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Gene: Pabpc6 (poly(A) binding protein, cytoplasmic 6) Rattus norvegicus

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Symbol:

Pabpc6

Name:

poly(A) binding protein, cytoplasmic 6

RGD ID:

1311201

Description:

Predicted to enable mRNA 3'-UTR binding activity; poly(A) binding activity; and poly(U) RNA binding activity. Predicted to be involved in RNA splicing and nuclear-transcribed mRNA catabolic process, nonsense-mediated decay. Predicted to be located in cytoplasm and lamellipodium. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasmic stress granule; cytosol; and nucleus. Orthologous to human PABPC3 (poly(A) binding protein cytoplasmic 3); INTERACTS WITH 1,2-dimethylhydrazine; bisphenol A; indole-3-methanol.

Type:

protein-coding

RefSeq Status:

VALIDATED

Previously known as:

LOC292295; Pabpc3; poly(A) binding protein, cytoplasmic 3; RGD1311201; similar to RIKEN cDNA 4932702K14

RGD Orthologs

Alliance Orthologs

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):	PABPC3 (poly(A) binding protein cytoplasmic 3)	HGNC	Ensembl, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Pabpc6 (poly(A) binding protein, cytoplasmic 6)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	PABPC3 (poly(A) binding protein cytoplasmic 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	PABPC3 (poly(A) binding protein cytoplasmic 3)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Other homologs ²
Homo sapiens (human):	PABPC1 (poly(A) binding protein cytoplasmic 1)	HGNC	EggNOG, Panther, PhylomeDB, Treefam
Homo sapiens (human):	OR2AK2 (olfactory receptor family 2 subfamily AK member 2)	HGNC	OMA
Alliance orthologs ³
Mus musculus (house mouse):	Pabpc6 (poly(A) binding protein, cytoplasmic 6)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Homo sapiens (human):	PABPC3 (poly(A) binding protein cytoplasmic 3)	Alliance	DIOPT (Ensembl Compara\|HGNC\|PANTHER)
Homo sapiens (human):	PABPC3 (poly(A) binding protein cytoplasmic 3)	Alliance	DIOPT (HGNC\|OrthoFinder\|PANTHER)
Danio rerio (zebrafish):	pabpc1a (poly(A) binding protein, cytoplasmic 1a)	Alliance	DIOPT (OrthoFinder\|PANTHER\|PhylomeDB)
Saccharomyces cerevisiae (baker's yeast):	PAB1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Saccharomyces cerevisiae (baker's yeast):	PAB1	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|SonicParanoid)
Drosophila melanogaster (fruit fly):	CG4612	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)
Drosophila melanogaster (fruit fly):	pAbp	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PANTHER\|SonicParanoid)
Drosophila melanogaster (fruit fly):	pAbp	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	pab-1	Alliance	DIOPT (Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	pab-2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|SonicParanoid)
Caenorhabditis elegans (roundworm):	pab-2	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PhylomeDB\|SonicParanoid)
Xenopus tropicalis (tropical clawed frog):	pabpc1	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|PANTHER)

Latest Assembly:

GRCr8 - GRCr8 Assembly

Position:

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	53,592,902 - 53,595,978 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	1	53,592,884 - 53,595,973 (+)	Ensembl				GRCr8
mRatBN7.2	1	51,045,264 - 51,048,340 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	51,045,233 - 51,048,340 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	1	51,767,244 - 51,770,320 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	57,753,614 - 57,756,690 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	51,842,793 - 51,845,869 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	51,619,875 - 51,622,951 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	51,619,875 - 51,622,942 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	1	52,894,340 - 52,897,416 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	1	45,590,368 - 45,593,517 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	1	46,823,047 - 46,826,123 (+)	NCBI		Celera
RGSC_v3.1	1	45,593,429 - 45,595,361 (+)	NCBI
Cytogenetic Map	1	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Annotation Click to see Annotation Detail View

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

(+)-catechin (ISO)

(-)-epigallocatechin 3-gallate (ISO)

1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene (ISO)

1,2-dimethylhydrazine (EXP)

2,2',4,4',5,5'-hexachlorobiphenyl (ISO)

2,2',5,5'-tetrachlorobiphenyl (ISO)

2,4,4'-trichlorobiphenyl (ISO)

2,6-dimethoxyphenol (ISO)

