CLIP4

CAP-Gly Domain Containing Linker Protein Family Member 4 is a protein that in humans is encoded by the CLIP4 gene.[6] In terms of conserved domains, the CLIP4 gene contains primarily ankyrin repeats and the eponymous CAP-Gly domains.[6] The structure of the CLIP4 protein is largely made up of coil, with alpha helices dominating the rest of the protein.[7] CLIP4 mRNA expression occurs largely in the adrenal cortex and atrioventricular node.[8] The literature encompassing CLIP4's conserved domains and paralogs points toward microtubule regulation as a possible function of CLIP4.

CLIP4 protein predicted tertiary structure. Taken from PhyreRisk.[1]

CLIP4
Available structures PDB Ortholog search: PDBe RCSB List of PDB id codes 2Z0W
Identifiers
Aliases	CLIP4, RSNL2, CAP-Gly domain containing linker protein family member 4
External IDs	MGI: 1919100 HomoloGene: 11662 GeneCards: CLIP4
Gene location (Human) Chr. Chromosome 2 (human)[2] Band 2p23.2 Start 29,097,705 bp[2] End 29,189,643 bp[2]
Gene location (Mouse) Chr. Chromosome 17 (mouse)[3] Band 17|17 E1.3 Start 71,768,473 bp[3] End 71,864,273 bp[3]
Orthologs
Species	Human	Mouse
Entrez	79745	78785
Ensembl	ENSG00000115295	ENSMUSG00000024059
UniProt	Q8N3C7	Q8CI96
RefSeq (mRNA)	NM_001287527 NM_001287528 NM_024692	NM_001271483 NM_001271484 NM_030179 NM_175378
RefSeq (protein)	NP_001274456 NP_001274457 NP_078968	NP_001258412 NP_001258413 NP_084455 NP_780587
Location (UCSC)	Chr 2: 29.1 – 29.19 Mb	Chr 17: 71.77 – 71.86 Mb
PubMed search	[4]	[5]
Wikidata
View/Edit Human View/Edit Mouse

Gene

The human CLIP4 gene, also known as Restin-Like Protein 2 (RSNL2),[9] is located on the plus strand of the short (p) arm of chromosome 2 at region 2, band 3[9] from base pair 29,096,676 to base pair 29,189,643. CLIP4 is 92,968 base pairs in length and consists of 23 exons.[9]

Transcript

Transcript variants

Transcript	mRNA size (nucleotides)
CLIP4 transcript variant 1[10]	4299
CLIP4 transcript variant 2[11]	4295
CLIP4 transcript variant 3[12]	2353

Protein

The human CLIP4 protein is 705 amino acids in length and is composed of two main types of conserved domains: Two CAP-Gly domains and numerous ankyrin repeats.[9] The secondary structure of CLIP4 consists largely of random coil, with alpha helices as the second-most abundant structure and beta sheets as the third-most abundant structure.[7]

The isoelectronic point of the unprocessed CLIP4 protein is slightly basic (8.62 pI), meaning there is a slight excess of basic amino acids compared to acidic amino acids.[13] The molecular weight is about 65 kD.[13] The most abundant amino acid in CLIP4 is Serine, which makes up 10.7% of the protein.[14] Aligned matching blocks of separated, tandem, and periodic repeats are found between positions 340-345 and 542-547, as well as 447-547 and 564-568.[14] The unusual 9-figure periodic element of a singular Lysine followed by eight other amino acids occurs five times within the protein when compared to the swp23s.q dataset.[14] Another unusual phenomenon is a 7-figure periodic element of a negatively charged amino acid followed by six other hydrophobic amino acids, which occurs six times within the protein when compared to the swp23s.q dataset.[14] There are two instances of Serine spacing and two instances of Phenylalanine spacing that comprise unusually large distances when compared to the swp23s.q dataset.[14]

Protein isoforms

Isoform	Protein size (amino acids)
CLIP4 isoform 1[15]	705
CLIP4 isoform 2[16]	599

