Pcgf6 (polycomb group ring finger 6)

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Gene: Pcgf6 (polycomb group ring finger 6) Ictidomys tridecemlineatus

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Symbol:

Pcgf6

Name:

polycomb group ring finger 6

RGD ID:

12602749

Description:

ENCODES a protein that exhibits metal ion binding (inferred); INVOLVED IN chromatin remodeling (inferred); negative regulation of DNA-templated transcription (inferred); negative regulation of transcription by RNA polymerase II (inferred); PARTICIPATES IN histone modification pathway; ASSOCIATED WITH desmoplastic/nodular medulloblastoma (ortholog); FOUND IN nucleus (inferred); PcG protein complex (inferred); PRC1 complex (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

polycomb group RING finger protein 6

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024407213	31,111,640 - 31,138,470 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936600	2,714,843 - 2,741,697 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936600	2,714,883 - 2,741,418 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

desmoplastic/nodular medulloblastoma (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

chromatin remodeling (IEA)

negative regulation of DNA-templated transcription (IEA)

negative regulation of transcription by RNA polymerase II (IEA)

Cellular Component

nucleus (IEA)

PcG protein complex (IEA)

PRC1 complex (IEA)

Molecular Function

metal ion binding (IEA)

protein binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

histone modification pathway (ISO)

References

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

Pcgf6
(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_024407213	31,111,640 - 31,138,470 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936600	2,714,843 - 2,741,697 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936600	2,714,883 - 2,741,418 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PCGF6
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	10	103,302,796 - 103,351,140 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	10	103,302,796 - 103,351,144 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	10	105,062,553 - 105,110,897 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	10	105,052,543 - 105,100,881 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	10	105,052,543 - 105,100,881	NCBI
Celera	10	98,802,479 - 98,850,828 (-)	NCBI		Celera
Cytogenetic Map	10	q24.33	NCBI
HuRef	10	98,693,204 - 98,741,643 (-)	NCBI		HuRef
CHM1_1	10	105,346,724 - 105,395,054 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	10	104,190,415 - 104,238,442 (-)	NCBI		T2T-CHM13v2.0

Pcgf6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	19	47,022,056 - 47,039,379 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	19	47,022,056 - 47,039,345 (-)	Ensembl		GRCm39 Ensembl
GRCm38	19	47,033,617 - 47,050,939 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	19	47,033,617 - 47,050,906 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	19	47,108,109 - 47,125,335 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	19	47,086,930 - 47,104,156 (-)	NCBI		MGSCv36	mm8
Celera	19	47,801,827 - 47,819,682 (-)	NCBI		Celera
Cytogenetic Map	19	C3	NCBI
cM Map	19	39.11	NCBI

Pcgf6
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	255,866,709 - 255,886,306 (-)	NCBI		GRCr8
mRatBN7.2	1	245,925,354 - 245,944,964 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	245,925,360 - 245,944,914 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	1	254,051,540 - 254,071,097 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	260,744,865 - 260,764,438 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	253,394,241 - 253,413,823 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	266,811,418 - 266,831,022 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	266,811,420 - 266,830,976 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	1	274,241,829 - 274,261,565 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	1	252,357,987 - 252,377,545 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	1	252,622,561 - 252,642,118 (-)	NCBI
Celera	1	241,697,022 - 241,716,581 (-)	NCBI		Celera
Cytogenetic Map	1	q54	NCBI

Pcgf6
(Chinchilla lanigera - long-tailed chinchilla)

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955485	7,196,626 - 7,227,536 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955485	7,196,626 - 7,228,918 (+)	NCBI	ChiLan1.0	ChiLan1.0

PCGF6
(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	8	115,188,317 - 115,236,309 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	10	115,193,649 - 115,241,653 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	10	99,901,760 - 99,949,733 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	10	103,353,439 - 103,426,283 (-)	NCBI	panpan1.1	PanPan1.1	panPan2

PCGF6
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	28	15,697,707 - 15,733,177 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	28	15,605,040 - 15,733,097 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	28	15,869,655 - 15,905,116 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	28	16,173,796 - 16,209,301 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	28	16,159,740 - 16,209,313 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	28	15,723,250 - 15,758,660 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	28	15,750,627 - 15,786,077 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	28	15,889,370 - 15,924,844 (-)	NCBI		UU_Cfam_GSD_1.0

PCGF6
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	14	114,249,820 - 114,287,434 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	14	114,062,457 - 114,287,458 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	14	124,190,350 - 124,210,490 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PCGF6
(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	9	96,349,418 - 96,396,083 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	9	96,349,423 - 96,395,650 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666048	57,462,812 - 57,509,143 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Pcgf6
(Heterocephalus glaber - naked mole-rat)

