Cdc5l (cell division cycle 5-like)

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Gene: Cdc5l (cell division cycle 5-like) Rattus norvegicus

Analyze

Symbol:

Cdc5l

Name:

cell division cycle 5-like

RGD ID:

70892

Description:

Exhibits enzyme binding activity; leucine zipper domain binding activity; and transcription corepressor binding activity. Involved in several processes, including cellular response to growth factor stimulus; cellular response to prolactin; and cellular response to wortmannin. Localizes to nuclear speck; perinuclear region of cytoplasm; and protein-DNA complex. Predicted to colocalize with DNA replication factor A complex. Human ortholog(s) of this gene implicated in osteosarcoma. Orthologous to human CDC5L (cell division cycle 5 like); PARTICIPATES IN spliceosome pathway; INTERACTS WITH ammonium chloride; bisphenol A; dimethylarsinic acid.

Type:

protein-coding

RefSeq Status:

PROVISIONAL

Also known as:

CDC5 (cell division cycle 5 S. pombe homolog)-like; CDC5 (cell division cycle 5, S. pombe, homolog)-like; CDC5 cell division cycle 5-like; CDC5 cell division cycle 5-like (S. pombe); cdc5-like protein; cell division cycle 5-like (S. pombe); cell division cycle 5-like protein; cell division cycle 5-related protein; pombe Cdc5-related protein

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):	CDC5L (cell division cycle 5 like)	HGNC	EggNOG, Ensembl, HomoloGene, Inparanoid, NCBI, OMA, OrthoDB, OrthoMCL, Panther, PhylomeDB, Treefam
Mus musculus (house mouse):	Cdc5l (cell division cycle 5-like (S. pombe))	HGNC	Treefam, EggNOG, OrthoMCL, NCBI, OMA, HomoloGene, Inparanoid, Panther, PhylomeDB, OrthoDB, Ensembl
Chinchilla lanigera (long-tailed chinchilla):	Cdc5l (cell division cycle 5 like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	CDC5L (cell division cycle 5 like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	CDC5L (cell division cycle 5 like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Ictidomys tridecemlineatus (thirteen-lined ground squirrel):	Cdc5l (cell division cycle 5 like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	CDC5L (cell division cycle 5 like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (African green monkey):	CDC5L (cell division cycle 5 like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Cdc5l (cell division cycle 5 like)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Alliance orthologs ³
Homo sapiens (human):	CDC5L (cell division cycle 5 like)	Alliance	DIOPT (Ensembl Compara\|HGNC\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Mus musculus (house mouse):	Cdc5l (cell division cycle 5-like (S. pombe))	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Danio rerio (zebrafish):	cdc5l (CDC5 cell division cycle 5-like (S. pombe))	Alliance	DIOPT (PhylomeDB\|TreeFam)
Saccharomyces cerevisiae (baker's yeast):	CEF1	Alliance	DIOPT (Ensembl Compara\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Drosophila melanogaster (fruit fly):	Cdc5	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB\|TreeFam)
Caenorhabditis elegans (roundworm):	cdc-5L	Alliance	DIOPT (Ensembl Compara\|Hieranoid\|InParanoid\|OMA\|OrthoFinder\|OrthoInspector\|PANTHER\|PhylomeDB)

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	9	15,564,949 - 15,603,453 (+)	NCBI
Rnor_6.0 Ensembl	9	17,949,764 - 17,988,509 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	9	17,949,764 - 17,988,514 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	9	16,838,171 - 16,876,921 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	9	11,165,631 - 11,204,135 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	9	11,162,952 - 11,201,455 (+)	NCBI
Celera	9	13,308,462 - 13,346,957 (+)	NCBI		Celera
Cytogenetic Map	9	q12	NCBI

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

CAKUT (ISO)

esophagus adenocarcinoma (ISO)

Lung Neoplasms (ISO)

osteosarcoma (ISO)

Gene-Chemical Interaction Annotations Click to see Annotation Detail View

1,2-dimethylhydrazine (ISO)

