Rpl39 (ribosomal protein L39) - Rat Genome Database

Name: Rpl39
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Rpl39 (ribosomal protein L39) Rattus norvegicus

Analyze

Symbol:

Rpl39

Name:

ribosomal protein L39

RGD ID:

3593

Description:

Predicted to be a structural constituent of ribosome. Predicted to be involved in antimicrobial humoral immune response mediated by antimicrobial peptide; cytoplasmic translation; and innate immune response in mucosa. Part of cytosolic large ribosomal subunit. Orthologous to human RPL39 (ribosomal protein L39); PARTICIPATES IN ribosome biogenesis pathway; translation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol; ammonium chloride.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

60S ribosomal protein L39; large ribosomal subunit protein eL39

RGD Orthologs

Alliance Genes

More Info

more info ...

More Info

Species	Gene symbol and name	Data Source	Assertion derived from	less info ...
Orthologs ¹				less info ...
Homo sapiens (human):	RPL39 (ribosomal protein L39)	HGNC	HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, Panther
Mus musculus (house mouse):	Rpl39 (ribosomal protein L39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Rpl39 (ribosomal protein L39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	RPL39 (ribosomal protein L39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	LOC100687285 (60S ribosomal protein L39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Rpl39 (ribosomal protein L39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	RPL39 (ribosomal protein L39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	RPL39 (ribosomal protein L39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Rpl39 (ribosomal protein L39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	RPL39 (ribosomal protein L39)	Alliance	DIOPT (HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Mus musculus (house mouse):	Rpl39 (ribosomal protein L39)	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Danio rerio (zebrafish):	rpl39 (ribosomal protein L39)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	rpl-39	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	RPL39	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Drosophila melanogaster (fruit fly):	RpL39	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	rpl39	Alliance	DIOPT (OMA\|OrthoFinder\|PANTHER)

Related Pseudogenes:

Rpl31-ps12 Rpl39-ps1 Rpl39-ps10 Rpl39-ps11 Rpl39-ps12 Rpl39-ps13 Rpl39-ps14

Latest Assembly:

mRatBN7.2 - mRatBN7.2 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	X	121,192,901 - 121,195,896 (-)	NCBI		GRCr8
mRatBN7.2	X	116,327,216 - 116,330,211 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	X	116,327,094 - 116,330,304 (-)	Ensembl		mRatBN7.2 Ensembl
mRatBN7.2 Ensembl	18	6,326,330 - 6,326,692 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	X	118,430,743 - 118,433,782 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	X	121,999,885 - 122,002,924 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	X	119,545,777 - 119,548,828 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	X	123,705,241 - 123,707,257 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	123,705,235 - 123,708,211 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	X	123,841,669 - 123,843,685 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	7,825,919 - 7,827,935 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	X	7,830,555 - 7,833,491 (+)	NCBI
Celera	X	115,554,572 - 115,556,588 (-)	NCBI		Celera
Cytogenetic Map	X	q35	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)

genetic disease (ISO)

syndromic X-linked intellectual disability 14 (ISO)

syndromic X-linked intellectual disability Cabezas type (ISO)

syndromic X-linked intellectual disability Lubs type (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(1->4)-beta-D-glucan (ISO)

1,2-dimethylhydrazine (ISO)

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

2,3',4,4',5-Pentachlorobiphenyl (ISO)

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

3-chloropropane-1,2-diol (EXP)

4-hydroxyphenyl retinamide (ISO)

acrylamide (ISO)

ammonium chloride (EXP)