3-isobutyl-1-methyl-7H-xanthine (ISO)

5-aza-2'-deoxycytidine (ISO)

antirheumatic drug (ISO)

arsane (ISO)

arsenic atom (ISO)

arsenous acid (ISO)

atrazine (ISO)

benzo[a]pyrene (ISO)

bis(2-ethylhexyl) phthalate (ISO)

bisphenol A (EXP,ISO)

CGP 52608 (ISO)

CU-O LINKAGE (ISO)

cyclosporin A (ISO)

dexamethasone (ISO)

diarsenic trioxide (ISO)

diazinon (ISO)

epoxiconazole (ISO)

fulvestrant (ISO)

furfural (ISO)

indole-3-methanol (EXP)

indometacin (ISO)

lead diacetate (ISO)

N,N-diethyl-m-toluamide (EXP)

PCB138 (ISO)

permethrin (EXP)

potassium chromate (ISO)

sodium arsenite (ISO)

sodium chloride (ISO)

sunitinib (ISO)

titanium dioxide (ISO)

vitamin E (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

nuclear-transcribed mRNA catabolic process, nonsense-mediated decay (IEA)

RNA splicing (IEA)

Cellular Component

cytoplasmic stress granule (IBA,IEA)

cytosol (IBA)

lamellipodium (IEA)

nucleus (IBA)

ribonucleoprotein complex (IBA)

spliceosomal complex (IEA)

Molecular Function

mRNA 3'-UTR binding (IBA)

nucleic acid binding (IEA)

poly(A) binding (IBA,ISO)

poly(U) RNA binding (IBA)

protein binding (ISO)

RNA binding (IEA)

References

References - curated

#	Reference Title	Reference Citation
1.	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.
2.	GOA pipeline	RGD automated data pipeline
3.	ClinVar Automated Import and Annotation Pipeline	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4.	Data Import for Chemical-Gene Interactions	RGD automated import pipeline for gene-chemical interactions

Additional References at PubMed

PMID:11328870	PMID:12477932	PMID:23533145

Genomics

Comparative Map Data

Pabpc6
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	1	53,592,902 - 53,595,978 (+)	NCBI	GRCr8	GRCr8		GRCr8
GRCr8 Ensembl	1	53,592,884 - 53,595,973 (+)	Ensembl				GRCr8
mRatBN7.2	1	51,045,264 - 51,048,340 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	1	51,045,233 - 51,048,340 (+)	Ensembl				mRatBN7.2
UTH_Rnor_SHR_Utx	1	51,767,244 - 51,770,320 (+)	NCBI	UTH_Rnor_SHR_Utx	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	1	57,753,614 - 57,756,690 (+)	NCBI	UTH_Rnor_SHRSP_BbbUtx_1.0	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	1	51,842,793 - 51,845,869 (+)	NCBI	UTH_Rnor_WKY_Bbb_1.0	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	1	51,619,875 - 51,622,951 (+)	NCBI	Rnor_6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	1	51,619,875 - 51,622,942 (+)	Ensembl			rn6	Rnor6.0
Rnor_5.0	1	52,894,340 - 52,897,416 (+)	NCBI	Rnor_5.0	Rnor_5.0	rn5
RGSC_v3.4	1	45,590,368 - 45,593,517 (+)	NCBI	RGSC_v3.4	RGSC_v3.4	rn4
Celera	1	46,823,047 - 46,826,123 (+)	NCBI		Celera
RGSC_v3.1	1	45,593,429 - 45,595,361 (+)	NCBI
Cytogenetic Map	1	q12	NCBI

PABPC3
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	13	25,096,136 - 25,099,254 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	13	25,096,136 - 25,099,254 (+)	Ensembl			hg38	GRCh38
GRCh37	13	25,670,274 - 25,673,392 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	13	24,568,276 - 24,570,705 (+)	NCBI	Build 36	Build 36	hg18	NCBI36
Build 34	13	24,568,275 - 24,570,705	NCBI
Celera	13	6,733,832 - 6,736,261 (+)	NCBI		Celera
Cytogenetic Map	13	q12.13	NCBI
HuRef	13	6,483,848 - 6,486,277 (+)	NCBI		HuRef
CHM1_1	13	25,638,844 - 25,641,273 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	13	24,304,920 - 24,308,038 (+)	NCBI		T2T-CHM13v2.0

