Wikipedia

SUHW4

Zinc finger protein 280D, also known as Suppressor Of Hairy Wing Homolog 4, SUWH4, Zinc Finger Protein 634, ZNF634, or KIAA1584, is a protein that in humans is encoded by the ZNF280D gene located on chromosome 15q21.3.[4][5]

ZNF280D
Identifiers
AliasesZNF280D, SUHW4, ZNF634, zinc finger protein 280D
External IDsMGI: 2384583 HomoloGene: 17151 GeneCards: ZNF280D
Orthologs
SpeciesHumanMouse
Entrez

54816

235469

Ensembl

ENSG00000137871

ENSMUSG00000038535

UniProt

Q6N043

Q68FE8

RefSeq (mRNA)

NM_001002843
NM_001002844
NM_001288588
NM_001288589
NM_017661

NM_146224
NM_001311105

RefSeq (protein)

NP_001002843
NP_001002844
NP_001275517
NP_001275518
NP_060131

NP_001298034
NP_666336

Location (UCSC)n/aChr 9: 72.18 – 72.27 Mb
PubMed search[2][3]
Wikidata
View/Edit HumanView/Edit Mouse

Gene edit

There are a total of 24 possible exons in any variant of the ZNF280D gene.[6] ZNF280D is oriented on the minus strand of Chromosome 15 and spans 288.396 kb.[7] Surrounding genes at the same locus include TEX9, HMGB1P33, MNS1, LOC645877, and LOC145783.[8]

 
Chromosomal location of the ZNF280D gene in humans with surrounding local genes
 
Chromosome 15 Location

mRNA edit

At least 24 spliced variants have been identified.[9] There are 7 probable alternative promoters. The mRNAs appear to differ by truncation of the 5' end, truncation of the 3' end, presence or absence of 12 cassette exons, overlapping exons with different boundaries, splicing versus retention of 5 introns.[9] The longest splice form contains 4428 bp.[10]

 
Most abundant alternative splice forms of ZNF280D mRNA.

Protein edit

Composition and Domains edit

 
Multiple sequence alignment of orthologs for DUF4195 reveals low conservation.
 
Multiple sequence alignment of orthologs for five zinc finger domains reveals high conservation.

The ZNF280D protein is 979 amino acids in length.[11] The protein contains a domain of unknown function (DUF4195) spanning from amino acid 45 to amino acid 230.[11] DUF4195 (pfam13826) is a family that is found at the N-terminus of metazoan proteins that carry PHD-like zinc-finger domains; the function is unknown.[12] ZNF280D protein also contains five highly conserved Cys2His2-type zinc finger domains.[13] Zinc fingers have the ability to bind DNA, which supports the speculative role of ZNF280D as a transcription factor.[14] The protein has a weight of approximately 109.3 kdal.[15] Charge cluster analysis reveals a negative charge cluster near the N-terminus from amino acids 16-43.[15] Charge clusters are associated with functional domains of cellular transcription factors, providing further support for ZNF280D as a possible transcription factor.[16]

Interactions edit

ZNF280D has been experimentally determined to interact with CBX5 and CBX3 proteins.[17] These proteins both play a role in the formation of heterochromatin, which presents a possible functional role of ZNF280D as a transcriptional repressor.[18][19]

SNPs edit

There are a number of SNPs that have been observed in the human population.[20] The image below lists some of the most frequently occurring.

 
Frequently observed SNPs in human genome.

Regulation edit

mRNA Level edit

 
Human ZNF280D promoter region and predicted transcription factor binding sites.

A number of transcription factors are predicted to bind to the predicted promoter region.[21]

Protein Level edit

ZNF280D protein contains 66 serine, 17 threonine, and 6 tyrosine residues all of which are potential phosphorylation sites.[22]

 
Candidate phosphorylation sites in human ZNF280D protein.

The glycine residue at position 2 is a probable candidate for N-terminal acetylation.[23] There are seven probable sumoylation sites.[24]

 
Probable sumoylation sites in ZNF280D protein.

Expression edit

 
GEO Profile expression analysis of ZNF280D protein in human tissues.

ZNF280D is ubiquitously expressed at relatively low levels throughout almost all tissues in the human body.[25]

In one study, the expression of ZNF280D was compared between endothelial progenitor cells in cord blood and peripheral blood. The results show that expression was significantly higher in cord blood. This supports a possible involvement of ZNF280D in embryonic development or cell differentiation.[26]

 
Expression data for ZNF280D in endothelial progenitor cells from cord blood and adult peripheral blood.

Evolution edit

A number of orthologs and distant homologs have been identified for the human ZNF280D protein. There are also four paralogs to ZNF280D in the human genome.[27]

