Psmd10 (proteasome 26S subunit, non-ATPase 10)

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Gene: Psmd10 (proteasome 26S subunit, non-ATPase 10) Rattus norvegicus

Analyze

Symbol:

Psmd10

Name:

proteasome 26S subunit, non-ATPase 10

RGD ID:

620350

Description:

Predicted to have transcription factor binding activity. Predicted to be involved in several processes, including negative regulation of signal transduction; positive regulation of cellular protein metabolic process; and regulation of transcription, DNA-templated. Predicted to colocalize with proteasome regulatory particle, base subcomplex. Orthologous to human PSMD10 (proteasome 26S subunit, non-ATPase 10); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2-acetamidofluorene; acetamide.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

26S proteasome non-ATPase regulatory subunit 10; 26S proteasome regulatory subunit p28; gankyrin; p28Gank; proteasome (prosome, macropain) 26S subunit, non-ATPase, 10

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

Alliance Genes

More Info

more info ...

Latest Assembly:

Rnor_6.0 - RGSC Genome Assembly v6.0

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	X	104,656,809 - 104,665,126 (-)	NCBI
Rnor_6.0 Ensembl	X	112,323,187 - 112,328,642 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	X	112,323,188 - 112,328,642 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	52,274,008 - 52,279,025 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.1	X	128,864,162 - 128,864,331 (+)	NCBI
Celera	3	43,276,201 - 43,283,816 (+)	NCBI		Celera
Cytogenetic Map	X	q33	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

autistic disorder (ISO)

syndromic X-linked intellectual disability Lubs type (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

2,2',4,4'-Tetrabromodiphenyl ether (ISO)

2,3,7,8-tetrachlorodibenzodioxine (EXP,ISO)

2-acetamidofluorene (EXP)

4,4'-diaminodiphenylmethane (ISO)

4-hydroxyphenyl retinamide (ISO)

acetamide (EXP)

aflatoxin B1 (ISO)

benzo[a]pyrene (ISO)

benzo[a]pyrene diol epoxide I (ISO)

bisphenol A (EXP)

carbon nanotube (ISO)

copper(II) sulfate (ISO)

cyclosporin A (ISO)

dibutyl phthalate (EXP)

dicrotophos (ISO)

doxorubicin (ISO)

enzyme inhibitor (ISO)

folic acid (ISO)

genistein (EXP)

microcystin RR (ISO)

phlorizin (ISO)

resveratrol (ISO)

sodium arsenite (ISO)

tamoxifen (ISO)

trichloroethene (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

apoptotic process (IEA)

cytoplasmic sequestering of NF-kappaB (IEA,ISO,ISS)

negative regulation of apoptotic process (ISO,ISS)

negative regulation of DNA damage response, signal transduction by p53 class mediator (IEA,ISO,ISS)

negative regulation of MAPK cascade (IEA,ISO,ISS)

negative regulation of NF-kappaB transcription factor activity (ISO,ISS)

negative regulation of release of cytochrome c from mitochondria (IEA,ISO,ISS)

negative regulation of transcription by RNA polymerase II (IEA,ISO,ISS)

positive regulation of cell growth (IEA,ISO,ISS)

positive regulation of cyclin-dependent protein serine/threonine kinase activity (IEA,ISO,ISS)

positive regulation of proteasomal ubiquitin-dependent protein catabolic process (IEA,ISO,ISS)

positive regulation of protein ubiquitination (IEA,ISO,ISS)

proteasome regulatory particle assembly (IEA,ISO,ISS)

Cellular Component

cytoplasm (ISO)

cytosol (IEA,ISO)

intermediate filament cytoskeleton (IEA,ISO)

nucleus (IEA,ISO)

proteasome complex (ISO)

proteasome regulatory particle, base subcomplex (IEA,ISO)

Molecular Function

protein binding (ISO)

References

References - curated


1.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2.	GOA data from the GO Consortium
3.	MGD data from the GO Consortium
4.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
5.	Rezvani K, etal., Biochem Soc Trans 2003 Apr;31(2):470-3.
6.	RGD automated data pipeline
7.	RGD automated import pipeline for gene-chemical interactions
8.	RGD, Sept. 2003

Additional References at PubMed

PMID:10613832	PMID:11301474	PMID:11900540	PMID:12477932	PMID:16023600	PMID:17323924	PMID:18040287	PMID:19490896	PMID:19729910