Expression

CLIP4 RNA expression is consistently measured to a high degree in the thyroid.[6] Additionally, high degrees of transcription occur in the adrenal cortex and atrioventricular node.[8] The Human Protein Atlas points toward high RNA expression values in the muscle tissues, as well as some in the skin, endocrine tissues, and proximal digestive tract.[17] Greatest protein expression values appeared in the muscle tissues as well, in addition to some in the lung, gastrointestinal tract, liver & gallbladder, and bone marrow & lymphoid tissues.[17]

CLIP4 protein expression seems to be highly expressed during Ada3 deficiency.[18] There also exists a higher trend towards higher CLIP4 expression in the absence of U28.[18]

Regulation

Gene

Common transcription factor binding sites

These transcription factors were chosen and organized based on proximity to the promoter and matrix similarity.[19]

Transcription Factor	Detailed Matrix Info	Anchor Base	Matrix Similarity	Sequence
NOLF	Early B-cell factor 1	17	0.98	taagagTCCCcagggcagaaaca
PAX2	Zebrafish PAX2 paired domain protein	18	0.8	aagagtccccagggcagAAACaa
AP2F	Transcription factor AP-2, alpha	16	0.98	ctgcCCTGgggactc
AP2F	Transcription factor AP-2, beta	16	0.899	gagTCCCcagggcag
SORY	SRY (sex-determining region Y) box 9, dimeric binding sites	35	0.768	aAACAaaatccagtgagggagag
HNF6	CUT-homeodomain transcription factor Onecut-2	32	0.827	aaacaaAATCcagtgag
PAX5	B-cell-specific activator protein	40	0.815	acaaaaTCCAgtgagggagagatgcaggg
ZF16	PR/SET domain 15	36	0.852	aaatccagtgaGGGA
SORY	HMGI(Y) high-mobility-group protein I (Y), architectural transcription factor organizing the framework of a nuclear protein-DNA transcriptional complex	78	0.945	tggaAATTttctaccttaggagc
NFAT	Nuclear factor of activated T-cells 5	83	0.955	ttttGGAAattttctacct
NFAT	Nuclear factor of activated T-cells 5	83	0.871	aggtAGAAaatttccaaaa
CEBP	CCAAT/enhancer binding protein (C/EBP), epsilon	89	0.975	agccttttGGAAatt
CAAT	Cellular and viral CCAAT box	110	0.91	gcagCCATttaatct
CAAT	Avian C-type LTR CCAAT box	165	0.875	cccaCCAAgcagtgg
CEBP	CCAAT/enhancer binding protein (C/EBP), gamma	650	0.866	ctaaTTGCtcaacgt
CEBP	CCAAT/enhancer binding protein alpha	651	0.971	cacgttgaGCAAtta
VTBP	Mammalian C-type LTR TATA box	680	0.903	tgctgTAAAaggcctaa
TF2B	Transcription factor II B (TFIIB) recognition element	983	1	ccgCGCC
TF2B	Transcription factor II B (TFIIB) recognition element	1157	1	ccgCGCC
TF2B	Transcription factor II B (TFIIB) recognition element	1228	1	ccgCGCC

Transcriptional

The human CLIP4 mRNA sequence has 12 stem-loop structures in its 5' UTR and 13 stem-loop structures in its 3' UTR. Of those secondary structures, there are 12 conserved stem-loop secondary structures in the 5'UTR as well as 1 conserved stem-loop secondary structure in the 3' UTR.[20]

Protein

The human CLIP4 protein is localized within the cellular nuclear membrane.[21] CLIP4 does not have a signal peptide due to its intracellular localization.[22] It also does not have N-linked glycosylation sites for that same reason.[23] CLIP4 is not cleaved.[24] However, numerous O-linked glycosylation sites are present.[25] A high density of phosphorylation sites are present in the 400-599 amino acid positions on the CLIP4 protein, although many are also present throughout the rest of the protein.[26]

Function

CAP-Gly domains are often associated with microtubule regulation.[27] In addition, ankyrin repeats are known to mediate protein-protein interactions.[28] Furthermore, CLIP1, a paralog of CLIP4 in humans, is known to bind to microtubules and regulate the microtubule cytoskeleton.[29] The CLIP4 protein is also predicted to interact with various microtubule-associated proteins.[30] As a result, it is likely that the CLIP4 protein, although uncharacterized, is associated with microtubule regulation.

