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CLIP4

From Wikipedia, the free encyclopedia
CLIP4 protein predicted tertiary structure. Taken from PhyreRisk.[1]
CLIP4
Available structures
PDBOrtholog search: PDBe RCSB
Identifiers
AliasesCLIP4, RSNL2, CAP-Gly domain containing linker protein family member 4
External IDsMGI: 1919100; HomoloGene: 11662; GeneCards: CLIP4; OMA:CLIP4 - orthologs
Orthologs
SpeciesHumanMouse
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 – 29.2 MbChr 17: 72.08 – 72.17 Mb
PubMed search[4][5]
Wikidata
View/Edit HumanView/Edit Mouse

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.

Gene

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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

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Transcript variants

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

Protein

[edit]

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

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

Expression

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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

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Gene

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Common transcription factor binding sites

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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

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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

[edit]

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

[edit]

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

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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

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Importance in various cancers

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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

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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 Systemic Lupus Arythematosus points to it having a potential role in the disease mechanism.[36]

Homology

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CLIP4 orthologs

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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

References

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  1. ^ "PhyreRisk". phyrerisk.bc.ic.ac.uk. Retrieved 2020-05-03.
  2. ^ a b c GRCh38: Ensembl release 89: ENSG00000115295 – Ensembl, May 2017
  3. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000024059 – Ensembl, May 2017
  4. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  5. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  6. ^ a b c "CLIP4 CAP-Gly domain containing linker protein family member 4 [Homo sapiens (human)] - Gene - NCBI". ncbi.nlm.nih.gov. Retrieved 2020-05-01.
  7. ^ a b "CFSSP: Chou & Fasman Secondary Structure Prediction Server". biogem.org. Retrieved 2020-05-03.
  8. ^ a b "BioGPS - your Gene Portal System". biogps.org. Retrieved 2020-05-01.
  9. ^ a b c d "CLIP4 Gene - GeneCards | CLIP4 Protein | CLIP4 Antibody". genecards.org. Retrieved 2020-05-01.
  10. ^ "Homo sapiens CAP-Gly domain containing linker protein family member 4 (CLIP4), transcript variant 1, mRNA". 2020-04-25. {{cite journal}}: Cite journal requires |journal= (help)
  11. ^ "Homo sapiens CAP-Gly domain containing linker protein family member 4 (CLIP4), transcript variant 2, mRNA". 2020-04-25. {{cite journal}}: Cite journal requires |journal= (help)
  12. ^ "Homo sapiens CAP-Gly domain containing linker protein family member 4 (CLIP4), transcript variant 3, mRNA". 2020-04-25. {{cite journal}}: Cite journal requires |journal= (help)
  13. ^ a b "ExPASy - Compute pI/Mw tool". web.expasy.org. Retrieved 2020-05-03.
  14. ^ a b c d e "SAPS < Sequence Statistics < EMBL-EBI". ebi.ac.uk. Retrieved 2020-05-03.
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  16. ^ "CAP-Gly domain-containing linker protein 4 isoform 2 [Homo sapiens] - Protein - NCBI". ncbi.nlm.nih.gov. Retrieved 2020-05-03.
  17. ^ a b "CLIP4 protein expression summary - The Human Protein Atlas". proteinatlas.org. Retrieved 2020-05-01.
  18. ^ a b "CLIP4 - GEO Profiles - NCBI". ncbi.nlm.nih.gov. Retrieved 2020-05-01.
  19. ^ "Sequence Utilities". bioline.com. Retrieved 2020-05-01.
  20. ^ "RNA secondary structure prediction". genebee.msu.su. Archived from the original on 2021-09-17. Retrieved 2020-05-01.
  21. ^ "PSORT II Prediction". psort.hgc.jp. Retrieved 2020-05-03.
  22. ^ "SignalP-5.0". cbs.dtu.dk. Retrieved 2020-05-03.
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  25. ^ "NetOGlyc 4.0 Server". cbs.dtu.dk. Retrieved 2020-05-03.
  26. ^ "NetPhos 3.1 Server". cbs.dtu.dk. Retrieved 2020-05-03.
  27. ^ Weisbrich A, Honnappa S, Jaussi R, Okhrimenko O, Frey D, Jelesarov I, et al. (October 2007). "Structure-function relationship of CAP-Gly domains". Nature Structural & Molecular Biology. 14 (10): 959–67. doi:10.1038/nsmb1291. PMID 17828277. S2CID 37088265.
  28. ^ Li J, Mahajan A, Tsai MD (December 2006). "Ankyrin repeat: a unique motif mediating protein-protein interactions". Biochemistry. 45 (51): 15168–78. doi:10.1021/bi062188q. PMID 17176038.
  29. ^ "UniProtKB - P30622 (CLIP1_HUMAN)". UniProt. Archived from the original on 2010-12-16. Retrieved 3 May 2020.
  30. ^ a b "CLIP4 protein (human) - STRING interaction network". string-db.org. Retrieved 2020-05-03.
  31. ^ "CLIP4 - CAP-Gly domain-containing linker protein 4 - Homo sapiens (Human) - CLIP4 gene & protein". uniprot.org. Retrieved 2020-05-01.
  32. ^ Pirini F, Noazin S, Jahuira-Arias MH, Rodriguez-Torres S, Friess L, Michailidi C, et al. (June 2017). "Early detection of gastric cancer using global, genome-wide and IRF4, ELMO1, CLIP4 and MSC DNA methylation in endoscopic biopsies". Oncotarget. 8 (24): 38501–38516. doi:10.18632/oncotarget.16258. PMC 5503549. PMID 28418867.
  33. ^ Pirini F, Noazin S, Jahuira-Arias MH, Rodriguez-Torres S, Friess L, Michailidi C, et al. (June 2017). "Early detection of gastric cancer using global, genome-wide and IRF4, ELMO1, CLIP4 and MSC DNA methylation in endoscopic biopsies". Oncotarget. 8 (24): 38501–38516. doi:10.18632/oncotarget.16258. PMC 5503549. PMID 28418867.
  34. ^ Kron K, Pethe V, Briollais L, Sadikovic B, Ozcelik H, Sunderji A, et al. (2009-03-13). "Discovery of novel hypermethylated genes in prostate cancer using genomic CpG island microarrays". PLOS ONE. 4 (3): e4830. Bibcode:2009PLoSO...4.4830K. doi:10.1371/journal.pone.0004830. PMC 2653233. PMID 19283074.
  35. ^ Gehrau R, Mas V, Archer K, Maluf D (2012-06-06). "Biomarkers of disease differentiation: HCV recurrence versus acute cellular rejection". Fibrogenesis & Tissue Repair. 5 (Suppl 1): S11. doi:10.1186/1755-1536-5-S1-S11. PMC 3368799. PMID 23259646.
  36. ^ "Barbara Dema". Discovery Medicine.
  37. ^ "Nucleotide BLAST: Search nucleotide databases using a nucleotide query". blast.ncbi.nlm.nih.gov. Retrieved 2020-05-03.
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