Pabpc6
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	9,885,426 - 9,888,633 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	17	9,885,424 - 9,888,646 (-)	Ensembl		GRCm39 Ensembl		GRCm39
GRCm38	17	9,666,497 - 9,669,704 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	9,666,495 - 9,669,717 (-)	Ensembl			mm10	GRCm38
MGSCv37	17	9,859,362 - 9,862,569 (-)	NCBI	MGSCv37	MGSCv37	mm9	NCBIm37
MGSCv36	17	9,509,854 - 9,513,053 (-)	NCBI		MGSCv36	mm8
Celera	17	9,716,507 - 9,719,711 (-)	NCBI		Celera
Cytogenetic Map	17	A1	NCBI
cM Map	17	7.47	NCBI

PABPC3
(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	14	24,690,355 - 24,693,376 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	13	15,799,986 - 15,803,673 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	13	6,386,455 - 6,388,651 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	13	24,669,780 - 24,671,978 (+)	NCBI	PanPan1.1	PanPan1.1	panPan2

PABPC3
(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	3	4,485,682 - 4,488,122 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666057	39,956,390 - 39,959,484 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Variants

Variants in Pabpc6
16 total Variants

miRNA Target Status (No longer updated)

Predicted Target Of

	Summary Value
Count of predictions:	104
Count of miRNA genes:	76
Interacting mature miRNAs:	91
Transcripts:	ENSRNOT00000023319
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.

QTLs in Region (GRCr8)

The following QTLs overlap with this region.

