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Gene: Pcbp1 (poly(rC) binding protein 1) Chinchilla lanigera

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Symbol:

Pcbp1

Name:

poly(rC) binding protein 1

RGD ID:

8756816

Description:

ENCODES a protein that exhibits DNA-binding transcription factor activity, RNA polymerase II-specific (ortholog); mRNA binding (ortholog); RNA binding (ortholog); INVOLVED IN positive regulation of transcription by RNA polymerase II (ortholog); viral RNA genome replication (ortholog); PARTICIPATES IN iron homeostasis pathway; iron storage pathway; ASSOCIATED WITH Breast Neoplasms (ortholog); COVID-19 (ortholog); genetic disease (ortholog); FOUND IN cytoplasm (ortholog); cytoplasmic ribonucleoprotein granule (ortholog); cytosol (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

poly(rC)-binding protein 1

RGD Orthologs

Alliance Orthologs

More Info

more info ...

Latest Assembly:

ChiLan1.0 - Chinchilla ChiLan1.0 Assembly

NCBI Annotation Information:

Annotation category: partial on reference assembly

Position:

Chinchilla Assembly	Chr	Position (strand)	Source	Genome Browsers
Chinchilla Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
ChiLan1.0 Ensembl	NW_004955424	15,046,011 - 15,047,081 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955424	15,045,642 - 15,047,184 (-)	NCBI	ChiLan1.0	ChiLan1.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

Breast Neoplasms (ISO)

COVID-19 (ISO)

genetic disease (ISO)

Neurodevelopmental Disorders (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

positive regulation of transcription by RNA polymerase II (ISO)

viral RNA genome replication (ISO)

Cellular Component

cytoplasm (ISO)

cytoplasmic ribonucleoprotein granule (ISO)

cytosol (ISO)

nuclear speck (ISO)

nucleoplasm (ISO)

nucleus (ISO)

postsynaptic density (ISO)

Molecular Function

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

mRNA binding (ISO)

protein binding (ISO)

RNA binding (ISO)

sequence-specific single stranded DNA binding (ISO)

single-stranded DNA binding (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

iron homeostasis pathway (ISO)

iron storage pathway (ISO)

References

References - curated

#	Reference Title	Reference Citation
1.	Transitive Annotation Pipeline	Automated assignment of GO, PW and RDO ISO annotations across species

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

Pcbp1
(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_004955424	15,046,011 - 15,047,081 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955424	15,045,642 - 15,047,184 (-)	NCBI	ChiLan1.0	ChiLan1.0

PCBP1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	70,087,477 - 70,089,203 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	70,087,477 - 70,089,203 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	70,314,609 - 70,316,335 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	70,168,203 - 70,169,836 (+)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	2	70,226,351 - 70,227,983	NCBI
Celera	2	70,165,361 - 70,167,111 (+)	NCBI		Celera
Cytogenetic Map	2	p13.3	NCBI
HuRef	2	70,051,034 - 70,052,784 (+)	NCBI		HuRef
CHM1_1	2	70,244,214 - 70,245,976 (+)	NCBI		CHM1_1
T2T-CHM13v2.0	2	70,099,201 - 70,100,927 (+)	NCBI		T2T-CHM13v2.0

Pcbp1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	6	86,501,462 - 86,503,171 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	6	86,501,474 - 86,503,303 (-)	Ensembl		GRCm39 Ensembl
GRCm38	6	86,524,480 - 86,526,189 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	6	86,524,492 - 86,526,321 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	6	86,474,488 - 86,476,165 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	6	86,490,128 - 86,491,801 (-)	NCBI		MGSCv36	mm8
Celera	6	88,462,456 - 88,464,133 (-)	NCBI		Celera
Cytogenetic Map	6	D1	NCBI
cM Map	6	37.72	NCBI

