Cfp (complement factor properdin)

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Gene: Cfp (complement factor properdin) Rattus norvegicus

Analyze

Symbol:

Cfp

Name:

complement factor properdin

RGD ID:

1594557

Description:

Predicted to be involved in complement activation, alternative pathway. Predicted to localize to extracellular space and secretory granule. Human ortholog(s) of this gene implicated in X-linked properdin deficiency. Orthologous to human CFP (complement factor properdin); INTERACTS WITH 1-naphthyl isothiocyanate; 17alpha-ethynylestradiol; 17beta-estradiol.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

Pfc; Pfc_mapped; properdin; properdin factor, complement; properdin factor, complement (mapped); Properdin P factor, complement

RGD Orthologs

Human

Mouse

Chinchilla

Bonobo

Dog

Squirrel

Pig

Green Monkey

Naked Mole-Rat

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):	CFP (complement factor properdin)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, Treefam
Mus musculus (house mouse):	Cfp (complement factor properdin)	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Cfp (complement factor properdin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CFP (complement factor properdin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CFP (complement factor properdin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	LOC101961626 (complement factor properdin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CFP (complement factor properdin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	LOC103231897 (properdin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Cfp (complement factor properdin)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	CFP (complement factor properdin)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Cfp (complement factor properdin)	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	si:ch73-237c6.1	Alliance	DIOPT (PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	cfp (complement factor properdin)	Alliance	DIOPT (PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	C36B7.5	Alliance	DIOPT (Ensembl Compara\|TreeFam)

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	1,162,014 - 1,167,576 (+)	NCBI
Rnor_6.0 Ensembl	X	1,311,121 - 1,316,682 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	X	1,311,121 - 1,316,683 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	X	2,126,142 - 2,131,704 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	12,584,709 - 12,590,271 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	X	1,730,903 - 1,736,462 (+)	NCBI		Celera
Cytogenetic Map	X	q11	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)

Experimental Liver Cirrhosis (ISO)

factor VIII deficiency (ISO)

hepatocellular carcinoma (ISO)

meningococcal meningitis (ISO)

syndromic X-linked intellectual disability Lubs type (ISO)

X-linked properdin deficiency (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

1-naphthyl isothiocyanate (EXP)

17alpha-ethynylestradiol (EXP,ISO)

17beta-estradiol (EXP,ISO)

17beta-estradiol 3-benzoate (EXP)

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

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

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

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

3H-1,2-dithiole-3-thione (EXP)

4,4'-diaminodiphenylmethane (EXP)

acrylamide (ISO)

aflatoxin B1 (EXP,ISO)

antirheumatic drug (ISO)

Aroclor 1254 (EXP)

benzene (ISO)

benzo[a]pyrene (ISO)

benzo[b]fluoranthene (ISO)

bisphenol A (EXP,ISO)

carbon nanotube (ISO)

cerium trichloride (ISO)

cisplatin (ISO)

copper atom (EXP)

copper(0) (EXP)

copper(II) sulfate (ISO)

endosulfan (EXP)

flutamide (EXP)

fumonisin B1 (ISO)

lead diacetate (ISO)

lipopolysaccharide (ISO)

N,N,N',N'-tetrakis(2-pyridylmethyl)ethylenediamine (ISO)

N-nitrosodimethylamine (EXP)

nickel atom (ISO)

niclosamide (ISO)

paracetamol (ISO)

phenobarbital (ISO)

pirinixic acid (ISO)

poly(I:C) (EXP)

resveratrol (EXP)

rotenone (EXP)

silicon dioxide (ISO)

Soman (EXP)

streptozocin (EXP)

sulforaphane (ISO)

testosterone (EXP)

tetrachloromethane (EXP,ISO)

thimerosal (ISO)

titanium dioxide (ISO)

trichloroethene (EXP)

troglitazone (ISO)

valproic acid (EXP,ISO)

versicolorin A (ISO)

vinclozolin (EXP)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

biological_process (ND)

complement activation, alternative pathway (ISO)

Cellular Component

cellular_component (ND)

extracellular space (ISO)

secretory granule (ISO)

Molecular Function

molecular_function (ND)

protein binding (ISO)

References

References - curated


1.	Goundis D and Reid KB, Nature 1988 Sep 1;335(6185):82-5.
2.	Online Mendelian Inheritance in Man, OMIM (TM).
3.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4.	RGD automated import pipeline for gene-chemical interactions
5.	RGD comprehensive gene curation
6.	Verroust F, etal., J Clin Lab Immunol. 1981 Sep;6(2):127-30.