Genomics

Comparative Map Data

Psmd10
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	X	104,656,809 - 104,665,126 (-)	NCBI
Rnor_6.0 Ensembl	X	112,323,187 - 112,328,642 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	X	112,323,188 - 112,328,642 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	3	52,274,008 - 52,279,025 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.1	X	128,864,162 - 128,864,331 (+)	NCBI
Celera	3	43,276,201 - 43,283,816 (+)	NCBI		Celera
Cytogenetic Map	X	q33	NCBI

PSMD10
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	X	108,084,207 - 108,091,549 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	X	108,084,207 - 108,091,542 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	X	107,327,437 - 107,334,772 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	X	107,214,093 - 107,221,504 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	X	107,133,581 - 107,140,993	NCBI
Celera	X	107,798,909 - 107,806,320 (-)	NCBI
Cytogenetic Map	X	q22.3	NCBI
HuRef	X	96,950,118 - 96,957,560 (-)	NCBI		HuRef
CHM1_1	X	107,238,312 - 107,245,750 (-)	NCBI		CHM1_1

Psmd10
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	139,849,174 - 139,857,460 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	X	139,849,178 - 139,857,477 (-)	Ensembl
GRCm38	X	140,948,425 - 140,956,711 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	140,948,429 - 140,956,728 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	137,482,964 - 137,491,250 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	X	136,294,902 - 136,303,045 (-)	NCBI			mm8
Celera	X	124,203,589 - 124,211,948 (-)	NCBI		Celera
Cytogenetic Map	X	F1	NCBI

Psmd10
(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_004955490	7,825,251 - 7,833,772 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955490	7,825,202 - 7,832,347 (+)	NCBI	ChiLan1.0	ChiLan1.0

PSMD10
(Pan paniscus - bonobo/pygmy chimpanzee)

Bonobo Assembly	Chr	Position (strand)	Source	Genome Browsers
Bonobo Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
PanPan1.1	X	107,552,180 - 107,559,616 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	X	107,552,186 - 107,559,616 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	X	97,182,090 - 97,189,523 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

PSMD10
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	X	81,625,288 - 81,632,175 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	X	81,625,141 - 81,632,129 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	X	67,744,887 - 67,752,996 (-)	NCBI
ROS_Cfam_1.0	X	83,273,600 - 83,281,719 (-)	NCBI
UMICH_Zoey_3.1	X	80,732,655 - 80,740,768 (-)	NCBI
UNSW_CanFamBas_1.0	X	82,445,205 - 82,453,318 (-)	NCBI
UU_Cfam_GSD_1.0	X	82,236,960 - 82,244,460 (-)	NCBI

Psmd10
(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	X	80,958,954 - 80,966,256 (-)	NCBI
SpeTri2.0	NW_004936499	6,691,758 - 6,698,515 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PSMD10
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	X	88,540,376 - 88,548,560 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	X	88,540,261 - 88,548,593 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	X	102,980,406 - 102,988,628 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PSMD10
(Chlorocebus sabaeus - African green monkey)

Vervet Assembly	Chr	Position (strand)	Source	Genome Browsers
Vervet Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChlSab1.1	X	95,931,710 - 95,939,145 (-)	NCBI
ChlSab1.1 Ensembl	X	95,931,466 - 95,939,218 (-)	Ensembl

Psmd10
(Heterocephalus glaber - naked mole-rat)

Molerat Assembly	Chr	Position (strand)	Source	Genome Browsers
Molerat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HetGla 1.0	NW_004624803	8,407,462 - 8,420,316 (+)	NCBI

Position Markers

RH129063

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	X	112,311,362 - 112,311,578	NCBI	Rnor6.0
Rnor_5.0	3	52,290,602 - 52,290,818	UniSTS	Rnor5.0
RGSC_v3.4	X	128,790,838 - 128,791,054	UniSTS	RGSC3.4
Celera	3	43,283,756 - 43,283,972	UniSTS
RH 3.4 Map	7	1125.31	UniSTS

RH130489

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	X	112,311,794 - 112,311,975	NCBI	Rnor6.0
Rnor_5.0	3	52,290,205 - 52,290,386	UniSTS	Rnor5.0
RGSC_v3.4	X	128,791,270 - 128,791,451	UniSTS	RGSC3.4
Celera	3	43,284,188 - 43,284,369	UniSTS
RH 3.4 Map	7	1125.61	UniSTS