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

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

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

aflatoxin B1 (ISO)

ammonium chloride (EXP)

antirheumatic drug (ISO)

Aroclor 1254 (ISO)

benzo[a]pyrene (ISO)

bisphenol A (EXP)

copper(II) sulfate (ISO)

coumestrol (ISO)

dicrotophos (ISO)

dimethylarsinic acid (EXP)

dorsomorphin (ISO)

doxorubicin (ISO)

enzyme inhibitor (ISO)

flavonoids (EXP)

folic acid (ISO)

glafenine (EXP)

hydrogen peroxide (ISO)

methyl methanesulfonate (ISO)

motexafin gadolinium (ISO)

N-nitrosodiethylamine (EXP)

nickel atom (ISO)

nimesulide (EXP)

paclitaxel (ISO)

paracetamol (ISO)

pentachlorophenol (ISO)

resveratrol (ISO)

SB 431542 (ISO)

tert-butyl hydroperoxide (ISO)

tetrachloromethane (EXP)

thapsigargin (ISO)

trichostatin A (ISO)

troglitazone (ISO)

tungsten (ISO)

valproic acid (ISO)

wortmannin (EXP)

zinc acetate (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cellular response to fibroblast growth factor stimulus (IEP)

cellular response to interleukin-2 (IEP)

cellular response to nerve growth factor stimulus (IDA)

cellular response to prolactin (IEP)

cellular response to wortmannin (IDA)

DNA repair (IEA)

G2/M transition of mitotic cell cycle (TAS)

mitotic cell cycle (IMP)

mRNA splicing, via spliceosome (IBA,ISO,ISS)

positive regulation of transcription by RNA polymerase II (ISO)

regulation of transcription by RNA polymerase II (IBA)

regulation of transcription, DNA-templated (TAS)

signal transduction involved in DNA damage checkpoint (ISO,ISS)

Cellular Component

catalytic step 2 spliceosome (ISO)

cytoplasm (ISO)

DNA replication factor A complex (ISO,ISS)

nuclear speck (IDA,ISO)

nucleoplasm (ISO)

nucleus (IDA,ISO)

perinuclear region of cytoplasm (IDA)

protein-DNA complex (IDA)

Prp19 complex (IBA,ISO,ISS)

spliceosomal complex (IBA)

U2-type catalytic step 2 spliceosome (ISO,ISS)

Molecular Function

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

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

leucine zipper domain binding (IPI)

protein binding (IPI,ISO)

protein kinase binding (IPI)

protein phosphatase 1 binding (IPI)

RNA binding (IEA)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (IBA,ISO)

transcription corepressor binding (IPI)

WD40-repeat domain binding (ISO,ISS)

Molecular Pathway Annotations Click to see Annotation Detail View

spliceosome pathway (IEA,ISO)

References

References - curated


1.	Bonner AE, etal., Oncogene. 2004 Feb 5;23(5):1166-76.
2.	Boudrez A, etal., J Biol Chem. 2000 Aug 18;275(33):25411-7.
3.	Chanarat S and Strasser K, Biochim Biophys Acta. 2013 Oct;1833(10):2126-34. doi: 10.1016/j.bbamcr.2013.05.023. Epub 2013 Jun 3.
4.	Engemann H, etal., Nucleic Acids Res 2002 Mar 15;30(6):1408-17.
5.	Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
6.	Hansel DE, etal., Am J Surg Pathol. 2005 Mar;29(3):390-9.
7.	Johnson LM and Too CK, Mol Cell Endocrinol. 2001 Nov 26;184(1-2):151-61.
8.	Lu XY, etal., Mol Cancer Res. 2008 Jun;6(6):937-46. doi: 10.1158/1541-7786.MCR-07-2115.
9.	MGD Curation, June 12, 2002
10.	MGD data from the GO Consortium
11.	NCBI rat LocusLink and RefSeq merged data July 26, 2002
12.	Pipeline to import KEGG annotations from KEGG into RGD
13.	RGD automated data pipeline
14.	RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
15.	RGD automated import pipeline for gene-chemical interactions
16.	Too CK Mol Cell Endocrinol 1997 Aug 8;131(2):221-32.
17.	Urano Y, etal., J Biol Chem. 2006 Mar 17;281(11):7498-514. Epub 2005 Dec 13.
18.	Urano-Tashiro Y, etal., J Neurosci Res. 2010 Oct;88(13):2787-97. doi: 10.1002/jnr.22455.