Additional References at PubMed

PMID:12477932	PMID:18292556	PMID:20551380	PMID:21135110	PMID:22815489

Genomics

Comparative Map Data

Cfp
(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	1,162,014 - 1,167,576 (+)	NCBI
Rnor_6.0 Ensembl	X	1,311,121 - 1,316,682 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	X	1,311,121 - 1,316,683 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	X	2,126,142 - 2,131,704 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	X	12,584,709 - 12,590,271 (-)	NCBI	RGSC3.4		rn4	RGSC3.4
Celera	X	1,730,903 - 1,736,462 (+)	NCBI		Celera
Cytogenetic Map	X	q11	NCBI

CFP
(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	47,623,172 - 47,630,305 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	X	47,623,282 - 47,630,305 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	X	47,482,681 - 47,489,704 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	X	47,368,569 - 47,374,648 (-)	NCBI	NCBI36		hg18	NCBI36
Build 34	X	47,239,878 - 47,245,958	NCBI
Celera	X	51,678,874 - 51,684,967 (-)	NCBI
Cytogenetic Map	X	p11.23	NCBI
HuRef	X	45,196,561 - 45,202,654 (-)	NCBI		HuRef
CHM1_1	X	47,514,712 - 47,520,808 (-)	NCBI		CHM1_1

Cfp
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	X	20,791,693 - 20,797,794 (-)	NCBI	GRCm39		mm39
GRCm39 Ensembl	X	20,791,693 - 20,797,794 (-)	Ensembl
GRCm38	X	20,925,454 - 20,931,555 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	X	20,925,454 - 20,931,555 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	X	20,502,661 - 20,508,650 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	X	20,082,494 - 20,088,465 (-)	NCBI			mm8
Celera	X	19,059,397 - 19,065,386 (-)	NCBI		Celera
Cytogenetic Map	X	A1.3	NCBI
cM Map	X	16.44	NCBI

Cfp
(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_004955516	449,993 - 456,492 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955516	449,993 - 455,897 (+)	NCBI	ChiLan1.0	ChiLan1.0

CFP
(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	47,956,191 - 47,961,965 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	X	47,956,191 - 47,961,965 (-)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	X	40,060,106 - 40,066,720 (-)	NCBI	Mhudiblu_PPA_v0		panPan3

CFP
(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	41,245,868 - 41,252,194 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	X	41,245,905 - 41,251,623 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	X	15,620,466 - 15,626,213 (-)	NCBI
ROS_Cfam_1.0	X	41,379,663 - 41,385,406 (-)	NCBI
UMICH_Zoey_3.1	X	41,367,204 - 41,372,947 (-)	NCBI
UNSW_CanFamBas_1.0	X	41,355,500 - 41,361,239 (-)	NCBI
UU_Cfam_GSD_1.0	X	41,448,168 - 41,453,913 (-)	NCBI

LOC101961626
(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	33,550,861 - 33,558,058 (-)	NCBI
SpeTri2.0	NW_004936502	13,391,613 - 13,398,723 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CFP
(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	42,143,805 - 42,174,939 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	X	42,145,754 - 42,152,879 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	X	47,326,173 - 47,335,086 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

LOC103231897
(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	44,801,388 - 44,807,177 (-)	NCBI
ChlSab1.1 Ensembl	X	44,801,354 - 44,807,402 (-)	Ensembl

Cfp
(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_004624978	180,352 - 194,467 (-)	NCBI

Position Markers

DXWox21

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	X	1,305,731 - 1,305,917	NCBI	Rnor6.0
Rnor_5.0	X	2,120,752 - 2,120,938	UniSTS	Rnor5.0
RGSC_v3.4	X	12,595,475 - 12,595,661	UniSTS	RGSC3.4
Celera	X	1,725,513 - 1,725,699	UniSTS
Cytogenetic Map	X	q12	UniSTS