RGD ID	Symbol	Name	LOD	P Value	Trait	Sub Trait	Chr	Start	Stop	Species
1331732	Srn4	Serum renin concentration QTL 4	4.467		renin activity (VT:0005581)	plasma renin activity level (CMO:0000116)	1	43457837	87558729	Rat
1357397	Bw41	Body weight QTL 41	4.19	0.0001	body mass (VT:0001259)	body weight (CMO:0000012)	1	29409279	74409279	Rat
1578649	Bmd8	Bone mineral density QTL 8	4.9		femur mineral mass (VT:0010011)	trabecular volumetric bone mineral density (CMO:0001729)	1	51940904	101229020	Rat
1358359	Sradr1	Stress Responsive Adrenal Weight QTL 1	4.74		adrenal gland mass (VT:0010420)	both adrenal glands wet weight (CMO:0000164)	1	39728272	132889942	Rat
4889929	Bss87	Bone structure and strength QTL 87	6.7		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	46302615	91302615	Rat
634314	Niddm44	Non-insulin dependent diabetes mellitus QTL 44			blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	51941022	208479811	Rat
1331792	Rf29	Renal function QTL 29	4.589		urine potassium amount (VT:0010539)	urine potassium level (CMO:0000128)	1	43457837	87558729	Rat
2313062	Bmd73	Bone mineral density QTL 73	3.9	0.0001	tibia mineral mass (VT:1000283)	compact volumetric bone mineral density (CMO:0001730)	1	46302615	91302615	Rat
8552900	Pigfal1	Plasma insulin-like growth factor 1 level QTL 1	7.4		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	43509952	88509952	Rat
1578654	Bss10	Bone structure and strength QTL 10	4		femur morphology trait (VT:0000559)	femoral neck cortical cross-sectional area (CMO:0001702)	1	51940904	168768703	Rat
1354643	Foco2	Food consumption QTL 2	7.17	0.0001	eating behavior trait (VT:0001431)	food intake rate (CMO:0000427)	1	42122968	87122968	Rat
2313065	Bss67	Bone structure and strength QTL 67	3.1	0.0001	tibia area (VT:1000281)	tibia total energy absorbed before break (CMO:0001736)	1	46302615	91302615	Rat
2313069	Bss68	Bone structure and strength QTL 68	2.9	0.0001	tibia size trait (VT:0100001)	tibia total energy absorbed before break (CMO:0001736)	1	46302615	91302615	Rat
70225	Bp58	Blood pressure QTL 58	3.3		arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34184556	172281316	Rat
2313075	Bss66	Bone structure and strength QTL 66	3.4	0.0001	tibia length (VT:0004357)	tibia length (CMO:0000450)	1	46302615	91302615	Rat
10059597	Bp377	Blood pressure QTL 377	3.42	0.025	arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	1	34565911	208798288	Rat
1331778	Rf28	Renal function QTL 28	4.66		urine potassium amount (VT:0010539)	urine potassium excretion rate (CMO:0000761)	1	43457837	87558729	Rat
2313077	Bss69	Bone structure and strength QTL 69	3.5	0.0001	tibia strength trait (VT:1000284)	bone polar moment of inertia (CMO:0001558)	1	46302615	91302615	Rat
2313402	Anxrr24	Anxiety related response QTL 24			aggression-related behavior trait (VT:0015014)	tameness/aggressiveness composite score (CMO:0002136)	1	51511344	153680016	Rat
1578756	Iddm22	Insulin dependent diabetes mellitus QTL 22	2.7		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	1	20508326	65508326	Rat
631508	Sald1	Serum aldosterone level QTL 1	3.7		blood aldosterone amount (VT:0005346)	serum aldosterone level (CMO:0000487)	1	11684464	56684464	Rat
1331785	Rf27	Renal function QTL 27	4.643		urine sodium amount (VT:0006274)	urine sodium level (CMO:0000129)	1	30708375	87558729	Rat
1300172	Bp172	Blood pressure QTL 172	3.56		arterial blood pressure trait (VT:2000000)	diastolic blood pressure (CMO:0000005)	1	34565726	79565726	Rat
4889962	Bss94	Bone structure and strength QTL 94	3.8		tibia area (VT:1000281)	tibia-fibula cortical bone endosteal cross-sectional area (CMO:0001722)	1	51909206	91302615	Rat
1558642	Prcr2	Prostate cancer resistance QTL 2	4.3		prostate integrity trait (VT:0010571)	area of ventral prostate occupied by tumorous lesions to total ventral prostate area ratio (CMO:0000899)	1	10379492	55379492	Rat
2313092	Bmd72	Bone mineral density QTL 72	2.5	0.0001	tibia mineral mass (VT:1000283)	total volumetric bone mineral density (CMO:0001728)	1	46302615	91302615	Rat
2313097	Bss70	Bone structure and strength QTL 70	3.5	0.0001	tibia strength trait (VT:1000284)	tibia total energy absorbed before break (CMO:0001736)	1	46302615	91302615	Rat
9589820	Insglur3	Insulin/glucose ratio QTL 3	10.75	0.001	blood insulin amount (VT:0001560)	calculated plasma insulin level (CMO:0002170)	1	43509952	88509952	Rat
152025249	Scl82	Serum cholesterol level QTL 82	4.77		blood cholesterol amount (VT:0000180)		1	52891222	109116986	Rat
1354599	Bw29	Body weight QTL 29	3.46	0.001	body mass (VT:0001259)	body weight (CMO:0000012)	1	42122968	87122968	Rat
2302038	Pia31	Pristane induced arthritis QTL 31	5.5	0.001	blood autoantibody amount (VT:0003725)	serum immunoglobulin M-type rheumatoid factor level relative to an arbitrary reference serum (CMO:0002111)	1	12820494	57820494	Rat
4889919	Bss86	Bone structure and strength QTL 86	4.1		tibia area (VT:1000281)	tibia midshaft total cross-sectional area (CMO:0001715)	1	46302615	91302615	Rat
8552948	Pigfal11	Plasma insulin-like growth factor 1 level QTL 11	4.7		blood insulin-like growth factor amount (VT:0010479)	plasma insulin-like growth factor 1 level (CMO:0001299)	1	43509952	88509952	Rat
634353	Rends2	Renal damage susceptibility QTL 2		0.05	kidney blood vessel morphology trait (VT:0000530)	organ lesion measurement (CMO:0000677)	1	20656420	65656420	Rat

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.

Download All Expressed Objects for this Gene

alimentary part of gastrointestinal system	appendage	circulatory system	ectoderm	endocrine system	endoderm	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	mesenchyme	mesoderm	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	sensory system	visual system
6	7	52	99	39	46	24	11	24	2	139	83	10	87	21	57	22	6	6

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106208	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC168959	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474059	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JAXUCZ010000001	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSRNOT00000023319 ⟹ ENSRNOP00000023319

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8 Ensembl	1	53,592,884 - 53,595,973 (+)	Ensembl
mRatBN7.2 Ensembl	1	51,045,233 - 51,048,340 (+)	Ensembl
Rnor_6.0 Ensembl	1	51,619,875 - 51,622,942 (+)	Ensembl