Additional References at PubMed

PMID:9038199	PMID:11082045	PMID:11991638	PMID:12477932	PMID:16332694	PMID:19946888	PMID:20176811	PMID:22681889	PMID:24332808	PMID:28076346

Genomics

Comparative Map Data

Cdc5l
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
mRatBN7.2	9	15,564,949 - 15,603,453 (+)	NCBI
Rnor_6.0 Ensembl	9	17,949,764 - 17,988,509 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_6.0	9	17,949,764 - 17,988,514 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_5.0	9	16,838,171 - 16,876,921 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	9	11,165,631 - 11,204,135 (+)	NCBI	RGSC3.4		rn4	RGSC3.4
RGSC_v3.1	9	11,162,952 - 11,201,455 (+)	NCBI
Celera	9	13,308,462 - 13,346,957 (+)	NCBI		Celera
Cytogenetic Map	9	q12	NCBI

CDC5L
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38.p13 Ensembl	6	44,387,706 - 44,450,425 (+)	Ensembl	GRCh38		hg38	GRCh38
GRCh38	6	44,387,706 - 44,450,425 (+)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh37	6	44,355,443 - 44,418,162 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
GRCh37	6	44,355,251 - 44,418,161 (+)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	6	44,463,280 - 44,522,758 (+)	NCBI	NCBI36		hg18	NCBI36
Build 34	6	44,463,279 - 44,522,757	NCBI
Celera	6	45,908,480 - 45,967,835 (+)	NCBI
Cytogenetic Map	6	p21.1	NCBI
HuRef	6	44,077,869 - 44,140,670 (+)	NCBI		HuRef
CHM1_1	6	44,358,890 - 44,421,686 (+)	NCBI		CHM1_1

Cdc5l
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	17	45,702,809 - 45,744,633 (-)	NCBI	GRCm39		mm39
GRCm38	17	45,391,887 - 45,433,707 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	17	45,391,884 - 45,433,737 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	17	45,528,836 - 45,570,656 (-)	NCBI	GRCm37		mm9	NCBIm37
MGSCv36	17	44,855,468 - 44,897,288 (-)	NCBI			mm8
Celera	17	48,822,530 - 48,866,019 (-)	NCBI		Celera
Cytogenetic Map	17	B3	NCBI

Cdc5l
(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_004955437	9,990,613 - 10,032,034 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955437	9,990,613 - 10,032,034 (+)	NCBI	ChiLan1.0	ChiLan1.0

CDC5L
(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	6	45,265,845 - 45,326,392 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	6	45,265,845 - 45,326,383 (+)	Ensembl	panpan1.1		panPan2
Mhudiblu_PPA_v0	6	43,983,840 - 44,043,029 (+)	NCBI	Mhudiblu_PPA_v0		panPan3

CDC5L
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1 Ensembl	12	12,780,010 - 12,822,801 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
CanFam3.1	12	12,779,936 - 12,822,978 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1

Cdc5l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
SpeTri2.0	NW_004936476	15,647,470 - 15,698,095 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

CDC5L
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	7	39,384,556 - 39,431,248 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	7	39,384,397 - 39,427,729 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	7	45,306,065 - 45,349,669 (+)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

CDC5L
(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	17	27,727,185 - 27,785,233 (-)	NCBI
ChlSab1.1 Ensembl	17	27,722,819 - 27,785,268 (-)	Ensembl

