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Gene: LOC100986487 (zinc finger protein 540) Pan paniscus

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Symbol:

LOC100986487 (Ensembl: ZNF540)

Name:

zinc finger protein 540

RGD ID:

11831407

Description:

ENCODES a protein that exhibits DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); mRNA regulatory element binding translation repressor activity (inferred); nucleic acid binding (inferred); INVOLVED IN negative regulation of DNA-templated transcription (inferred); negative regulation of translation (inferred); regulation of DNA-templated transcription (inferred); ASSOCIATED WITH COVID-19 (ortholog); FOUND IN cytoplasm (inferred); cytosol (inferred); intracellular membrane-bounded organelle (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

ZNF540

RGD Orthologs

Human

Squirrel

Green Monkey

Alliance Orthologs

More Info

more info ...

Latest Assembly:

Mhudiblu_PPA_v0 - Bonobo Mhudiblu_PPA_v0 Assembly

Position:

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	20	43,723,723 - 43,743,014 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	19	45,602,254 - 45,621,545 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	19	34,536,659 - 34,555,850 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	19	42,212,283 - 42,231,497 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	19	42,213,165 - 42,227,855 (-)	Ensembl	panpan1.1		panPan2

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

COVID-19 (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

negative regulation of DNA-templated transcription (IEA)

negative regulation of translation (IEA)

regulation of DNA-templated transcription (IEA)

regulation of transcription by RNA polymerase II (IEA)

Cellular Component

cytoplasm (IEA)

cytosol (IEA)

intracellular membrane-bounded organelle (IEA)

nucleoplasm (IEA)

nucleus (IEA)

Molecular Function

DNA-binding transcription factor activity, RNA polymerase II-specific (IEA)

mRNA regulatory element binding translation repressor activity (IEA)

nucleic acid binding (IEA)

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IEA)

zinc ion binding (IEA)

References

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

LOC100986487
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
NHGRI_mPanPan1-v2	20	43,723,723 - 43,743,014 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	19	45,602,254 - 45,621,545 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	19	34,536,659 - 34,555,850 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	19	42,212,283 - 42,231,497 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	19	42,213,165 - 42,227,855 (-)	Ensembl	panpan1.1		panPan2

ZNF540
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	19	37,551,374 - 37,614,179 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	19	37,551,406 - 37,614,179 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	19	38,042,276 - 38,105,080 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	19	42,734,148 - 42,796,836 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	19	42,734,147 - 42,796,834	NCBI
Celera	19	34,886,421 - 34,905,691 (+)	NCBI		Celera
Cytogenetic Map	19	q13.12	NCBI
HuRef	19	34,492,440 - 34,555,196 (+)	NCBI		HuRef
CHM1_1	19	38,042,735 - 38,105,552 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	19	40,353,192 - 40,415,937 (+)	NCBI		T2T-CHM13v2.0

Znf540
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024409349	12,329,783 - 12,364,075 (+)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936801	481,223 - 528,848 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ZNF540
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	6	32,272,552 - 32,292,480 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666073	10,209,707 - 10,230,039 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Expression

RNA-SEQ Expression

Click on a value in the shaded box below the category label to view a detailed expression data table for that system.

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_008960850	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_034945203	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_034945204	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_034945205	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_034945206	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_055103120	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_055103121	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JARIFH020000020	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSPPAT00000036773 ⟹ ENSPPAP00000014097

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
PanPan1.1 Ensembl	19	42,213,165 - 42,227,209 (-)	Ensembl

Ensembl Acc Id:

ENSPPAT00000036778 ⟹ ENSPPAP00000014102

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
PanPan1.1 Ensembl	19	42,214,834 - 42,227,855 (-)	Ensembl

RefSeq Acc Id:

XM_008960850 ⟹ XP_008959098

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
NHGRI_mPanPan1-v2	20	43,723,723 - 43,743,014 (+)	NCBI
NHGRI_mPanPan1	19	45,602,254 - 45,621,545 (+)	NCBI
Mhudiblu_PPA_v0	19	34,536,659 - 34,555,850 (+)	NCBI
PanPan1.1	19	42,212,283 - 42,231,497 (-)	NCBI

Sequence:

show sequence

TGTACGACGTTGCGCAGCGACGCGGGGGCCTTCGGGAAATGTAGTCTACAACTGGAAACCGGCC
GGATCGTGTCTGCGCAGGCCCAGCAGCTAAGATCGGGTCCGGCGCTCCAGAACAGAACGATCCC
TGAGGCTCCCTTGCTCGAACTGTGGGACTTACCCTACTATGGTCCGAGCCTACCCTATTTCATT
ATACTCAAGTAACGCCCCAGAAATTCCAGAGAATCTCACACAAAGAGGTTGAGTCTTGCCGTGG
TGCCTTCAGGGGAATGTCATCCCGGGCTAGAAGAGCTGCAAAAGGCTGTCAGGCTTCTCAGAAC
TTTGCTTCTCCAGCAGAATAATCCTGCGGAAGACTGAGCAGTTCTTGTGAGTGTAAAACCATGG
CCCATGCATTGGTGACGTTCAGGGATGTGGCTATAGACTTCTCTCAGAAGGAATGGGAGTGCCT
GGACACTACCCAGAGGAAATTGTACAGAGATGTGATGTTGGAGAATTATAATAACTTGGTCTCA
CTGGGATATTCTGGCTCAAAGCCAGATGTGATTACCTTACTGGAGCAAGGGAAAGAGCCCTGCG
TGGCGGCGAGGGATGTGACAGGAAGACAGTGCCCCGGTTTGTTATCCCTGCATAAGACCAAGAA
ATTATCTTCAGAAAAGGACATTCATGAAATCAGTTTATCCAAAGGGAGTATAATAGAAAAAAGT
AAAACTCTTCATGTGAAAGGATCCATTTTTAGAAATGAGTGGCAGAACAAAAGTGAGTTTGAGG
GTCAACAGGGACTTAAAGAAAGATCTATCAGTCAAAAGAAAATCGTCTCTAAAAAAATGTCAAC
TGATAGAAAACATCCCTCTTTTACTCTGAATCAGAGAATTCATAATAGTGAGAAAAGCTGTGAC
TCAAACTTGGTTCAACATGGGAAAATAGATTCTGATGTGAAACATGATTGTAAAGAATGTGGGA
GTACTTTTAATAATGTCTATCAGCTTACTCTCCATCAGAAAATTCATACTGGTGAAAAATCCTG
TAAATGTGAGAAATGTGGGAAAGTTTTTAGTCATAGCTATCAACTTACTCTGCATCAGAGATTT
CATACTGGTGAGAAACCCTATGAATGTCAAGAATGTGGGAAGACCTTTATTCTTTACCCACAAC
TTAATCGACATCAGAAAATTCACACTGGTAAAAAACCCTATATGTGTAAGAAATGTGATAAGGG
TTTTTTTAGTAGATTAGAACTTACTCAACATAAAAGAATTCATACTGGTAAGAAATCTTATGAA
TGTAAAGAATGTGGAAAAGTTTTTCAACTTATTTTCTACTTTAAAGAACATGAGAGAATTCATA
CAGGTAAGAAACCCTATGAATGTAAGGAGTGTGGGAAAGCTTTTAGTGTATGCGGACAACTTAC
CCGTCATCAGAAAATTCATACTGGTGTAAAACCCTACGAATGTAAGGAATGTGGAAAGACCTTT
AGACTTNAGTTTTACCTTACTGAACACAGAAGAACTCATGCAGGTAAGAAACCTTATGAATGTA
AGGAGTGCGGGAAATCATTTAATGTGCGTGGACAGCTTAATCGGCATAAAACAATCCATACTGG