Naked Mole-Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Naked Mole-Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624831	2,549,951 - 2,587,885 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

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_005333606	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_021731832	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_040273052	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_040273053	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_040273054	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005728240	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010002273	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSSTOT00000014519 ⟹ ENSSTOP00000013010

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936600	2,714,843 - 2,741,697 (+)	Ensembl

RefSeq Acc Id:

XM_005333606 ⟹ XP_005333663

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024407213	31,111,645 - 31,138,470 (+)	NCBI
SpeTri2.0	NW_004936600	2,714,883 - 2,741,418 (+)	NCBI

Sequence:

show sequence

CTGAACTCCCGCGCTCTCCCGTCGCGGCACTTAGCTTTTCAGGTCCGATTTTTGCCGGGGCCAT
GGAAGGGGTCGCGGCGATCACGGCAGGCAACGCGGGCGCTGCCAAGGCGGAGGGAGCCGCAGTC
ATGCCGCCGCCGCCTCCCGTGTCCCCACCTGCCCTCACCCCGCCGCCCGTGGCCGGCGAGGAGG
GCCCGGCTCCTCTGCCCGAGGTGGGGGCTCCAGGCTGCTCCGGCTCCCGGCCCCCTGAGTTAGA
GCCCGAGCGCAGCCTGGGCCGCTTGAGGGGCCGCTTCGAAGACTACGACGAGGAGCTGGAAGAG
GATGAGGAGTTGGAGGAGGAAGAGGAGGAGGAGGAGGAAGAGCTGAGCCACTTCTCGCTGAGGC
TGGAAGGGGGCCGGCCGGACTCTGAGGACGAAGAGGAGCGCCTGATTAATCTTGCTGAGCTGAC
ACCATATATCTTGTGTTCCATTTGCAAGGGTTATTTAATAGATGCAACTACCATTACAGAATGT
CTTCATACGTTTTGTAAAAGCTGCATTGTAAGACATTTTTACTATAGCAACAGATGTCCAAAAT
GCAACGTAGTTGTACATCAGACACAACCACTTTACAATATAAGGTTGGACCGACAATTACAAGA
TATAGTGTACAAATTAGTGATCAATCTAGAGGAAAGAGAAAAAAAGCAAATGCATGATTTCTAT
AAAGAAAGAGGTCTAGAAGTACCTAAACCTGCTGTTCCACAGTCAGTCCCTTCAAGCAAAGGAA
GAACTAAGAAAGTCCTAGAATCAGTATTTCGTATTCCACCTGAACTTGACATGTCTTTATTACT
GGAGTTCATTGGTGCTAATGAAGGCACGGGACATTTTAAGCCATTAGAAAAGAAGTTTGTTCGA
GTTTCAGGAGAAGCCACTATTGGACATGTAGAAAAATTCCTCCGAAGAAAAATGGGTCTTGATC
CAGCTTGTCAGGTAGATATCATCTGTGGTGATCACTTGCTGGAGCAGTACCAGACTCTAAGGGA
GATCCGACGTGCAATAGGTGATGCAGCAATGCAAGATGGTCTGCTTGTCCTTCATTATGGTCTT
GTGGTTTCTCCTCTGAAAATAACTTGAAGATGCTAGGCATATTATGAGGAAGGAAGCAAACAAA
GTAAGGAAATTTCTACAGGACTGTATTTCACCAAAGATTTCCACAAAACATGTAATCACTACCA
CGTTGTGCTGTTCAAGACATACCTTATCTATTTTCAGCACCAAAAATCCTAAGTACAATTGGAA
TGAAGGAATGCACCTGTTTCACTAGAGACTATATGTAAAAAGCACTAGAGCTCAGGGGAATTTT
TCCAAAACAGCATATTTTAAAATTCCGTATACTTTGATGTTGATTTTTGCTTCCCATCTTTGAG
GTAAAGTGATCACTGTTTTCTCCTTTGTTGAGCCATATCCCTTTAAAGTTGGCAGTAAGGATTC
TGTTCTGTGGAACAGCATCAGTTGGACAGTCATCCTTTTGGGAAAAAGAGGTATGCTTTTGAAT
GGGAGATTCAAAGCCAGTCTTTGTTAAACCACAGGGTATACTCTCAAAAGACCAAAACTACTGG
CTGCTTTTGTATTTGCCATCATATTTTAAACTTGTAGAGTTTCCCCCCCCCTTAAACCAGCAAT
ACTACTAAAGAAATGTTTGTTCATAAAATGGATGAATTATCATTATCTGTGTGAAGACACTGTG
TCATAAGCCTTCAGTGTAATAAGACTTCTTAACATATCTTACAATAAGAGGTGCTTATTTGTGA
TGACATATTTAATTTTATTTGCATACAAAGTATGATTTGTTGATAACCTGTAATGGCACTCCTT
CTGAAAGTAATAATAAAACATTTCAGGTGAATTTCAGAAGTTTACAGAATACTTTTTGTTTCCT
CAGCAAGTCAGCTTAATATTCA

hide sequence

RefSeq Acc Id:

XM_040273052 ⟹ XP_040128986

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024407213	31,111,641 - 31,138,470 (+)	NCBI

RefSeq Acc Id:

XM_040273053 ⟹ XP_040128987

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024407213	31,111,642 - 31,138,470 (+)	NCBI

RefSeq Acc Id:

XM_040273054 ⟹ XP_040128988

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024407213	31,111,644 - 31,138,470 (+)	NCBI

RefSeq Acc Id:

XR_005728240

Type:

NON-CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024407213	31,111,640 - 31,133,702 (+)	NCBI

Protein Sequences


Protein RefSeqs	XP_005333663	(Get FASTA)	NCBI Sequence Viewer
	XP_040128986	(Get FASTA)	NCBI Sequence Viewer
	XP_040128987	(Get FASTA)	NCBI Sequence Viewer
	XP_040128988	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000013010.3

RefSeq Acc Id:	XP_005333663 ⟸ XM_005333606
- Peptide Label:	isoform X4
- UniProtKB:	I3MN33 (UniProtKB/TrEMBL)
- Sequence:	show sequence MEGVAAITAGNAGAAKAEGAAVMPPPPPVSPPALTPPPVAGEEGPAPLPEVGAPGCSGSRPPEL EPERSLGRLRGRFEDYDEELEEDEELEEEEEEEEEELSHFSLRLEGGRPDSEDEEERLINLAEL TPYILCSICKGYLIDATTITECLHTFCKSCIVRHFYYSNRCPKCNVVVHQTQPLYNIRLDRQLQ DIVYKLVINLEEREKKQMHDFYKERGLEVPKPAVPQSVPSSKGRTKKVLESVFRIPPELDMSLL LEFIGANEGTGHFKPLEKKFVRVSGEATIGHVEKFLRRKMGLDPACQVDIICGDHLLEQYQTLR EIRRAIGDAAMQDGLLVLHYGLVVSPLKIT hide sequence

RefSeq Acc Id:	XP_040128986 ⟸ XM_040273052
- Peptide Label:	isoform X1

RefSeq Acc Id:	XP_040128987 ⟸ XM_040273053
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_040128988 ⟸ XM_040273054
- Peptide Label:	isoform X3

Ensembl Acc Id:

ENSSTOP00000013010 ⟸ ENSSTOT00000014519

Protein Domains

RING-type

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000014511	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000014519.3	UniProtKB/TrEMBL
Gene3D-CATH	3.30.40.10	UniProtKB/TrEMBL
InterPro	PcG_RING_finger	UniProtKB/TrEMBL
	PCGF6	UniProtKB/TrEMBL
	PCGF6_RAWUL	UniProtKB/TrEMBL
	RAWUL	UniProtKB/TrEMBL
	Ubiquitin-like_domsf	UniProtKB/TrEMBL
	Znf_RING	UniProtKB/TrEMBL
	Znf_RING/FYVE/PHD	UniProtKB/TrEMBL
	Znf_RING_CS	UniProtKB/TrEMBL
NCBI Gene	Pcgf6	ENTREZGENE
PANTHER	POLYCOMB GROUP RING FINGER PROTEIN	UniProtKB/TrEMBL
	POLYCOMB GROUP RING FINGER PROTEIN 6	UniProtKB/TrEMBL
Pfam	RAWUL	UniProtKB/TrEMBL
	zf-C3HC4_2	UniProtKB/TrEMBL
PROSITE	ZF_RING_1	UniProtKB/TrEMBL
	ZF_RING_2	UniProtKB/TrEMBL
SMART	RING	UniProtKB/TrEMBL
Superfamily-SCOP	RING/U-box	UniProtKB/TrEMBL
	SSF54236	UniProtKB/TrEMBL
UniProt	I3MN33	ENTREZGENE, UniProtKB/TrEMBL

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)

Imported Disease Annotations - ClinVar

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Imported Disease Annotations - ClinVar

RGD Manual Annotations