Cdc5l
(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_004624754	15,477,188 - 15,517,656 (-)	NCBI

Position Markers

RH125755

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	9	17,988,173 - 17,988,426	NCBI	Rnor6.0
Rnor_5.0	9	16,876,580 - 16,876,833	UniSTS	Rnor5.0
RGSC_v3.4	9	11,203,794 - 11,204,047	UniSTS	RGSC3.4
Celera	9	13,346,616 - 13,346,869	UniSTS
Cytogenetic Map	9	q12	UniSTS

RH131317

Rat Assembly	Chr	Position (strand)	Source	JBrowse
Rnor_6.0	9	17,988,114 - 17,988,294	NCBI	Rnor6.0
Rnor_5.0	9	16,876,521 - 16,876,701	UniSTS	Rnor5.0
RGSC_v3.4	9	11,203,735 - 11,203,915	UniSTS	RGSC3.4
Celera	9	13,346,557 - 13,346,737	UniSTS
RH 3.4 Map	9	78.6	UniSTS
Cytogenetic Map	9	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
70226	Eae4	Experimental allergic encephalomyelitis QTL 4			nervous system integrity trait (VT:0010566)	experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)	9	1	29467098	Rat
9589055	Scfw5	Subcutaneous fat weight QTL 5	5.55	0.001	subcutaneous adipose mass (VT:1000472)	abdominal subcutaneous fat pad weight (CMO:0002069)	9	1	40383872	Rat
9589158	Gluco65	Glucose level QTL 65	6.82	0.001	blood glucose amount (VT:0000188)	plasma glucose level (CMO:0000042)	9	1	40383872	Rat
7411592	Foco8	Food consumption QTL 8	7.4	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	9	1	40383872	Rat
1300124	Cm4	Cardiac mass QTL 4	3.55		heart mass (VT:0007028)	heart weight to body weight ratio (CMO:0000074)	9	1	45029794	Rat
10054125	Srcrt7	Stress Responsive Cort QTL 7	3.33	0.0011	blood corticosterone amount (VT:0005345)	plasma corticosterone level (CMO:0001173)	9	1055222	93442944	Rat
1298088	Edpm11	Estrogen-dependent pituitary mass QTL 11	2.5		pituitary gland mass (VT:0010496)	pituitary gland wet weight (CMO:0000853)	9	2355722	47355722	Rat
1641911	Alcrsp13	Alcohol response QTL 13			response to alcohol trait (VT:0010489)	brain neurotensin receptor 1 density (CMO:0002068)	9	2355722	47355722	Rat
61425	Cia15	Collagen induced arthritis QTL 15	4.6		joint integrity trait (VT:0010548)	joint inflammation composite score (CMO:0000919)	9	2880977	47375681	Rat
631211	Bw4	Body weight QTL4	5.31		retroperitoneal fat pad mass (VT:0010430)	retroperitoneal fat pad weight to body weight ratio (CMO:0000635)	9	2880977	47880977	Rat
1354650	Despr5	Despair related QTL 5	4.01	0.0017	locomotor behavior trait (VT:0001392)	amount of time spent in voluntary immobility (CMO:0001043)	9	4986095	49986095	Rat
2303559	Gluco54	Glucose level QTL 54	2		blood glucose amount (VT:0000188)	blood glucose level (CMO:0000046)	9	4986095	49986095	Rat
61450	Ciaa3	CIA Autoantibody QTL 3	6.5		blood autoantibody amount (VT:0003725)	calculated serum anti-type 2 collagen antibody titer (CMO:0001279)	9	5724254	25692342	Rat
11353947	Bp392	Blood pressure QTL 392			arterial blood pressure trait (VT:2000000)	systolic blood pressure (CMO:0000004)	9	12216771	57216771	Rat
9589133	Insul26	Insulin level QTL 26	17.96	0.001	blood insulin amount (VT:0001560)	plasma insulin level (CMO:0000342)	9	12425463	57425463	Rat
7411609	Foco16	Food consumption QTL 16	25.6	0.001	eating behavior trait (VT:0001431)	feed conversion ratio (CMO:0001312)	9	12425463	57425463	Rat
1600365	Mcs20	Mammary carcinoma susceptibility QTL 20	3		mammary gland integrity trait (VT:0010552)	mammary tumor growth rate (CMO:0000344)	9	15554901	47249201	Rat