TATAAAACCTTTTGCATGTAAGGTGTGTGAGAAGGCTTTTAGTTATAGTGGTGACCTCAGAGTA
CATTCTAGAATTCATACTGGAGAGAAACCATATGAATGTAAGGAATGTGGGAAAGCCTTTATGC
TTCGTTCAGTCCTTACTGAACATCAGAGACTTCATACTGGTGTGAAGCCCTACGAATGTAAGGA
ATGTGGGAAGACCTTTCGAGTTCGTTCTCAAATTAGTCTACATAAGAAAATTCATACTGATGTG
AAGCCCTACAAATGTGTACGATGTGGGAAGACCTTTAGATTTGGTTTCTACCTTACTGAACACC
AGAGAATTCACACTGGTGAAAAGCCCTATAAATGTAAAGAATGTGGAAAGGCCTTTATTCGTAG
AGGGAATCTTAAAGAACATCTGAAAATTCATTCTGGTTTAAAACCCTATGACTGTAAAGAATGT
GGGAAGTCCTTTAGTCGGCGTGGGCAGTTCACTGAACATCAGAAAATTCATACGGGTGTAAAAC
CATACATATGTAAAGAATGTGGGAAGGCCTTTAGTCGTAGTGTAGACCTTAGAATACATCAAAG
AATTCATACTGGTGAGAAACCCTATGAGTGTAAACAATGTGGGAAGGCCTTTAGACTTAATTCA
CACCTTACTGAACATCAGAGAATTCATACTGGTGAGAAACCCTATGAGTGTAAGGTATGTAGAA
AGGCCTTTAGACAATATTCACATCTTTATCAACATCAGAAAACTCATAATGTAATTTAATATAA
GAAAAAGTTTCCATGTCATGCTCTATTTATAGAATATCAAAATATTTATGGCCAGAAGTTCTGT
CAATGTGTTGATGTTTTTTTACACATATTAACTTAATAAATGTGTGAGTCTTAAATACCTCTTA
GTTCTCCTTAAATTTAGGAAAATTCACACTAGAAAATAAAGCTGTTAATGTAACAGTTGTGGAA
AAGTGTTCTAGCAACAGCATATACTTATCATCATTGCCTTTCCACTACTCTACTATCTGTGTGA
TATTAGACAAAATATTTGCTTCTTGGTACCTCAGCTGTAAAATGAAACACACCTAAAAGTGTGG
TTGTTTCCAACATGTATAATACAGCAACAACTATCTGGCCCAAACTGCTTTGGATTAATATTGG
ATATTACTGTTTTTATTATCATCAACATTATTATTAGTGGATTTCTTAATAGGAAGATGCAATG
GAGATGACAAATTTGGAAAAACCACTCATCACTTATATTTCATGAAGTACTTCTTTGATAAAAT
CTGTTATGGGCTGAATGTTTGTGTTCCTGTAACAATTCCTATGTTGAAACACGAATCCCAAGGT
GATGGTATTTGAAGGTAGGGCCTTTAGGAAGTAACAATTCCTATGTTGAAACACGAATCCCAAG
GTGATGGTATTTGAAGGTAGGGCCTTTAGGAAGAAATTAGGTCATGAGGGTGGAGCCTTCATGA
GTGGAATTACTGCCTTTATAAGAAGAAGCCAAAGAGCCAGCTAGCTCTTTCAACCACATGAGGT
TACAGCAAGAAGTCAGCAGTCTACAGTGCAAAAGAGGGCCTTCACCAGAACCCAAGCATGCTGG
CACCTTGACCTTGGACTTTCAGCCTCCAAAACTGTGAGAAATAAA

hide sequence

RefSeq Acc Id:

XM_034945203 ⟹ XP_034801094

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
NHGRI_mPanPan1-v2	20	43,723,723 - 43,743,014 (+)	NCBI
NHGRI_mPanPan1	19	45,602,254 - 45,621,545 (+)	NCBI
Mhudiblu_PPA_v0	19	34,536,659 - 34,555,850 (+)	NCBI