Aroclor 1254 (ISO)

arsenite(3-) (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP,ISO)

bisphenol F (ISO)

cadmium dichloride (ISO)

carbon nanotube (ISO)

chlordecone (ISO)

chloropicrin (ISO)

chromium(6+) (ISO)

cisplatin (ISO)

clobetasol (ISO)

copper(II) sulfate (ISO)

cylindrospermopsin (ISO)

dibutyl phthalate (EXP)

dicrotophos (ISO)

elemental selenium (ISO)

epoxiconazole (ISO)

ethanol (ISO)

fenvalerate (EXP)

flavonoids (EXP)

folic acid (ISO)

fulvestrant (ISO)

genistein (EXP)

hydralazine (ISO)

hydrogen peroxide (ISO)

methidathion (ISO)

mifepristone (ISO)

ozone (ISO)

paracetamol (ISO)

perfluorooctane-1-sulfonic acid (ISO)

resveratrol (ISO)

selenium atom (ISO)

simvastatin (ISO)

sodium arsenite (ISO)

sunitinib (ISO)

temozolomide (ISO)

tetrachloromethane (EXP)

trichloroethene (EXP)

tungsten (ISO)

valproic acid (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

antimicrobial humoral immune response mediated by antimicrobial peptide (ISO)

cytoplasmic translation (ISO)

innate immune response in mucosa (ISO)

translation (IEA)

Cellular Component

cytoplasm (ISO)

cytosolic large ribosomal subunit (IBA,IDA,IEA,ISO)

cytosolic ribosome (ISO)

extracellular space (ISO)

ribonucleoprotein complex (IEA)

ribosome (IEA)

Molecular Function

protein binding (ISO)

structural constituent of ribosome (IEA,ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

ribosome biogenesis pathway (ISO)

translation pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Structures of the human and Drosophila 80S ribosome.	Anger AM, etal., Nature. 2013 May 2;497(7447):80-5. doi: 10.1038/nature12104.
2.	Normalization and subtraction: two approaches to facilitate gene discovery.	Bonaldo MF, etal., Genome Res 1996 Sep;6(9):791-806.
3.	The primary structures of rat ribosomal proteins: the characterization of the cDNAs for S21 and L39, corrections in the sequences of L7 and L18a, and the identification of L33.	Chan YL, etal., Biochem Biophys Res Commun 1995 Aug 24;213(3):1042-50.
4.	Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
5.	Rat ISS GO annotations from MGI mouse gene data--August 2006	MGD data from the GO Consortium
6.	Electronic Transfer of LocusLink and RefSeq Data	NCBI rat LocusLink and RefSeq merged data July 26, 2002
7.	GOA pipeline	RGD automated data pipeline
8.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions
9.	Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences.	Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
10.	Tentative Sequence Identification Numbers	Tentative Sequence Data IDs. TIGR Gene Index, Rat Data
11.	Isolation of eukaryotic ribosomal proteins. Purification and characterization of the 60 S ribosomal subunit proteins L4, L5, L7, L9, L11, L12, L13, L21, L22, L23, L26, L27, L30, L33, L35', L37, and L39.	Tsurugi K, etal., J Biol Chem. 1976 Dec 25;251(24):7940-6.

Additional References at PubMed

PMID:6706949	PMID:12860195	PMID:12962325	PMID:15489334	PMID:17154719	PMID:25957688

Genomics

Comparative Map Data

Rpl39
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	X	121,192,901 - 121,195,896 (-)	NCBI		GRCr8
mRatBN7.2	X	116,327,216 - 116,330,211 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	X	116,327,094 - 116,330,304 (-)	Ensembl		mRatBN7.2 Ensembl
mRatBN7.2 Ensembl	18	6,326,330 - 6,326,692 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	X	118,430,743 - 118,433,782 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	X	121,999,885 - 122,002,924 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	X	119,545,777 - 119,548,828 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	X	123,705,241 - 123,707,257 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	X	123,705,235 - 123,708,211 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	X	123,841,669 - 123,843,685 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	7,825,919 - 7,827,935 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	X	7,830,555 - 7,833,491 (+)	NCBI
Celera	X	115,554,572 - 115,556,588 (-)	NCBI		Celera
Cytogenetic Map	X	q35	NCBI