miRNA Target Status

Predicted Target Of

	Summary Value
Count of predictions:	54
Count of miRNA genes:	45
Interacting mature miRNAs:	53
Transcripts:	ENSRNOT00000027264
Prediction methods:	Miranda, Rnahybrid, Targetscan
Result types:	miRGate_prediction

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

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

Expression

RNA-SEQ Expression

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

	alimentary part of gastrointestinal system	circulatory system	endocrine system	exocrine system	hemolymphoid system	hepatobiliary system	integumental system	musculoskeletal system	nervous system	renal system	reproductive system	respiratory system	appendage
High
Medium	3	43	57	41	19	41	8	11	74	35	41	11	8
Low
Below cutoff

View RNA-SEQ Expression Data

Sequence

Nucleotide Sequences


RefSeq Transcripts	NM_053527	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AF000578	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC087007	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC111403	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	BC161839	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	CH473987	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	JACYVU010000213	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

Reference Sequences

RefSeq Acc Id:

ENSRNOT00000027264 ⟹ ENSRNOP00000027264

RefSeq Status:

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
Rnor_6.0 Ensembl	9	17,949,764 - 17,988,509 (+)	Ensembl

RefSeq Acc Id:

NM_053527 ⟹ NP_445979

RefSeq Status:

PROVISIONAL

Type:

CODING

Position:

Rat Assembly	Chr	Position (strand)	Source
mRatBN7.2	9	15,564,949 - 15,603,453 (+)	NCBI
Rnor_6.0	9	17,949,764 - 17,988,514 (+)	NCBI
Rnor_5.0	9	16,838,171 - 16,876,921 (+)	NCBI
RGSC_v3.4	9	11,165,631 - 11,204,135 (+)	RGD
Celera	9	13,308,462 - 13,346,957 (+)	RGD

Sequence:

show sequence

GGTCGCTCTTGGAGGAAGTGGCCTCTTTGCGTCCCGTGACCGAAGCGCCGTTACTACTTTCTCG
AAGCTCCACTCGGCCGCTTGCCGGACACTCCGCCGCCAAGATGCCCCGGATTATGATCAAAGGG
GGCGTGTGGAGGAATACGGAGGATGAAATTCTTAAAGCAGCGGTAATGAAATATGGGAAAAACC
AGTGGTCTAGGATTGCCTCATTGCTGCATAGGAAATCGGCAAAGCAGTGCAAAGCCAGATGGTA
CGAATGGCTGGACCCAAGTATTAAGAAAACTGAATGGTCCAGAGAAGAGGAAGAAAAGCTCTTG
CACTTGGCCAAGCTGATGCCAACGCAGTGGAGGACCATTGCTCCAATCATAGGAAGGACAGCAG
CCCAGTGCTTGGAGCACTATGAATTCCTCCTGGACAAAACTGCCCAAAGGGACAATGAAGAGGA
AACAACAGATGACCCCCGAAAACTTAAGCCTGGAGAGATAGATCCAAATCCAGAAACCAAACCA
GCCCGGCCTGATCCAATTGACATGGATGAGGATGAACTTGAGATGCTTTCTGAGGCTCGAGCCC
GTTTGGCCAATACTCAAGGAAAGAAGGCTAAGAGGAAAGCAAGAGAAAAGCAGTTGGAAGAAGC
AAGGCGCCTTGCTGCCCTCCAGAAAAGACGGGAACTTCGAGCAGCTGGCATAGAGATTCAGAAG
AAAAGGAAAAAGAAGAGAGGAGTTGATTATAATGCTGAAATCCCATTTGAAAAAAAGCCTGCTC
TTGGTTTTTATGATACTTCTGAGGAGAATTACCAGGCCCTTGATGCTGATTTCAGGAAATTACG
ACAGCAGGATCTTGACGGGGAGCTAAGATCTGAAAAAGAAGGAAGAGATAGAAAAAAAGACAAA
CAGCATTTAAAAAGGAAAAAAGAATCTGATTTACCATCTGCTATCCTTCAAACTAGTGGTGTCT
CTGAGTTTACTAAAAAGAGAAGCAAACTTGTGCTGCCTGCCCCTCAGATTTCAGATGCTGAACT
CCAGGAAGTTGTCAAGGTAGGCCAGGCCAGTGAAGTTGCACGGCAGACTGCGGAGGAGTCTGGG
ATCACAAACTCTGCTTCTAGCACTCTCCTGTCTGAGTACAATGTCACAAACAACAGCATTGCTC
TGAGAACACCACGGACTCCAGCCTCCCAAGACAGGATTCTACAGGAAGCTCAGAACCTCATGGC
CTTGACCAATGTGGACACTCCACTGAAAGGTGGGCTTAACACCCCACTGCACGAGAGTGACTTC
TCTGGTGTGACGCCACAGCGGCAGGTTGTGCAGACTCCAAATACGGTTCTGTCTACCCCTTTCA
GGACTCCTTCTAATGGAGCTGAAGGGCTGACTCCCCGGAGTGGAACAACCCCGAAACCAGTCAC
TAACGCCACCCCAGGTAGAACACCACTTAGAGACAAATTAAACATTAATCCAGAGGATGGAATG
GCAGACTACAGTGACCCCTCTTACGTGAAGCAGATGGAAAGAGAATCTCGTGAACATCTCCGTC
TAGGGTTGTTAGGCCTCCCTGCACCGAAGAATGATTTTGAAATTGTTCTGCCAGAAAATGCGGA
GAAGGAACTGGAAGAACGTGAAATGGATGACACGTACATCGAGGATGCTGCTGATGTGGATGCT
CGAAAGCAGGCCATACGAGATGCTGAGCGTGTAAAGGAAATGAAACGAATGCACAAAGCTGTTC
AGAAGGATCTACCCAGACCGTCTGAAGTAAATGAAACTATTTTAAGACCTTTAAATGTAGAACC
ACCTCTAACAGATTTGCAGAAAAGTGAGGAACTGATCAAAAAAGAGATGATTACGATGCTTCAT
TATGACCTGCTGCATCACCCCTACGAGCCGTCTGGGAATAAGAAAGGGAAAAACGTCGGGTTTG
CTACCAACAATTCAGAGCACATTACCTATCTTGAGCATAGCCCTTATGAGAAGTTCTCCAAAGA
GGATCTAAAAAAGGCCCAGGATGTTCTGGTGCAAGAGATGGAAGTGGTAAAACAAGGAATGAGC
CACGGAGAACTCTCCAGTGAAGCTTACAACCAGGTGTGGGAGGAATGCTACAGTCAAGTCCTCT
ATCTTCCTGCTCAGAGCCGCTACACACGGGCTAATCTTGCTAGCAAAAAGGACAGAATTGAATC
ACTTGAAAAGAGACTTGAGATAAACAGGGGTCACATGACAACAGAAGCCAAGAGAGCTGCAAAG
ATGGAAAAAAAGATGAAGATTTTGCTGGGTGGTTACCAGTCCCGCGCCATGGGGCTCCTGAAGC
AGCTGAACGACCTGTGGGACCAAATCGAGCAGGCGCACCTGGAGCTGCGCACCTTTGAGGAACT
CAAGAAACACGAAGACTCTGCTATTCCCCGTAGGCTAGAGTGTCTAAAGGAAGATGTGCAGCGG
CAACAGGAAAGAGAGAAAGAGCTTCAGCAAAGATATGCGGATTTGCTGATGGAGAAAGAGACTT
TACAGGCAAAGTTCTGAAGCACAGAGGACGCTCTGCCTCAGAAGAACTAGTTGCTGGTTTCGTA
CTCAGCAAGGCCGAGACTGACCTTTCTCCTCATTGACAAAGTCACCCAGCACCTGTGGGCTCTC
GGTTGCTTGTTTTGAATGATACTGATCTTGCGTGTTCTGTGTTACAAACTTGGACTCCAGGATA
ATAAGGGTTTAAATTATCCAGATGCTCATTCTTTGCCAGTGTCATATTTACAAAATTTCGTAGT
TTAGGCCTTTAATTTAAAAAGCCTGATTTTAAATACTGCCTGCAAGTAAACCCTTGAATAAAAA
GAACATGTGAAGAAAAAAAAAAAAAAAAAAA