Interacting Proteins

The CLIP4 protein is predicted to interact with many proteins associated with microtubules; namely, MAPRE1, MAPRE2, and MAPRE3. It is also predicted to interact with CKAP5 and DCTN1, a cytoskeleton-associated protein and dynactin-associated protein respectively.[30]

Clinical significance

Importance in various cancers

CLIP4 activity is correlated with the spread of renal cell carcinomas (RCCs) within the host and could therefore be a potential biomarker for RCC metastasis in cancer patients.[31] Additionally, measurement of promotor methylation levels of CLIP4 using a Global Methylation DNA Index reveals that higher methylation of CLIP4 is associated with an increase in severity of gastritis to possibly gastric cancer.[32] This indicates that CLIP4 could be used for early detection of gastric cancer.[33] A similar finding was also documented for prostate cancer, in which CLIP4 was found to be hypermethylated in patients with prostate cancer.[34]

Importance in other diseases

The presence of CLIP4 was found to be highly increased in samples with predicted severe fibrosis as a result of Chronic Hepatitis C virus (HCV).[35] Additionally, the presence of CLIP4 as a novel self-antigen in Systmic Lupus Arythematosus points to it having a potential role in the disease mechanism.[36]

Homology

CLIP4 orthologs

These orthologs were chosen and organized based on estimated date of divergence from the human protein as well as the global sequence identity.[37]

Binomial Nomenclature	Common Name	Taxonomic Group	Estimated DoD from Human (MYA)	Accession Number	Sequence Length (AA)	Global Sequence Identity to Human Protein (%)	Global Sequence Similarity to Human Protein (%)
Homo sapiens (Hsa)	Human	Primate	0	AAP97312	601	100	100
Aotus nancymaae (Ana)	Ma's night monkey	Primate	43.2	XP_012330895	704	83.5	83.7
Sorex araneus (Sar)	Common shrew	Eulipotyphla	96	XP_004620056	707	74	78.5
Antrostomus carolinensis (Aca)	Chuck-will's-widow	Aves	312	XP_028942997	702	66.5	75.4
Gekko japonicus (Gja)	Schlegel's Japanese gecko	Reptilia	312	XP_015270366	702	63.8	73.1
Rhinatrema bivittatum (Rbi)	Two-lined caecilian	Amphibians	351.8	XP_029448862	707	59.5	70.5
Callorhinchus milii (Cmi)	Elephant shark	Chondrichthyes	473	XP_007895016	715	52.5	65.6
Branchiostoma floridae (Bfl)	Florida lancelet	Leptocardii	684	XP_002606824	481	40.4	52.8
Saccoglossus kowalevskii (Sko)	Acorn worm	Enteropneusta	684	XP_006822686	648	35.7	47.5
Ixodes scapularis (Isc)	Black-legged tick	Arachnid	797	XP_029831090	527	38.9	53
Limulus polyphemus (Lpo)	Atlantic horseshoe crab	Arachnid	797	XP_013786376	462	38	51.6
Lottia gigantea (Lgi)	Owl limpet	Gastropods	797	XP_009046843	669	36.3	49.3
Mizuhopecten yessoensis (Mye)	Yesso scallop	Bivalvia	797	XP_021359747	633	35.4	47.2
Parasteatoda tepidariorum (Pte)	Common house spider	Arachnid	797	XP_015914966	616	34.7	47.6
Aplysia californica (Aca)	California sea hare	Gastropods	797	XP_012945346	653	33.7	45.7
Crassostrea virginica (Cvi)	Eastern oyster	Bivalvia	797	XP_022315879	646	32.7	45.1
Tetranychus urticae (Tur)	Two-spotted spider mite	Arachnid	797	XP_015790536	652	31.9	43.5
Centruroides sculpturatus (Csc)	Bark scorpion	Arachnid	797	XP_023229484	605	30.6	43.4
Penaeus vannamei (Pva)	Pacific white shrimp	Malacostracans	797	XP_027206746	681	22.9	34
Monosiga brevicollis (Mbr)	Choanoflagellate	Choanoflagellatea	1023	XP_001748580	576	25.3	40.8

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