RPL39
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	X	119,786,504 - 119,791,630 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	X	119,786,504 - 119,791,630 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	X	118,920,467 - 118,925,593 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	X	118,804,497 - 118,809,634 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	X	118,702,350 - 118,707,488	NCBI
Celera	X	119,375,089 - 119,380,226 (-)	NCBI		Celera
Cytogenetic Map	X	q24	NCBI
HuRef	X	108,414,000 - 108,419,138 (-)	NCBI		HuRef
CHM1_1	X	118,831,549 - 118,836,703 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	X	118,161,629 - 118,166,754 (-)	NCBI		T2T-CHM13v2.0

Rpl39
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	36,346,169 - 36,348,852 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	X	36,346,173 - 36,349,055 (-)	Ensembl		GRCm39 Ensembl
GRCm38	X	37,082,518 - 37,085,222 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	37,082,520 - 37,085,402 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	34,622,515 - 34,625,179 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	X	33,513,965 - 33,516,629 (-)	NCBI		MGSCv36	mm8
Celera	X	23,806,150 - 23,808,814 (-)	NCBI		Celera
Cytogenetic Map	X	A3.3	NCBI
cM Map	X	21.5	NCBI

Rpl39
(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	NW_004955534	200,591 - 203,827 (+)	NCBI	ChiLan1.0	ChiLan1.0

RPL39
(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	X	119,167,811 - 119,173,033 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	X	119,171,415 - 119,176,588 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	X	108,818,773 - 108,823,935 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	X	119,243,623 - 119,248,916 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	X	119,243,624 - 119,248,916 (-)	Ensembl	panpan1.1		panPan2

LOC100687285
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	35	3,404,495 - 3,411,279 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	35	3,412,178 - 3,419,003 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	35	3,461,129 - 3,467,957 (-)	NCBI		ROS_Cfam_1.0
UMICH_Zoey_3.1	35	3,336,550 - 3,343,086 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	35	3,358,282 - 3,365,107 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	35	4,690,923 - 4,697,748 (-)	NCBI		UU_Cfam_GSD_1.0

Rpl39
(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	90,850,993 - 90,854,543 (-)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936479	10,132,965 - 10,136,506 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

RPL39
(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	98,178,150 - 98,181,332 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	X	98,178,148 - 98,181,439 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	X	113,430,973 - 113,434,240 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

RPL39
(Chlorocebus sabaeus - green monkey)

Green Monkey Assembly	Chr	Position (strand)	Source	Genome Browsers
Green Monkey Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Vero_WHO_p1.0	NW_023666065	32,567,895 - 32,573,168 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Rpl39
(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_004624895	3,748,059 - 3,752,199 (-)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Variants

Variants in Rpl39
16 total Variants

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	111
Count of miRNA genes:	91
Interacting mature miRNAs:	98
Transcripts:	ENSRNOT00000064521
Prediction methods:	Microtar, Miranda, Pita, 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.

QTLs in Region (mRatBN7.2)

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	14843113	120568734	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	41052407	146860749	Rat
61431	Cia19	Collagen induced arthritis QTL 19	4.4		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	X	65612192	120568734	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	75294106	120294106	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	93956491	138956491	Rat
738025	Stresp3	Stress response QTL 3	4.61	0.0066	stress-related behavior trait (VT:0010451)	defensive burying - approach	X	100567703	150256146	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	103312877	148312877	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	103312877	148312877	Rat
738029	Stresp2	Stress response QTL 2	3.4	0.0004	stress-related behavior trait (VT:0010451)	defensive burying - approach	X	112934952	138400867	Rat
5685004	Bss104	Bone structure and strength QTL 104	3.9		tibia area (VT:1000281)	tibia area measurement (CMO:0001382)	X	113805422	126975220	Rat
10059603	Bw174	Body weight QTL 174	3.4	0.025	body mass (VT:0001259)	body weight (CMO:0000012)	X	113937816	152453651	Rat