RefSeq Acc Id:

XM_034945204 ⟹ XP_034801095

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
NHGRI_mPanPan1-v2	20	43,723,723 - 43,743,014 (+)	NCBI
NHGRI_mPanPan1	19	45,602,254 - 45,621,545 (+)	NCBI
Mhudiblu_PPA_v0	19	34,536,691 - 34,555,850 (+)	NCBI

RefSeq Acc Id:

XM_034945205 ⟹ XP_034801096

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
NHGRI_mPanPan1-v2	20	43,724,279 - 43,743,014 (+)	NCBI
NHGRI_mPanPan1	19	45,602,807 - 45,621,545 (+)	NCBI
Mhudiblu_PPA_v0	19	34,537,103 - 34,555,850 (+)	NCBI

RefSeq Acc Id:

XM_034945206 ⟹ XP_034801097

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
NHGRI_mPanPan1-v2	20	43,724,298 - 43,743,014 (+)	NCBI
NHGRI_mPanPan1	19	45,602,821 - 45,621,545 (+)	NCBI
Mhudiblu_PPA_v0	19	34,537,106 - 34,555,850 (+)	NCBI

RefSeq Acc Id:

XM_055103120 ⟹ XP_054959095

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
NHGRI_mPanPan1-v2	20	43,723,723 - 43,743,014 (+)	NCBI
NHGRI_mPanPan1	19	45,602,254 - 45,621,545 (+)	NCBI

RefSeq Acc Id:

XM_055103121 ⟹ XP_054959096

Type:

CODING

Position:

Bonobo Assembly	Chr	Position (strand)	Source
NHGRI_mPanPan1-v2	20	43,724,230 - 43,743,014 (+)	NCBI
NHGRI_mPanPan1	19	45,602,761 - 45,621,545 (+)	NCBI

Protein Sequences


Protein RefSeqs	XP_008959098	(Get FASTA)	NCBI Sequence Viewer
	XP_034801094	(Get FASTA)	NCBI Sequence Viewer
	XP_034801095	(Get FASTA)	NCBI Sequence Viewer
	XP_034801096	(Get FASTA)	NCBI Sequence Viewer
	XP_034801097	(Get FASTA)	NCBI Sequence Viewer
	XP_054959095	(Get FASTA)	NCBI Sequence Viewer
	XP_054959096	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSPPAP00000014097.1
	ENSPPAP00000014102.1

RefSeq Acc Id:

XP_008959098 ⟸ XM_008960850

- Peptide Label:

isoform X2

- Sequence:

show sequence

MAHALVTFRDVAIDFSQKEWECLDTTQRKLYRDVMLENYNNLVSLGYSGSKPDVITLLEQGKEP
CVAARDVTGRQCPGLLSLHKTKKLSSEKDIHEISLSKGSIIEKSKTLHVKGSIFRNEWQNKSEF
EGQQGLKERSISQKKIVSKKMSTDRKHPSFTLNQRIHNSEKSCDSNLVQHGKIDSDVKHDCKEC
GSTFNNVYQLTLHQKIHTGEKSCKCEKCGKVFSHSYQLTLHQRFHTGEKPYECQECGKTFILYP
QLNRHQKIHTGKKPYMCKKCDKGFFSRLELTQHKRIHTGKKSYECKECGKVFQLIFYFKEHERI
HTGKKPYECKECGKAFSVCGQLTRHQKIHTGVKPYECKECGKTFRLXFYLTEHRRTHAGKKPYE
CKECGKSFNVRGQLNRHKTIHTGIKPFACKVCEKAFSYSGDLRVHSRIHTGEKPYECKECGKAF
MLRSVLTEHQRLHTGVKPYECKECGKTFRVRSQISLHKKIHTDVKPYKCVRCGKTFRFGFYLTE
HQRIHTGEKPYKCKECGKAFIRRGNLKEHLKIHSGLKPYDCKECGKSFSRRGQFTEHQKIHTGV
KPYICKECGKAFSRSVDLRIHQRIHTGEKPYECKQCGKAFRLNSHLTEHQRIHTGEKPYECKVC
RKAFRQYSHLYQHQKTHNVI