hide sequence

Protein Sequences


Protein RefSeqs	NP_445979	(Get FASTA)	NCBI Sequence Viewer
GenBank Protein	AAD05365	(Get FASTA)	NCBI Sequence Viewer
	AAI61839	(Get FASTA)	NCBI Sequence Viewer
	EDM18727	(Get FASTA)	NCBI Sequence Viewer
	O08837	(Get FASTA)	NCBI Sequence Viewer

Reference Sequences

RefSeq Acc Id:

NP_445979 ⟸ NM_053527

- UniProtKB:

O08837 (UniProtKB/Swiss-Prot), B1WBQ0 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MPRIMIKGGVWRNTEDEILKAAVMKYGKNQWSRIASLLHRKSAKQCKARWYEWLDPSIKKTEWS
REEEEKLLHLAKLMPTQWRTIAPIIGRTAAQCLEHYEFLLDKTAQRDNEEETTDDPRKLKPGEI
DPNPETKPARPDPIDMDEDELEMLSEARARLANTQGKKAKRKAREKQLEEARRLAALQKRRELR
AAGIEIQKKRKKKRGVDYNAEIPFEKKPALGFYDTSEENYQALDADFRKLRQQDLDGELRSEKE
GRDRKKDKQHLKRKKESDLPSAILQTSGVSEFTKKRSKLVLPAPQISDAELQEVVKVGQASEVA
RQTAEESGITNSASSTLLSEYNVTNNSIALRTPRTPASQDRILQEAQNLMALTNVDTPLKGGLN
TPLHESDFSGVTPQRQVVQTPNTVLSTPFRTPSNGAEGLTPRSGTTPKPVTNATPGRTPLRDKL
NINPEDGMADYSDPSYVKQMERESREHLRLGLLGLPAPKNDFEIVLPENAEKELEEREMDDTYI
EDAADVDARKQAIRDAERVKEMKRMHKAVQKDLPRPSEVNETILRPLNVEPPLTDLQKSEELIK
KEMITMLHYDLLHHPYEPSGNKKGKNVGFATNNSEHITYLEHSPYEKFSKEDLKKAQDVLVQEM
EVVKQGMSHGELSSEAYNQVWEECYSQVLYLPAQSRYTRANLASKKDRIESLEKRLEINRGHMT
TEAKRAAKMEKKMKILLGGYQSRAMGLLKQLNDLWDQIEQAHLELRTFEELKKHEDSAIPRRLE
CLKEDVQRQQEREKELQQRYADLLMEKETLQAKF

hide sequence

RefSeq Acc Id:

ENSRNOP00000027264 ⟸ ENSRNOT00000027264

Protein Domains

HTH myb-type

Transcriptome

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

Promoters

RGD ID:

13696548

Promoter ID:

EPDNEW_R7072

Type:

multiple initiation site

Name:

Cdc5l_1

Description:

cell division cycle 5-like

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	9	17,949,752 - 17,949,812	EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)

ACI/EurMcwi (MCW)

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

ACI/EurMcwi (RGD)

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

ACI/N (MCW)

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

BBDP/Wor (RGD)