RH141135

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	X	1,309,135 - 1,309,319	NCBI	Rnor6.0
Rnor_5.0	X	2,124,156 - 2,124,340	UniSTS	Rnor5.0
RGSC_v3.4	X	12,592,073 - 12,592,257	UniSTS	RGSC3.4
Celera	X	1,728,917 - 1,729,101	UniSTS
RH 3.4 Map	6	789.4	UniSTS
Cytogenetic Map	X	q12	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
731181	Uae27	Urinary albumin excretion QTL 27	2.7	0.0059	urine albumin amount (VT:0002871)	urine albumin excretion rate (CMO:0000757)	X	1	44092703	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	58
Count of miRNA genes:	48
Interacting mature miRNAs:	50
Transcripts:	ENSRNOT00000038909
Prediction methods:	Microtar, 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	20	56	41	19	41			70	25	34	11
Low		23	1				8	11	4	10	7		8
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_001106757	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	BC158889	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH474009	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ209917	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	FQ212442	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000335	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000038909 ⟹ ENSRNOP00000031039

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	X	1,311,121 - 1,316,682 (+)	Ensembl

RefSeq Acc Id:

NM_001106757 ⟹ NP_001100227

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	X	1,162,014 - 1,167,576 (+)	NCBI
Rnor_6.0	X	1,311,121 - 1,316,683 (+)	NCBI
Rnor_5.0	X	2,126,142 - 2,131,704 (+)	NCBI
RGSC_v3.4	X	12,584,709 - 12,590,271 (-)	RGD
Celera	X	1,730,903 - 1,736,462 (+)	RGD

Sequence:

show sequence

CAGAAACATAGTGTTCACAATGCCCGTTGGAATGCAAGCCCCTCAGTGGCTCCTGCTCCTATTG
CTTATCCTGCCAACCACAGGCTCAGACCCTGTGCTCTGCTTCACCCAGTATGAGGAGCCCTCTG
GCAGGTGCAAAGGCCTACTTGGAAGAGACATCAGGGTGGAAGATTGCTGTCTCAACACTGCCTA
TGCCTTCCAGGAACATGATGGGGGCCTCTGTCAGTCATGCAGGTCCCCACAATGGTCAGCATGG
TCCTCATGGGGGCCCTGCTCAGTTACATGCTCTGAGGGGTCCCAGCTGCGACACAGGCGCTGTG
TGGGTAGGGGTGGACAGTGCTCTGAGAAGGCGGCTCCTGGAACTCTTGAGTGGCAGCTACAGGC
CTGTGAGGATCAGCTATGCTGTCCAGAGATGGGTGGCTGGTCTGAGTGGGGACCCTGGGGGCCT
TGCTCTGTCACCTGCTCCAAAGGAACCCAGACCCGTCAACGACTATGTGATAATCCTGCTCCTA
AGTGTGGAGGCCATTGCCCCGGAGAGGCCCAGCAATCACAGGCCTGTGACACTCAGAAGATCTG
CCCCACACATGGGGCCTGGGCATCCTGGGGCCCCTGGAGCGCCTGCTCAGGATCATGCCTTGGC
GGAGCTCAAGAACCTAAGGAGACACGAAGCCGCTCATGTTCTGCACCAGCACCTTCACACCAAC
CCCCTGGGAAGCCCTGCTCAGGAACAGCCTATGAGCATCGGGGCTGTAGTGGCCTACCACCTTG
CCCAGTGGCTGGTGGCTGGGGACCATGGGGCCCTTCAAGTCCCTGCCCGGTGACTTGTGGCCTG
GGCCAGACCCTAGAACGACGGACATGTGATCACCCTGTACCCCGTCATGGGGGCCCCTTTTGTG
CTGGTGATGCCACTCGGAAACACGTCTGTAACACAGCCATGCCTTGCCCTGTAAATGGAGAGTG
GGAGGCCTGGGGAAAATGGAGTCACTGCAGCCGTGTGAGAATGAAGTCCATCAGCTGTGATGAA
ATCCCAGGCCAGCAGTCACGTTCAAGGAGCTGTGGTGGCCGCAAATTTGATGGGCAGCCATGTA
CTGGGAAACTCCAAGATATTCGACACTGCTATGACATCCATAACTGTGTCTTGAAAGGTTCATG
GTCACAGTGGAGTACCTGGGGTCTGTGCACACCACCATGTGGACCCAACCCCACCCGTGTCCGT
CAGCGACTCTGCACACCTTTGCTCCCCAAGTACTCGCCTACAGTTTCCATGGTTGAAGGTCAGG
GTGAGAAGAATGTTACCTTCTGGGGGATCCCACGGCCACTGTGTGAGGTGCTACAGGGGCAGAA
GCTGGTGGTGGAAGAGAAACGGCCATGTCTACATGTGCCTTCCTGCAGAGATCCAGAAGAGAAG
AAACCCTAAAATCCCTTGCCTCCATTCTGACCCCCTGACCTTCTAAACCTCAATAAACCAGCCT
TTCTAGAAAAAAAAAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_001100227	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAI58890	(Get FASTA)	NCBI Sequence Viewer
	EDL97727	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:	NP_001100227 ⟸ NM_001106757
- Peptide Label:	precursor
- UniProtKB:	B0BNN4 (UniProtKB/TrEMBL)
- Sequence:	show sequence MPVGMQAPQWLLLLLLILPTTGSDPVLCFTQYEEPSGRCKGLLGRDIRVEDCCLNTAYAFQEHD GGLCQSCRSPQWSAWSSWGPCSVTCSEGSQLRHRRCVGRGGQCSEKAAPGTLEWQLQACEDQLC CPEMGGWSEWGPWGPCSVTCSKGTQTRQRLCDNPAPKCGGHCPGEAQQSQACDTQKICPTHGAW ASWGPWSACSGSCLGGAQEPKETRSRSCSAPAPSHQPPGKPCSGTAYEHRGCSGLPPCPVAGGW GPWGPSSPCPVTCGLGQTLERRTCDHPVPRHGGPFCAGDATRKHVCNTAMPCPVNGEWEAWGKW SHCSRVRMKSISCDEIPGQQSRSRSCGGRKFDGQPCTGKLQDIRHCYDIHNCVLKGSWSQWSTW GLCTPPCGPNPTRVRQRLCTPLLPKYSPTVSMVEGQGEKNVTFWGIPRPLCEVLQGQKLVVEEK RPCLHVPSCRDPEEKKP hide sequence