RefSeq Acc Id:

NM_001106208 ⟹ NP_001099678

RefSeq Status:

VALIDATED

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
GRCr8	1	53,592,902 - 53,595,978 (+)	NCBI
mRatBN7.2	1	51,045,264 - 51,048,340 (+)	NCBI
Rnor_6.0	1	51,619,875 - 51,622,951 (+)	NCBI
Rnor_5.0	1	52,894,340 - 52,897,416 (+)	NCBI
RGSC_v3.4	1	45,590,368 - 45,593,517 (+)	RGD
Celera	1	46,823,047 - 46,826,123 (+)	NCBI

Sequence:

show sequence

CATTCCGGTTGACTTCTGTTCCTGTGCCGGTCCCTCTCCCTGTTCAGCTTTGTGCAGACATGAA
CCCCAGCGACCCCAGCTACTCCTTGGCTTCACTCTATGTGGGGGACCTGCACCCCGACGTGACC
GAGGCGATGCTCTACGAGAAATTCAGCCCGGCAGGGCCCATCCTCTCCATCCGGGTGTACAGGG
ACAGAACCACCCGCCGCTCGCTGGGCTACGCGTCTGTAAACTTCCAGCAGCTGGAGGATGCCGA
GCGGGCCTTGGACACCATGAATTTCGATGTGATAAAGGGCAAGCCGGTTCGCATCATGTGGTCT
CAGCGGGACCCATCGCTGCGCAAGAGTGGGGTAGGCAACATATTCGTCAAAAATCTGGACAGAT
CCATTGACAGTAAAACGCTGTATGATACGTTTTCTGCCTTCGGTAACATCCTTTCCTGTAAGGT
GGTGTGTGATGAGAATGGTTCCAAGGGTTATGGATTCGTACACTTCGAGACACAGGAAGAAGCC
GAACGAGCAATTGAGAAAATGAACGGGATGTTCCTAAATGACCGCAAAGTGTTCGTTGGGCGCT
TTAAGTCTCGTAGAGACCGGCAGGCTGAACTTGGAGCCAGGGCCAAGGAGTTCACCAACGTTTA
CATCAAGAATTTGGGAGAAGACATGGATGATGAAAGACTCCAGGATCTCTTCAGCAGATTTGGG
CCTGCCTTAAGTGTTAAAGTCATGACTGATGAAAGTGGAAAGTCCAAAGGATTCGGATTTGTAA
GCTTTGAAAGGCATGAAGATGCACGAAAGGCAGTGGATGAAATGAACGGAAAAGACCTCAATGG
AAAACAAATTTATGTAGGTCGAGCTCAGAAAAAGGTGGAACGACAGACTGAACTGAAGCACAAA
TTCGGGCAGATGAAGCAAGATAAGCCCAAAATTGAACAGGTACCACAAGATAGAAGCGTCAGAT
GCCAAGGTGTTAACCTTTACGTGAAAAACCTCGATGATGGTATTGATGACGAGCGTCTCCGGAA
GGAGTTTTCTCCGTTTGGGACTATCACTAGTGCAAAGGTAACGATGGAGGGTGGGCGCAGCAAA
GGATTTGGTTTTGTATGTTTCTCCTCTCCAGAAGAAGCCACCAAAGCCGTTACAGAAATGAATG
GCAGAATAGTGGCAACCAAACCACTGTACGTAGCTTTAGCTCAACGCAAAGAGGAGCGCCAGGC
TCACCTCAGTAACCAGTACATGCAGAGAATGGCAAGCACCAGTGCCGTGCCCAACCCAGGCATC
AACCCTTTCCAGCCAGCACAGGGTCTTTCAGGATACTTCATGACAGCTACAGCACCGACTCAGA
ACCGTGGGACATACTATGCTCCTAACCAAACTACTCAGCAAGGACCAAGTGCCCGTGGGAGTGC
TCAGGGTACCAGAGCGCATCCATTCCAAAACATGTCTAGTGCCATCCACCCATCTAATACTATG