Markers in Region

AI408836

Rat Assembly	Chr	Position (strand)	Source	JBrowse
mRatBN7.2	X	116,327,367 - 116,327,610 (+)	MAPPER	mRatBN7.2
Rnor_6.0	X	123,705,387 - 123,705,629	NCBI	Rnor6.0
Rnor_5.0	X	123,841,815 - 123,842,057	UniSTS	Rnor5.0
RGSC_v3.4	X	7,827,547 - 7,827,789	UniSTS	RGSC3.4
Celera	X	115,554,718 - 115,554,960	UniSTS
Cytogenetic Map	X	q12	UniSTS

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	43	57	41	19	41	8	9	74	34	37	11	8
Low					1			4		1	8
Below cutoff	1	1	1	1	1	1		1	2	6	6

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_012875	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AC107580	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC058489	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473991	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ209995	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ210251	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ210527	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ212282	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ212463	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ213937	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ217566	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ217683	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ220172	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ221060	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ221172	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ221447	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ221527	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ221776	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ221814	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ221828	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ221961	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ222151	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ222241	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ222485	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ222523	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ222748	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ222761	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ222859	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ222874	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ222880	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ223028	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ223152	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ223343	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ223533	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ228454	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ228621	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ229531	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ230058	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ230173	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000021	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	X82551	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSRNOT00000046536 ⟹ ENSRNOP00000049665

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	20	17,253,931 - 17,254,086 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000051137 ⟹ ENSRNOP00000041329

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	7	29,834,988 - 29,835,143 (+)	Ensembl

RefSeq Acc Id:

ENSRNOT00000059010 ⟹ ENSRNOP00000055790

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2 Ensembl	X	31,984,332 - 31,984,487 (-)	Ensembl

RefSeq Acc Id:

NM_012875 ⟹ NP_037007

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	X	121,192,901 - 121,195,896 (-)	NCBI
mRatBN7.2	X	116,327,216 - 116,330,211 (-)	NCBI
Rnor_6.0	X	123,705,241 - 123,707,257 (-)	NCBI
Rnor_5.0	X	123,841,669 - 123,843,685 (-)	NCBI
RGSC_v3.4	X	7,825,919 - 7,827,935 (+)	RGD
Celera	X	115,554,572 - 115,556,588 (-)	RGD

Sequence:

show sequence

TCTCTCTTGATTCAGATCCTCGCCATGTCTTCTCACAAGACTTTCAGAATCAAGCGATTCCTGG
CAAAGAAACAAAAGCAAAATCGTCCTATTCCTCAATGGATTCGGATGAAAACTGGTAACAAAAT
CAGGTACAACTCTAAGAGAAGACACTGGAGGAGAACGAAGCTGGGTCTATAAGGAGTCACACTA
CGGCCAGACTGAGGATTTCTACTGAATCACCGTCATCGATCAGTCCGACCAGATGGATTTCAAC
ATTTTTAACCTAGAGATTTACTTGTGTCTGAACTAATTTGTCCAGTAATAAAATTTAGAACCTT
TCA

hide sequence

Protein Sequences


Protein RefSeqs	NP_037007	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAH58489	(Get FASTA)	NCBI Sequence Viewer
	CAA57900	(Get FASTA)	NCBI Sequence Viewer
	EDM10836	(Get FASTA)	NCBI Sequence Viewer
	EDM10837	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000041329.2
	ENSRNOP00000044553.1
	ENSRNOP00000049665.2
	ENSRNOP00000049713.1
	ENSRNOP00000055790.1
	ENSRNOP00000075910.2
	ENSRNOP00055011827
	ENSRNOP00055012496
	ENSRNOP00055032226
	ENSRNOP00055036674
	ENSRNOP00055039587
	ENSRNOP00055041964
	ENSRNOP00055044087
	ENSRNOP00060009617
	ENSRNOP00060012851
	ENSRNOP00060029631
	ENSRNOP00060032692
	ENSRNOP00060042538
	ENSRNOP00060044934
	ENSRNOP00060045054
	ENSRNOP00065007973
	ENSRNOP00065012566
	ENSRNOP00065018215
	ENSRNOP00065033563
	ENSRNOP00065041070
	ENSRNOP00065047676
GenBank Protein	P62893	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:	NP_037007 ⟸ NM_012875
- UniProtKB:	P62893 (UniProtKB/Swiss-Prot), A6JMH4 (UniProtKB/TrEMBL)
- Sequence:	show sequence MSSHKTFRIKRFLAKKQKQNRPIPQWIRMKTGNKIRYNSKRRHWRRTKLGL hide sequence