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

BN/SsN (MCW)

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

Buf/N (MCW)

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

COP/CrCrl (MCW & UW)

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

F344/NCrl (RGD)

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

F344/NRrrc (MCW)

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

FHH/EurMcwi (MCW)

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

FHH/EurMcwi (RGD)

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

FHL/EurMcwi (MCW)

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

FHL/EurMcwi (RGD)

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

GH/OmrMcwi (MCW)

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

GK/Ox (RGD)

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

LE/Stm (RGD)

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

LEW/Crl (RGD)

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

LEW/NCrlBR (RGD)

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

LH/MavRrrc (RGD)

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

LL/MavRrrc (RGD)

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

LN/MavRrrc (RGD)

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

M520/N (MCW)

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

MHS/Gib (RGD)

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

MNS/Gib (RGD)

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

MR/N (MCW)

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

SBH/Ygl (MCW)

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

SBH/Ygl (RGD)

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

SBN/Ygl (MCW)

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

SBN/Ygl (RGD)

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

SHR/NHsd (RGD)

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

SHRSP/Gcrc (RGD)

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

SR/JrHsd (MCW)

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

SR/JrHsd (RGD)

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

SS/Jr (RGD)

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

SS/JrHsdMcwi (MCW)

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

SS/JrHsdMcwi (RGD)

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

WAG/Rij (RGD)

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

WKY/Gcrc (RGD)

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

WKY/N (MCW)

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

WKY/NCrl (RGD)

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

WKY/NHsd (RGD)

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

WN/N (MCW)

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

Damaging Variants

Assembly: Rnor_6.0

Chromosome	Start Pos	End Pos	Reference Nucleotide	Variant Nucleotide	Variant Type	Strain
9	17975859	17975860	A	C	snv	WKY/NHsd (RGD)
9	17975864	17975865	C	A	snv	WKY/NHsd (RGD)
9	17975865	17975866	C	T	snv	WKY/NHsd (RGD)

Additional Information

External Database Links

Database	Acc Id	Source(s)
AGR Gene	RGD:70892	AgrOrtholog
Ensembl Genes	ENSRNOG00000019975	Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein	ENSRNOP00000027264	ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript	ENSRNOT00000027264	ENTREZGENE, UniProtKB/Swiss-Prot
IMAGE_CLONE	IMAGE:7125496	IMAGE-MGC_LOAD
	IMAGE:9101355	IMAGE-MGC_LOAD
InterPro	Cdc5p/Cef1	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Homeobox-like_sf	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	Myb_dom	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
	SANT/Myb	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report	rno:85434	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE	MGC:187349	IMAGE-MGC_LOAD
	MGC:93301	IMAGE-MGC_LOAD
NCBI Gene	85434	ENTREZGENE
Pfam	Myb_Cef	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen	Cdc5l	PhenoGen
PROSITE	HTH_MYB	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART	SANT	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt	B1WBQ0	ENTREZGENE, UniProtKB/TrEMBL
	CDC5L_RAT	UniProtKB/Swiss-Prot, ENTREZGENE

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2013-01-23	Cdc5l	cell division cycle 5-like	Cdc5l	CDC5 cell division cycle 5-like (S. pombe)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2008-09-26	Cdc5l	CDC5 cell division cycle 5-like (S. pombe)	Cdc5l	cell division cycle 5-like (S. pombe)	Nomenclature updated to reflect human and mouse nomenclature	1299863	APPROVED
2002-07-09	Cdc5l	cell division cycle 5-like (S. pombe)			Symbol and Name updated to reflect Human and Mouse nomenclature	70877	APPROVED

RGD Curation Notes

Note Type	Note	Reference
gene_physical_interaction	binds the leucine zipper domain of DAP-like kinase (Dlk), binding occurs via the Cdc5l C-terminal region between residues 500 and 802	619664
gene_regulation	differential display shows transcription upregulated by prolactin	61637

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

RGD Manual Annotations

Imported Annotations - KEGG (archival)