hide sequence

RefSeq Acc Id:	XP_034801094 ⟸ XM_034945203
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_034801095 ⟸ XM_034945204
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_034801096 ⟸ XM_034945205
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_034801097 ⟸ XM_034945206
- Peptide Label:	isoform X1

Ensembl Acc Id:

ENSPPAP00000014102 ⟸ ENSPPAT00000036778

Ensembl Acc Id:

ENSPPAP00000014097 ⟸ ENSPPAT00000036773

RefSeq Acc Id:	XP_054959095 ⟸ XM_055103120
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_054959096 ⟸ XM_055103121
- Peptide Label:	isoform X2

Protein Domains

C2H2-type KRAB

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSPPAG00000030207	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSPPAT00000036773.1	UniProtKB/TrEMBL
	ENSPPAT00000036778.1	UniProtKB/TrEMBL
Gene3D-CATH	6.10.140.140	UniProtKB/TrEMBL
	Classic Zinc Finger	UniProtKB/TrEMBL
InterPro	KRAB	UniProtKB/TrEMBL
	KRAB_dom_sf	UniProtKB/TrEMBL
	Znf_C2H2_sf	UniProtKB/TrEMBL
	Znf_C2H2_type	UniProtKB/TrEMBL
NCBI Gene	ZNF540	ENTREZGENE
PANTHER	ZINC FINGER PROTEIN	UniProtKB/TrEMBL
	ZINC FINGER PROTEIN 566	UniProtKB/TrEMBL
Pfam	KRAB	UniProtKB/TrEMBL
	zf-C2H2	UniProtKB/TrEMBL
	zf-C2H2_6	UniProtKB/TrEMBL
PROSITE	KRAB	UniProtKB/TrEMBL
	ZINC_FINGER_C2H2_1	UniProtKB/TrEMBL
	ZINC_FINGER_C2H2_2	UniProtKB/TrEMBL
SMART	KRAB	UniProtKB/TrEMBL
	ZnF_C2H2	UniProtKB/TrEMBL
Superfamily-SCOP	SSF109640	UniProtKB/TrEMBL
	SSF57667	UniProtKB/TrEMBL
UniProt	A0A2R9AFF4_PANPA	UniProtKB/TrEMBL
	A0A2R9AFF9_PANPA	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2024-03-13	LOC100986487	zinc finger protein 540	ZNF540	zinc finger protein 540	Symbol and/or name change	5135510	APPROVED

Gene Annotator (Functional Annotation) unavailable	Gene Annotator (Annotation Distribution) unavailable	Variant Visualizer (Genomic Variants) unavailble Variant Visualizer (Genomic Variants) unavailable
Gene Annotator (Functional Annotation)	Gene Annotator (Annotation Distribution)	Variant Visualizer (Genomic Variants)

InterViewer (Protein-Protein Interactions) unavailable	Gviewer (Genome Viewer) unavailable	Variant Visualizer (Damaging Variants) unavailble Variant Visualizer (Damaging Variants) unavailable
InterViewer (Protein-Protein Interactions)	GViewer (Genome Viewer)	Variant Visualizer (Damaging Variants)

Gene Annotator (Annotation Comparison) unavailable	OLGA (Gene List Generator) unavailable
Gene Annotator (Annotation Comparison)	OLGA (Gene List Generator)	Excel (Download)

MOET (Multi-Ontology Enrichement) unavailable	GOLF (Gene-Ortholog Location Finder) unavailable
MOET (Multi-Ontology Enrichement)	GOLF (Gene-Ortholog Location Finder)

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