CCATCATTTAGTACTTCAGGACCCACTTCCTCACAGGCTGTACGACACCGTACTGCCAGCACAT
CCACACAGATGATGGGTCCACATCCTGCAGCTGCTTCTACTGCAGCTGCTCCTGCCGCCCGCAC
AGTTACTCAGTATAAATATACTGCTGGAGTCCGAAATCCCCCTCAGCATCTTAATACACAGCCA
CAGGTCACCACGCAGCGGTCTGCTGTTTCTGCCCAAGGTAAAGAATCTTTGACTGTCTCCATGT
TGGCATCTGCTCCTCCTCAAGCTCAAAAGCAAATGTTAGGGGAATGGCTATTTTCTCTTATTCA
GGCCATGCACCCTGCCCTTGCCGGTAAAATCACCGGTATGCTGTTGGAAATTGATAATTTAGAG
CTACGCCACATGCTTGAGTCTCCAGAGTGTCTCCACACCAAAGTCGATGAAGCCATAGCTGTAC
TGCAAGCCCACCAAGCTAAAGAGACTTCCCAGAAAGCAGTCAGCAGTGTTGCTGGTGTCCCAAC
TTCTTAAAGTTGAGCAAAAGAAAACCTCCTGCTTCACTGAAGAAAAAAAAAATCTAGACACCAA
AAAACTGTGACAACAAAAAGAAAACTAGAAACTAAGCGAAAAGGAAAGGAACTTATAATCTCCT
GTGCCATCAGTGTCAGGTCTAGTGTGCAATGCAAACCCCAGGTCACTTGGTTTAAGACAACAGA
TAACAGAAATAGTGACATTTAAAATCAGATTAATGTTATCGACTTTGGGGAAATGATTTTCTTT
TAACAAAGTGCAAAAATTTAAAGCCTTTACTTCAATTATAATTCAAATAGCTCAAGAAGTCATT
TCTAAGTAACAGAATTGATACTTGAACAAGGACCATGGTTCAGATCATAATATCCTTGCTTTAC
TAAAGCTTCCTTAAAGAGTAGAAGGGGGGAAAAGGCATCACTATTGGCTAATAATACCTCTAAG
ACTTCTGGAAGGCTACTTCTGTCTTGTGGCCAGCTGTATTTCCGCTCAGTTGTTGCCGGATATA
AAACACACCCCACACTATCTGTAATTCACATAATTGATATACCAAAGAACCCCCCTTCAATTTA
GAAGCTTGTGTCTGTGGCATGAACTACAGAAAGTGAATTTTAACCGCCATAAAAGTTACCTTCA
TAGTCTCTGGACTTCACTAACTTACGTAAATATGTGCCTTCTTCACACTCAGTCTAACATTCAG
ATTACATTTATGCAGTGGCATTTTGCTGTGCTTTGGAAGATACAGGAGTTCTGGTTTTTTTGGA
GCTGTGTTTTGGTGGAATAGATGTATTAGATCACTAAATACATACTCTACAAAAACAGAGGAAA
AGAGAGGGAAGAAGGGAGATAGGAGGCTTCGGAGGGGAGAGGATTAATCTGCTTTTTTTTCAGG
CCCCGAGAAAACGCAAACACATCAGGAAGGCATGTGTGCCCTCTGGAGCATATATGAGCTAAGT
GGATTCTAGAGAGAGAAGAGCTGGGGTGTGTGGCTTTCTCCACACAAAGAGGGAGGATTGGAGT
AGAAAAGCAACGAAGGGGGTTTTCATGAATTTCGATCTATACAATAAAGCTGTTTTTCACAAAT
ACAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001099678	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI68959	(Get FASTA)	NCBI Sequence Viewer
	EDL83096	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSRNOP00000023319
	ENSRNOP00000023319.2

