus |
| RP9 | RP9 pre-mRNA splicing factor | Co-Expression, Experimental/Biochemical Data | 0.527 | Target protein for PM1 kinase, B-cell proliferation | Ubiquitous | nucleus, vesicles, and cytosol |
| CSNK2A2 | casein kinase 2 alpha 2 | Co-Expression, Experimental/Biochemical Data | 0.505 | Regulates numerous cellular processes | testes | nucleus |
| SREK1IP1 | SREK1 interacting protein 1 | Co-Expression, Experimental/Biochemical Data | 0.502 | Possible splicing regulator related to cell survival | Ubiquitous | nucleus |
| SYF2 | SYF2 pre-mRNA splicing factor | Co-Expression, Experimental/Biochemical Data | 0.482 | component of spliceosome, pre-mRNA splicing | Ubiquitous | nucleus |
Preliminary findings in three published studies suggest that deletion of the NKAPD1 gene, both complete and partial, are associated with the development of paraganglioma, a rare tumor of the head and neck. This research suggest that these deletions often occur hand-in-hand with deletions of several other nearby genes as well, most prominently SDHD, DLAT, PIHD2, and TIMM8B. [18] [19] [20]
Succinate dehydrogenase [ubiquinone] cytochrome b small subunit, mitochondrial (CybS), also known as succinate dehydrogenase complex subunit D (SDHD), is a protein that in humans is encoded by the SDHD gene. Names previously used for SDHD were PGL and PGL1. Succinate dehydrogenase is an important enzyme in both the citric acid cycle and the electron transport chain. Hereditary PGL-PCC syndrome is caused by a parental imprint of the SDHD gene. Screening can begin by 6 years of age.
Succinate dehydrogenase complex subunit C, also known as succinate dehydrogenase cytochrome b560 subunit, mitochondrial, is a protein that in humans is encoded by the SDHC gene. This gene encodes one of four nuclear-encoded subunits that comprise succinate dehydrogenase, also known as mitochondrial complex II, a key enzyme complex of the tricarboxylic acid cycle and aerobic respiratory chains of mitochondria. The encoded protein is one of two integral membrane proteins that anchor other subunits of the complex, which form the catalytic core, to the inner mitochondrial membrane. There are several related pseudogenes for this gene on different chromosomes. Mutations in this gene have been associated with pheochromocytomas and paragangliomas. Alternatively spliced transcript variants have been described.
KIAA0895 is a protein that in Homo sapiens is encoded by the KIAA0895 gene. The gene encodes a protein commonly known as the KIAA0895 protein. It's aliases include hypothetical protein LOC23366, OTTHUMP00000206979, OTTHUMP00000206980, 9530077C05Rik, and 1110003N12Rik. It is located at 7p14.2.
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.
Chromosome 8 open reading frame 58 is an uncharacterised protein that in humans is encoded by the C8orf58 gene. The protein is predicted to be localized in the nucleus.
Chromosome 21 Open Reading Frame 58 (C21orf58) is a protein that in humans is encoded by the C21orf58 gene.
Chromosome 16 open reading frame 46 is a protein of yet to be determined function in Homo sapiens. It is encoded by the C16orf46 gene with NCBI accession number of NM_001100873. It is a protein-coding gene with an overlapping locus.
C15orf39 is a protein that in humans is encoded by the Chromosome 15 open reading frame 15 (C15orf39) gene.
Chromosome 1 open reading frame (C1orf167) is a protein which in humans is encoded by the C1orf167 gene. The NCBI accession number is NP_001010881. The protein is 1468 amino acids in length with a molecular weight of 162.42 kDa. The mRNA sequence was found to be 4689 base pairs in length.
C16orf90 or chromosome 16 open reading frame 90 produces uncharacterized protein C16orf90 in homo sapiens. C16orf90's protein has four predicted alpha-helix domains and is mildly expressed in the testes and lowly expressed throughout the body. While the function of C16orf90 is not yet well understood by the scientific community, it has suspected involvement in the biological stress response and apoptosis based on expression data from microarrays and post-translational modification data.
Coiled-coil domain containing 121 (CCDC121) is a protein encoded by the CCDC121 gene in humans. CCDC121 is located on the minus strand of chromosome 2 and encodes three protein isoforms. All isoforms of CCDC121 contain a domain of unknown function referred to as DUF4515 or pfam14988.
C6orf136 is a protein in humans encoded by the C6orf136 gene. The gene is conserved in mammals, mollusks, as well some porifera. While the function of the gene is currently unknown, C6orf136 has been shown to be hypermethylated in response to FOXM1 expression in Head Neck Squamous Cell Carcinoma (HNSCC) tissue cells. Additionally, elevated expression of C6orf136 has been associated with improved survival rates in patients with bladder cancer. C6orf136 has three known isoforms.
Transmembrane protein 101 (TMEM101) is a protein that in humans is encoded by the TMEM101 gene. The TMEM101 protein has been demonstrated to activate the NF-κB signaling pathway. High levels of expression of TMEM101 have been linked to breast cancer.
C1orf159 is a protein that in human is encoded by the C1orf159 gene located on chromosome 1. This gene is also found to be an unfavorable prognosis marker for renal and liver cancer, and a favorable prognosis marker for urothelial cancer.
Chromosome 13 Open Reading Frame 46 is a protein which in humans is encoded by the C13orf46 gene. In humans, C13orf46 is ubiquitously expressed at low levels in tissues, including the lungs, stomach, prostate, spleen, and thymus. This gene encodes eight alternatively spliced mRNA transcript, which produce five different protein isoforms.
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.
Chromosome 19 open reading frame 22 (c19orf22) is a protein which in humans is encoded by the c19orf22 gene. The primary alias of the gene is R3H domain containing 4 (R3HDM4), but it is commonly referred to as c19orf22.
Family with sequence similarity 13 member B is a protein which in humans is encoded by the FAM13B gene, also known as C5ORF5. The FAM13B gene is found in vertebrates and jawed fish. FAM13B is expressed ubiquitously in human tissues and has been linked to maglinant myelomas susceptibility to atrial fibrillation, a cardiac arrhythmia.
Transmembrane protein 61 (TMEM61) is a protein that is encoded by the TMEM61 gene in humans. TMEM61 is located on the first chromosome in humans.TMEM61 is highly expressed in the intestinal regions predominantly the kidney, adrenal gland and pituitary tissues. The protein unlike other transmembrane protein in the region does not promote cancer growth. However, the TMEM61 protein when inhibited by secondary factors restricts normal activity in the kidney. The human protein shares many Orthologs and has been prevalent on Earth for millions of years.
Zinc Finger Protein 62, also known as "ZNF62," "ZNF755," or "ZET," is a protein that in humans is encoded by the ZFP62 gene. ZFP62 is part of the C2H2 Zinc Finger family of genes.