Pcbp1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	4	120,530,100 - 120,532,107 (-)	NCBI		GRCr8
mRatBN7.2	4	118,972,698 - 118,974,705 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	4	118,972,661 - 118,976,500 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	4	124,445,392 - 124,447,399 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	4	120,220,133 - 120,222,140 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	4	118,844,388 - 118,846,395 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	4	118,327,185 - 118,329,223 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	4	118,327,533 - 118,328,602 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	4	182,898,435 - 182,899,895 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	4	120,719,092 - 120,732,363 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	4	107,943,493 - 107,944,933 (-)	NCBI		Celera
Cytogenetic Map	4	q34	NCBI

PCBP1
(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	12	56,307,462 - 56,309,279 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2A	56,311,405 - 56,313,146 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2A	70,144,217 - 70,145,938 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2A	71,260,610 - 71,262,047 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2A	71,258,331 - 71,261,658 (+)	Ensembl	panpan1.1		panPan2

PCBP1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	10	68,686,278 - 68,687,916 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
Dog10K_Boxer_Tasha	10	68,575,170 - 68,576,820 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	10	69,707,654 - 69,709,307 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	10	69,707,756 - 69,709,266 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	10	69,426,436 - 69,428,082 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	10	69,688,634 - 69,690,278 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	10	69,987,443 - 69,989,093 (+)	NCBI		UU_Cfam_GSD_1.0

Pcbp1
(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_024406292	14,289,144 - 14,290,682 (-)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936491	14,280,695 - 14,281,765 (+)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936491	14,280,616 - 14,282,148 (+)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PCBP1
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	3	72,379,025 - 72,380,095 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	72,378,643 - 72,380,364 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	3	75,813,906 - 75,815,624 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

PCBP1
(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	14	37,013,486 - 37,015,119 (-)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	14	37,013,880 - 37,014,947 (-)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666045	74,989,204 - 74,990,938 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Pcbp1
(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_004624762	3,330,978 - 3,332,582 (-)	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_005385632	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AGCD01024682	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBBH01003850	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBDK01016452	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Ensembl Acc Id:

ENSCLAT00000026083 ⟹ ENSCLAP00000025783

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0 Ensembl	NW_004955424	15,046,011 - 15,047,081 (-)	Ensembl

RefSeq Acc Id:

XM_005385632 ⟹ XP_005385689

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955424	15,045,642 - 15,047,184 (-)	NCBI

Sequence:

show sequence

GCCGCTCCCGGCCCCGCTCGCCCCCTCCGCCGCCGCCGCCCGCCCCTGCGACGACGCCGCGGCC
TCCCGCCCGCGCCCGCTCGCTCCCGCGGCCCTCGCTCGCCTCGCGCCGGCAGTTTCGGGCCTAC
ACCTCCCCTCCCCCCGCCAGCCGCCAAAGACTTGACCACGTAACGAGCCCAACTCCCCCGAACG
CCGCCCGCCGCTCGCCATGGATGCCGGTGTGACCGAAAGCGGACTAAACGTGACTCTCACCATT
CGGCTCCTGATGCACGGGAAGGAAGTGGGAAGCATCATCGGGAAGAAAGGGGAGTCGGTGAAGC
GGATCCGCGAGGAGAGCGGCGCGCGGATCAACATCTCGGAGGGGAACTGCCCCGAGAGGATCAT
CACCCTCACCGGGCCCACCAATGCCATCTTCAAGGCCTTCGCCATGATCATCGACAAGCTGGAG
GAAGACATCAACAGCTCCATGACCAACAGCACGGCGGCCAGCCGGCCCCCGGTGACCCTGCGGC
TGGTGGTGCCCGCCACGCAGTGCGGCTCCCTGATCGGCAAGGGCGGCTGCAAGATCAAGGAGAT
CCGCGAGAGCACGGGCGCGCAGGTGCAGGTGGCGGGGGACATGCTGCCCAACTCCACCGAGCGG
GCCATCACCATCGCGGGCGTGCCGCAGTCCGTCACCGAGTGCGTCAAGCAGATCTGCCTGGTCA
TGCTGGAGACGCTCTCGCAGTCCCCGCAGGGCCGCGTCATGACCATCCCCTACCAGCCCATGCC
GGCCGGCTCCCCGGTCATCTGCGCGGGCGGCCAGGACCGCTGCGGCGACGCTGCGGGCTACCCG
CACGCCACCCACGACCTGGAGGGGCCCCCGCTGGACGCCTACTCGATCCAGGGACAACACACCA
TCTCGCCGCTCGATCTGGCCAAGCTGAACCAGGTGGCGAGGCAACAGTCGCACTTTGCCATGAT
GCACGGCGGGACCGGGTTCGCGGGCATTGACTCCAGCTCCCCCGAGGTGAAGGGCTACTGGGCC
AGTCTGGACGCGTCCACCCAGACCACGCACGAACTCACCATTCCCAATAACTTGATCGGCTGCA
TAATCGGGCGCCAGGGCGCCAACATCAACGAGATCCGCCAGATGTCCGGGGCGCAGATCAAAAT
CGCCAACCCCGTGGAGGGCTCCTCCGGCCGGCAGGTCACCATCACCGGCTCGGCCGCCAGCATC
AGCCTGGCGCAGTATCTCATCAACGCCCGGCTCTCCTCCGAGAAGGGCATGGGCTGCAGCTAGA
GCGGCGGCCCCCGAACCCCGCGCTGTTTCCCATGATCCAACTGTGTAATTTCTGGTCAGTGATT
CCAGGTTTTAAATAATTTGTAAGTGTTCAGTTTCTACACCTTCTCATCCGCTAAGAATTTAAGA
AAATCACATTCTCTCTGTTCAGCTGTTAACGCTGGGATCCATATTTAGTTTTATAAGCTTTTTT
TCCCTGTTTTTAGTTTTTTTTTTGTTTTGGGTTTTTTTTTTTGGCTCATGGATTTTATTTTCTG
TTTGTCGATAAGAAATGTAAGAGTGGAATGTTAATTTCAGTTTAGTTCTGTAATGTCAAGAATT
TAAGAATTAAAAAATGGATTGGTTAAAAACTGCTTCCTATTTGAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	XP_005385689	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCLAP00000025783
	ENSCLAP00000025783.1

RefSeq Acc Id:

XP_005385689 ⟸ XM_005385632

- UniProtKB:

A0A8C2YV85 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MDAGVTESGLNVTLTIRLLMHGKEVGSIIGKKGESVKRIREESGARINISEGNCPERIITLTGP
TNAIFKAFAMIIDKLEEDINSSMTNSTAASRPPVTLRLVVPATQCGSLIGKGGCKIKEIRESTG
AQVQVAGDMLPNSTERAITIAGVPQSVTECVKQICLVMLETLSQSPQGRVMTIPYQPMPAGSPV
ICAGGQDRCGDAAGYPHATHDLEGPPLDAYSIQGQHTISPLDLAKLNQVARQQSHFAMMHGGTG
FAGIDSSSPEVKGYWASLDASTQTTHELTIPNNLIGCIIGRQGANINEIRQMSGAQIKIANPVE
GSSGRQVTITGSAASISLAQYLINARLSSEKGMGCS

hide sequence

Ensembl Acc Id:

ENSCLAP00000025783 ⟸ ENSCLAT00000026083

Protein Domains

K Homology

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCLAG00000017909	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCLAT00000026083	ENTREZGENE
	ENSCLAT00000026083.1	UniProtKB/TrEMBL
Gene3D-CATH	3.30.1370.10	UniProtKB/TrEMBL
InterPro	KH_dom	UniProtKB/TrEMBL
	KH_dom_type_1	UniProtKB/TrEMBL
	KH_dom_type_1_sf	UniProtKB/TrEMBL
NCBI Gene	Pcbp1	ENTREZGENE
PANTHER	KH DOMAIN CONTAINING RNA BINDING PROTEIN	UniProtKB/TrEMBL
	POLY(RC)-BINDING PROTEIN 1	UniProtKB/TrEMBL
Pfam	KH_1	UniProtKB/TrEMBL
PROSITE	KH_TYPE_1	UniProtKB/TrEMBL
SMART	SM00322	UniProtKB/TrEMBL
Superfamily-SCOP	SSF54791	UniProtKB/TrEMBL
UniProt	A0A8C2YV85	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)

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