RefSeq Acc Id:

NP_001099678 ⟸ NM_001106208

- UniProtKB:

B5DF80 (UniProtKB/TrEMBL), F7FIM0 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MNPSDPSYSLASLYVGDLHPDVTEAMLYEKFSPAGPILSIRVYRDRTTRRSLGYASVNFQQLED
AERALDTMNFDVIKGKPVRIMWSQRDPSLRKSGVGNIFVKNLDRSIDSKTLYDTFSAFGNILSC
KVVCDENGSKGYGFVHFETQEEAERAIEKMNGMFLNDRKVFVGRFKSRRDRQAELGARAKEFTN
VYIKNLGEDMDDERLQDLFSRFGPALSVKVMTDESGKSKGFGFVSFERHEDARKAVDEMNGKDL
NGKQIYVGRAQKKVERQTELKHKFGQMKQDKPKIEQVPQDRSVRCQGVNLYVKNLDDGIDDERL
RKEFSPFGTITSAKVTMEGGRSKGFGFVCFSSPEEATKAVTEMNGRIVATKPLYVALAQRKEER
QAHLSNQYMQRMASTSAVPNPGINPFQPAQGLSGYFMTATAPTQNRGTYYAPNQTTQQGPSARG
SAQGTRAHPFQNMSSAIHPSNTMPSFSTSGPTSSQAVRHRTASTSTQMMGPHPAAASTAAAPAA
RTVTQYKYTAGVRNPPQHLNTQPQVTTQRSAVSAQGKESLTVSMLASAPPQAQKQMLGEWLFSL
IQAMHPALAGKITGMLLEIDNLELRHMLESPECLHTKVDEAIAVLQAHQAKETSQKAVSSVAGV
PTS

hide sequence

Ensembl Acc Id:

ENSRNOP00000023319 ⟸ ENSRNOT00000023319

Protein Domains

PABC RRM

Protein Structures

Name	Modeler	Protein Id	AA Range	Protein Structure
AF-B5DF80-F1-model_v2	AlphaFold	B5DF80	1-643	view protein structure

Transcriptome

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

Promoters

RGD ID:

13689626

Promoter ID:

EPDNEW_R150

Type:

initiation region

Name:

Pabpc6_1

Description:

poly binding protein, cytoplasmic 6

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	1	51,619,857 - 51,619,917	EPDNEW

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1311201	AgrOrtholog
BioCyc Gene	G2FUF-61529	BioCyc
Ensembl Genes	ENSRNOG00000017367	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000023319	ENTREZGENE
	ENSRNOT00000023319.6	UniProtKB/TrEMBL
Gene3D-CATH	3.30.70.330	UniProtKB/TrEMBL
	c-terminal domain of poly(a) binding protein	UniProtKB/TrEMBL
InterPro	Euk_RNA-bind_prot	UniProtKB/TrEMBL
	Nucleotide-bd_a/b_plait_sf	UniProtKB/TrEMBL
	PABP-dom	UniProtKB/TrEMBL
	PABP_1234	UniProtKB/TrEMBL
	PABP_HYD	UniProtKB/TrEMBL
	PABP_RRM1	UniProtKB/TrEMBL
	RBD_domain_sf	UniProtKB/TrEMBL
	RRM2_I_PABPs	UniProtKB/TrEMBL
	RRM_dom_euk	UniProtKB/TrEMBL
	RRM_RNP1	UniProtKB/TrEMBL
KEGG Report	rno:292295	UniProtKB/TrEMBL
NCBI Gene	292295	ENTREZGENE
PANTHER	OS02G0815200 PROTEIN	UniProtKB/TrEMBL
	RRM DOMAIN-CONTAINING PROTEIN	UniProtKB/TrEMBL
Pfam	PABP	UniProtKB/TrEMBL
	RRM_1	UniProtKB/TrEMBL
PhenoGen	Pabpc6	PhenoGen
PROSITE	PABC	UniProtKB/TrEMBL
	RRM	UniProtKB/TrEMBL
RatGTEx	ENSRNOG00000017367	RatGTEx
SMART	PolyA	UniProtKB/TrEMBL
	RRM	UniProtKB/TrEMBL
	RRM_1	UniProtKB/TrEMBL
Superfamily-SCOP	PABP_HYD	UniProtKB/TrEMBL
	SSF54928	UniProtKB/TrEMBL
UniProt	B5DF80	ENTREZGENE, UniProtKB/TrEMBL
	F7FIM0	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2012-10-05	Pabpc6	poly(A) binding protein, cytoplasmic 6	Pabpc3	poly(A) binding protein, cytoplasmic 3	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-02-27	Pabpc3	poly(A) binding protein, cytoplasmic 3	RGD1311201_predicted	similar to RIKEN cDNA 4932702K14 (predicted)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2005-01-20	RGD1311201_predicted	similar to RIKEN cDNA 4932702K14 (predicted)	LOC292295_predicted		Symbol and Name status set to approved	1331353	APPROVED
2005-01-12	LOC292295_predicted	similar to RIKEN cDNA 4932702K14 (predicted)			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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