QTLs in Region (Rnor_6.0)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
61430	Cia18	Collagen induced arthritis QTL 18	3.1		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	X	15688119	127888215	Rat
1598837	Memor13	Memory QTL 13	3.2		exploratory behavior trait (VT:0010471)	difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)	X	44320616	158345622	Rat
738035	Stresp1	Stress response QTL 1	4.96	0.000011	stress-related behavior trait (VT:0010451)	defensive burying - coping	X	44557974	120045269	Rat
61431	Cia19	Collagen induced arthritis QTL 19	4.4		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	X	70352120	127888215	Rat
724551	Glom1	Glomerulus QTL 1	2.8	0.0004	kidney glomerulus morphology trait (VT:0005325)	count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)	X	82930791	127930791	Rat
1598872	Memor14	Memory QTL 14	4.5		exploratory behavior trait (VT:0010471)	difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)	X	101333032	146333032	Rat
738025	Stresp3	Stress response QTL 3	4.61	0.0066	stress-related behavior trait (VT:0010451)	defensive burying - approach	X	107886746	152409805	Rat
1598809	Memor15	Memory QTL 15	4.4		exploratory behavior trait (VT:0010471)	difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)	X	110957467	155957467	Rat
1598856	Memor1	Memory QTL 1	1.9		exploratory behavior trait (VT:0010471)	total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)	X	110957467	155957467	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	19
Count of miRNA genes:	14
Interacting mature miRNAs:	18
Transcripts:	ENSRNOT00000074133
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.

Expression

RNA-SEQ Expression

High: > 1000 TPM value Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM Below Cutoff: < 0.5 TPM

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	4	38	22	19	22	1	1	74	35	40	11	1
Low		39	19	19		19	7	10			1		7
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053925	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039099411	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XM_039099412	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AB022014	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC158584	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473949	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ235019	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000448	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000083150 ⟹ ENSRNOP00000071060

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	X	112,323,187 - 112,328,642 (-)	Ensembl

RefSeq Acc Id:

NM_053925 ⟹ NP_446377

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	104,657,504 - 104,665,080 (-)	NCBI
Rnor_6.0	X	112,323,188 - 112,328,642 (-)	NCBI
Rnor_5.0	3	52,274,008 - 52,279,025 (+)	NCBI
Celera	3	43,276,201 - 43,283,816 (+)	RGD

Sequence:

show sequence

ATGGAGGGGTGTGTGTCTAACCTAATGGTCTGTAACCTGGCCTACAACGGGAAGCTGGATGAGT
TGAAGGAAAGCATTTTGGCTGATAAGTCTCTGGCCACTAGAACTGATCAGGACAGCAGAACAGC
ATTGCACTGGGCATGCTCAGCTGGTCATACAGAAATTGTTGAATTCTTGCTGCAACTTGGAGTG
CCAGTAAATGAAAAAGACGATGCAGGTTGGTCTCCTCTTCATATTGCTGCTTCCGCTGGCCGGG
ATGAGATTGTAAAAGCCCTTCTGATAAAAGGGGCACAAGTGAATGCCGTCAATCAGAATGGCTG
CACGGCCCTTCATTATGCAGCTTCCAAGAATAGGCATGAGATTGCTGTTATGTTACTAGAAGGT
GGGGCTAATCCAGATGCTAAGAACCATTATGATGCTACAGCAATGCACCGGGCAGCAGCCAAGG
GTAACTTGAAGATGGTTCATATCCTTCTGTTCTACAAAGCATCCACAAACATCCAAGATACTGA
GGGTAACACTCCTCTACACTTAGCCTGTGATGAGGAGAGAGTGGAAGAAGCAAAATTGCTGGTG
ACCCAAGGAGCAAGTATTTACATTGAAAATAAGGAAGAAAAGACACCGCTGCAAGTCGCCAAAG
GGGGCCTGGGTTTAATACTCAAAAGAATCGCAGAAAGTGAAGAGGCTTCTATGTAG

hide sequence

RefSeq Acc Id:

XM_039099411 ⟹ XP_038955339

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	104,656,809 - 104,665,125 (-)	NCBI

RefSeq Acc Id:

XM_039099412 ⟹ XP_038955340

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	104,656,809 - 104,665,126 (-)	NCBI

Protein Sequences


Protein RefSeqs	NP_446377	(Get FASTA)	NCBI Sequence Viewer
	XP_038955339	(Get FASTA)	NCBI Sequence Viewer
	XP_038955340	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI58585	(Get FASTA)	NCBI Sequence Viewer
	BAA36954	(Get FASTA)	NCBI Sequence Viewer
	EDL78959	(Get FASTA)	NCBI Sequence Viewer
	EDL78960	(Get FASTA)	NCBI Sequence Viewer
	EDL78961	(Get FASTA)	NCBI Sequence Viewer
	Q9Z2X3	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_446377 ⟸ NM_053925