RefSeq Acc Id:

ENSRNOP00000031039 ⟸ ENSRNOT00000038909

Transcriptome

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

Promoters

RGD ID:

13701690

Promoter ID:

EPDNEW_R12212

Type:

initiation region

Name:

Cfp_1

Description:

complement factor properdin

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	1,311,120 - 1,311,180	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

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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)

Visual

CSV

TAB

Printer

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)

Visual

CSV

TAB

Printer

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

Damaging Variants

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
X	1313770	1313771	G	A	snv	ACI/N (MCW), Buf/N (MCW), WN/N (MCW), M520/N (MCW), MR/N (MCW), F344/NRrrc (MCW)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:1594557	AgrOrtholog
Ensembl Genes	ENSRNOG00000025811	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein	ENSRNOP00000031039	ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSRNOT00000038909	ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH	2.20.100.10	UniProtKB/TrEMBL
IMAGE_CLONE	IMAGE:8375684	IMAGE-MGC_LOAD
InterPro	Thrombospondin_1_rpt	UniProtKB/TrEMBL
	TSP1_rpt_sf	UniProtKB/TrEMBL
KEGG Report	rno:299314	UniProtKB/TrEMBL
MGC_CLONE	MGC:188620	IMAGE-MGC_LOAD
NCBI Gene	299314	ENTREZGENE
Pfam	TSP_1	UniProtKB/TrEMBL
PhenoGen	Cfp	PhenoGen
PROSITE	TSP1	UniProtKB/TrEMBL
SMART	TSP1	UniProtKB/TrEMBL
Superfamily-SCOP	TSP1	UniProtKB/TrEMBL
UniProt	B0BNN4	ENTREZGENE, UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2008-03-06	Cfp	complement factor properdin	Pfc	properdin factor, complement	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2007-04-13		properdin factor, complement	Pfc	properdin factor, complement (mapped)	Name updated	737654	APPROVED
2007-04-11	Pfc	properdin factor, complement (mapped)	Pfc_mapped	properdin factor, complement (mapped)	Data Merged	737654	APPROVED
2006-11-20	Pfc	properdin factor, complement (mapped)			Symbol and Name status set to provisional	70820	PROVISIONAL
2005-11-17	Pfc_mapped	properdin factor, complement (mapped)	Pfc	properdin factor, complement	Symbol and Name updated	1556543	APPROVED
2002-06-10	Pfc	Properdin P factor, complement			Symbol and Name status set to approved	70586	APPROVED

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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