RefSeq Acc Id:

ENSRNOP00000055790 ⟸ ENSRNOT00000059010

RefSeq Acc Id:

ENSRNOP00000049665 ⟸ ENSRNOT00000046536

RefSeq Acc Id:

ENSRNOP00000041329 ⟸ ENSRNOT00000051137

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-P62893-F1-model_v2	AlphaFold	P62893	1-51	view protein structure

Transcriptome

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

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:3593	AgrOrtholog
BioCyc Gene	G2FUF-1299	BioCyc
Ensembl Genes	ENSRNOG00000029267	Ensembl, UniProtKB/Swiss-Prot
	ENSRNOG00000034237	Ensembl, UniProtKB/Swiss-Prot
	ENSRNOG00000043348	Ensembl, UniProtKB/TrEMBL
	ENSRNOG00000048073	Ensembl, UniProtKB/Swiss-Prot
	ENSRNOG00000050393	Ensembl, UniProtKB/Swiss-Prot
	ENSRNOG00000067660	Ensembl, UniProtKB/Swiss-Prot
	ENSRNOG00055008771	UniProtKB/Swiss-Prot
	ENSRNOG00055009210	UniProtKB/Swiss-Prot
	ENSRNOG00055023110	UniProtKB/Swiss-Prot
	ENSRNOG00055025936	UniProtKB/Swiss-Prot
	ENSRNOG00055027780	UniProtKB/Swiss-Prot
	ENSRNOG00055029405	UniProtKB/Swiss-Prot
	ENSRNOG00055030736	UniProtKB/Swiss-Prot
	ENSRNOG00060007696	UniProtKB/Swiss-Prot
	ENSRNOG00060009753	UniProtKB/Swiss-Prot
	ENSRNOG00060020780	UniProtKB/Swiss-Prot
	ENSRNOG00060022808	UniProtKB/Swiss-Prot
	ENSRNOG00060029471	UniProtKB/Swiss-Prot
	ENSRNOG00060031243	UniProtKB/Swiss-Prot
	ENSRNOG00060031377	UniProtKB/Swiss-Prot
	ENSRNOG00065006928	UniProtKB/Swiss-Prot
	ENSRNOG00065010244	UniProtKB/Swiss-Prot
	ENSRNOG00065014186	UniProtKB/Swiss-Prot
	ENSRNOG00065023966	UniProtKB/Swiss-Prot
	ENSRNOG00065028942	UniProtKB/Swiss-Prot
	ENSRNOG00065033698	UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000043244.3	UniProtKB/Swiss-Prot
	ENSRNOT00000046536.4	UniProtKB/Swiss-Prot
	ENSRNOT00000050345.2	UniProtKB/Swiss-Prot
	ENSRNOT00000051137.3	UniProtKB/Swiss-Prot
	ENSRNOT00000059010.2	UniProtKB/Swiss-Prot
	ENSRNOT00000092456.2	UniProtKB/TrEMBL
	ENSRNOT00055014807	UniProtKB/Swiss-Prot
	ENSRNOT00055015581	UniProtKB/Swiss-Prot
	ENSRNOT00055039689	UniProtKB/Swiss-Prot
	ENSRNOT00055044771	UniProtKB/Swiss-Prot
	ENSRNOT00055048092	UniProtKB/Swiss-Prot
	ENSRNOT00055050938	UniProtKB/Swiss-Prot
	ENSRNOT00055053326	UniProtKB/Swiss-Prot
	ENSRNOT00060012680	UniProtKB/Swiss-Prot
	ENSRNOT00060016443	UniProtKB/Swiss-Prot
	ENSRNOT00060036010	UniProtKB/Swiss-Prot
	ENSRNOT00060039506	UniProtKB/Swiss-Prot
	ENSRNOT00060051128	UniProtKB/Swiss-Prot
	ENSRNOT00060054198	UniProtKB/Swiss-Prot
	ENSRNOT00060054400	UniProtKB/Swiss-Prot
	ENSRNOT00065010795	UniProtKB/Swiss-Prot
	ENSRNOT00065016522	UniProtKB/Swiss-Prot
	ENSRNOT00065023410	UniProtKB/Swiss-Prot
	ENSRNOT00065041101	UniProtKB/Swiss-Prot
	ENSRNOT00065049991	UniProtKB/Swiss-Prot