Protein Name Species Date of Divergence (Million Years Ago)[28] Accession Number Sequence Length (# amino acids) Sequence Identity E Value
ZNF280D Mouse (Mus musculus) 92.3 NP_666336 974 76% 0
ZNF280D Isoform X1 Cow (Bos taurus) 94.2 XP_002690904 974 88% 0
ZNF280D African bush elephant (Loxodonta africana) 98.7 XP_003418437 979 90% 0
ZNF280D Isoform X1 Chinese softshell turtle (Pelodiscus sinensis) 296 XP_006112544 993 61% 0
ZNF280D Saker falcon (Falco cherrug) 296 XP_005435548 939 60% 0
ZNF280D Ground tit (Pseudopdoces humilis) 296 XP_005521527 936 57% 0
ZNF280D Isoform X1 Chinese alligator (Alligator sinensis) 296 XP_006018037 277 50% 1E-64
ZNF280D Western clawed frog (Xenopus tropicalis) 371.2 XP_002940298 1071 49% 0
ZNF280D Isoform X1 Zebrafish (Danio rerio) 400.1 XP_005166581 879 43% 2E-172
ZNF280D-like Acorn worm (Saccoglossus kowalevskii) 661.2 XP_006811912 733 32% 5E-50
Zinc Finger Protein 36 Sea squirt (Ciona intestinalis) 722.5 NP_001041459 581 32% 7E-58
GL11474 Fruit fly (Drosophila persimilis) 782.7 XP_002016218 1271 29% 5E-16
Zinc Finger Protein Eye worm (Loa loa) 937.5 XP_003139663 495 33% 6E-19
Zap1p Yeast (Saccharomyces cerevisiae S288c) 12158 NP_012479 880 33% 2E-7
Table of select number of orthologs and distant homologs for human ZNF280D protein
Paralog Name Accession Number Sequence Length (# amino acids) Sequence Identity E Value
ZNF280C NP_060136 737 68% 0
ZNF280B NP_542942 543 54% 0
ZNF280A NP_542778 542 49% 6E-148
ZNF280E (pogo transposable element with ZNF domain isoform 1) NP_055915 1410 44% 4E-134
Table of paralogs for human ZNF280D protein

References edit

  1. ^ a b c GRCm38: Ensembl release 89: ENSMUSG00000038535 – Ensembl, May 2017
  2. ^ "Human PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  3. ^ "Mouse PubMed Reference:". National Center for Biotechnology Information, U.S. National Library of Medicine.
  4. ^ Nagase T, Kikuno R, Nakayama M, Hirosawa M, Ohara O (August 2000). "Prediction of the coding sequences of unidentified human genes. XVIII. The complete sequences of 100 new cDNA clones from brain which code for large proteins in vitro". DNA Research. 7 (4): 273–81. doi:10.1093/dnares/7.4.271. PMID 10997877.
  5. ^ "Entrez Gene: SUHW4 suppressor of hairy wing homolog 4 (Drosophila)".
  6. ^ "Genetic Testing Registry". NCBI. Retrieved 7 May 2014.
  7. ^ "GeneCards". Retrieved 7 May 2014.
  8. ^ "ZNF280D zinc finger protein 280D [ Homo sapiens (human) ]". NCBI. Retrieved 9 May 2014.
  9. ^ a b "Homo sapiens complex locus ZNF280D, encoding zinc finger protein 280D and hypothetical LOC145783". NCBI AceView. Retrieved 7 May 2014.
  10. ^ "Homo sapiens zinc finger protein 280D, mRNA (cDNA clone MGC:168023 IMAGE:9020400), complete cds". NCBI. 12 May 2008. Retrieved 7 May 2014.
  11. ^ a b "Zinc finger protein 280D [Homo sapiens]". NCBI. Retrieved 7 May 2014.
  12. ^ "pfam13836: DUF4195". NCBI. Retrieved 7 May 2014.
  13. ^ "Q6N043 (Z280D_HUMAN)". UniProt. Retrieved 7 May 2014.
  14. ^ Klug A (October 1999). "Zinc finger peptides for the regulation of gene expression". Journal of Molecular Biology. 293 (2): 215–8. doi:10.1006/jmbi.1999.3007. PMID 10529348.
  15. ^ a b Brendel, Voker. "SAPS Statistical Analysis of PS". SDSC Workbench. Retrieved 7 May 2014.[permanent dead link]
  16. ^ Brendel V, Karlin S (August 1989). "Association of charge clusters with functional domains of cellular transcription factors". Proceedings of the National Academy of Sciences of the United States of America. 86 (15): 5698–702. Bibcode:1989PNAS...86.5698B. doi:10.1073/pnas.86.15.5698. PMC 297697. PMID 2569737.
  17. ^ "STRING input ZNF280D (Homo sapiens)". STRING. Retrieved 10 May 2014.
  18. ^ "CBX5 [Homo sapiens]". NCBI. Retrieved 10 May 2014.
  19. ^ "CBX3 [Homo sapiens]". NCBI. Retrieved 10 May 2014.
  20. ^ "SNP linked to Gene ZNF280D(geneID:54816) Via Contig Annotation". NCBI. Retrieved 10 May 2014.
  21. ^ "Genomatix". Genomatix. Retrieved 7 May 2014.
  22. ^ Blom N, Gammeltoft S, Brunak S (December 1999). "Sequence and structure-based prediction of eukaryotic protein phosphorylation sites". Journal of Molecular Biology. 294 (5): 1351–62. doi:10.1006/jmbi.1999.3310. PMID 10600390.
  23. ^ Kiemer, Lars (2005). "NetAcet: Prediction of N-terminal acetylation sites". Bioinformatics. 21 (7). NetAcet: 1269–1270. doi:10.1093/bioinformatics/bti130. PMID 15539450. Retrieved 7 May 2014.
  24. ^ "SUMOplot™ Analysis Program". Retrieved 7 May 2014.
  25. ^ "GDS596 / 221213_s_at / ZNF280D". GEO Profile. NCBI. Retrieved 7 May 2014.
  26. ^ "ZNF280D – Endothelial progenitor cells from cord blood and adult peripheral blood". NCBI. Retrieved 9 May 2014.
  27. ^ "NCBI Basic Local Alignment Search Tool". NCBI. Retrieved 10 May 2014.
  28. ^ "TimeTree". TimeTree. Retrieved 10 May 2014.

Further reading edit

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