- UniProtKB:

Q9Z2X3 (UniProtKB/Swiss-Prot)

- Sequence:

show sequence

MEGCVSNLMVCNLAYNGKLDELKESILADKSLATRTDQDSRTALHWACSAGHTEIVEFLLQLGV
PVNEKDDAGWSPLHIAASAGRDEIVKALLIKGAQVNAVNQNGCTALHYAASKNRHEIAVMLLEG
GANPDAKNHYDATAMHRAAAKGNLKMVHILLFYKASTNIQDTEGNTPLHLACDEERVEEAKLLV
TQGASIYIENKEEKTPLQVAKGGLGLILKRIAESEEASM

hide sequence

RefSeq Acc Id:

ENSRNOP00000071060 ⟸ ENSRNOT00000083150

RefSeq Acc Id:	XP_038955340 ⟸ XM_039099412
- Peptide Label:	isoform X2

RefSeq Acc Id:	XP_038955339 ⟸ XM_039099411
- Peptide Label:	isoform X1

Protein Domains

ANK_REP_REGION

Transcriptome

eQTL		View at Phenogen
WGCNA		View at Phenogen
Tissue/Strain Expression		View at Phenogen

Promoters

RGD ID:

13701958

Promoter ID:

EPDNEW_R12482

Type:

initiation region

Name:

Psmd10_1

Description:

proteasome 26S subunit, non-ATPase 10

SO ACC ID:

SO:0000170

Source:

EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)

Experiment Methods:

Single-end sequencing.

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0	X	112,328,671 - 112,328,731	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

ACI/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

ACI/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

BBDP/Wor (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

BN/SsN (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Buf/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

COP/CrCrl (MCW & UW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob) University of Wisconsin (Dr. James Shull)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Charles River Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)

F344/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

F344/NRrrc (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

FHH/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHH/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

FHL/EurMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

FHL/EurMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

GH/OmrMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

GK/Ox (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LE/Stm (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/Crl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LEW/NCrlBR (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LH/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LL/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

LN/MavRrrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

M520/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

MHS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MNS/Gib (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

MR/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

SBH/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBH/Ygl sequenced by MCW

SBH/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SBN/Ygl (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	SBN/Ygl sequenced by MCW

SBN/Ygl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHR/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SHRSP/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SR/JrHsd (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Harlan Laboratories
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SR/JrHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/Jr (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

SS/JrHsdMcwi (MCW)

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Sequenced By:	Medical College of Wisconsin (Dr. Howard Jacob)
Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA v0.7.7 and GATK v3.2-2
Breeder:	Medical College of Wisconsin
Description:	Provided by the Medical College of Wisconsin (Dr. Howard Jacob)

SS/JrHsdMcwi (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WAG/Rij (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/Gcrc (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

WKY/NCrl (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WKY/NHsd (RGD)

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Platform:	Illumina HiSeq 2000
Secondary Analysis:	BWA mem 0.7.15, GATK v.3.6-0
Description:	Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD

WN/N (MCW)

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Sequenced By:	Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen) Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform:	SOLiD 4 and 5500
Secondary Analysis:	liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder:	National Institutes of Health
Description:	Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:620350	AgrOrtholog
Ensembl Genes	ENSRNOG00000057649	Ensembl, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000071060	UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000083150	UniProtKB/TrEMBL
Gene3D-CATH	1.25.40.20	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:8369120	IMAGE-MGC_LOAD
InterPro	Ankyrin_rpt	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Ankyrin_rpt-contain_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Ankyrin_rpt-contain_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	PSMD10-like	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:116722	UniProtKB/Swiss-Prot
MGC_CLONE	MGC:187342	IMAGE-MGC_LOAD
NCBI Gene	116722	ENTREZGENE
PANTHER	PTHR24126:SF24	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Ank	UniProtKB/TrEMBL
	Ank_2	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Psmd10	PhenoGen
PRINTS	ANKYRIN	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE	ANK_REP_REGION	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	ANK_REPEAT	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	ANK	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF48403	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	A0A0G2JZI5_RAT	UniProtKB/TrEMBL
	B0BMV9_RAT	UniProtKB/TrEMBL
	PSD10_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2015-08-19	Psmd10	proteasome 26S subunit, non-ATPase 10	Psmd10	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2004-02-26	Psmd10	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10			Symbol and Name status set to approved	625702	APPROVED
2002-08-07	Psmd10	proteasome (prosome, macropain) 26S subunit, non-ATPase, 10			Symbol and Name status set to provisional	70820	PROVISIONAL

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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Imported Disease Annotations - ClinVar