	ENSRNOT00065057891	UniProtKB/Swiss-Prot
Gene3D-CATH	1.10.1620.10	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:6887843	IMAGE-MGC_LOAD
InterPro	Ribosomal_L39	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Ribosomal_L39_CS	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Ribosomal_L39e_dom_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:103690821	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	rno:103692785	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	rno:103693375	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	rno:103694169	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	rno:103694404	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	rno:25347	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE	MGC:72904	IMAGE-MGC_LOAD
NCBI Gene	25347	ENTREZGENE
PANTHER	60S RIBOSOMAL PROTEIN L39	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	RIBOSOMAL PROTEIN L39E	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam	Ribosomal_L39	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Rpl39	PhenoGen
PROSITE	RIBOSOMAL_L39E	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000029267	RatGTEx
	ENSRNOG00000034237	RatGTEx
	ENSRNOG00000043348	RatGTEx
	ENSRNOG00000048073	RatGTEx
	ENSRNOG00000050393	RatGTEx
	ENSRNOG00000067660	RatGTEx
	ENSRNOG00055008771	RatGTEx
	ENSRNOG00055009210	RatGTEx
	ENSRNOG00055023110	RatGTEx
	ENSRNOG00055025936	RatGTEx
	ENSRNOG00055027780	RatGTEx
	ENSRNOG00055029405	RatGTEx
	ENSRNOG00055030736	RatGTEx
	ENSRNOG00060007696	RatGTEx
	ENSRNOG00060009753	RatGTEx
	ENSRNOG00060020780	RatGTEx
	ENSRNOG00060022808	RatGTEx
	ENSRNOG00060029471	RatGTEx
	ENSRNOG00060031243	RatGTEx
	ENSRNOG00060031377	RatGTEx
	ENSRNOG00065006928	RatGTEx
	ENSRNOG00065010244	RatGTEx
	ENSRNOG00065014186	RatGTEx
	ENSRNOG00065023966	RatGTEx
	ENSRNOG00065028942	RatGTEx
	ENSRNOG00065033698	RatGTEx
Superfamily-SCOP	SSF48662	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR	TC218127
UniProt	A0A8L2RBV8_RAT	UniProtKB/TrEMBL
	A6JMH4	ENTREZGENE, UniProtKB/TrEMBL
	A6JMH5_RAT	UniProtKB/TrEMBL
	P62893	ENTREZGENE, UniProtKB/Swiss-Prot
UniProt Secondary	P02404	UniProtKB/Swiss-Prot
	P39025	UniProtKB/Swiss-Prot
	Q9BYF2	UniProtKB/Swiss-Prot

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2002-06-10	Rpl39	Ribosomal protein L39			Symbol and Name status set to approved	70586	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_other	9 to 11 copies of the gene	633962
gene_protein	50 amino acids and a molecular weight of 6,271	633962

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

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