Krt39 (keratin 39) - Rat Genome Database

Name: Krt39
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Krt39 (keratin 39) Ictidomys tridecemlineatus

Analyze

Symbol:

Krt39

Name:

keratin 39

RGD ID:

12475856

Description:

ENCODES a protein that exhibits structural molecule activity (inferred); INVOLVED IN epithelial cell differentiation (inferred); intermediate filament organization (inferred); ASSOCIATED WITH genetic disease (ortholog); FOUND IN cytoskeleton (inferred); intermediate filament (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

keratin, type I cytoskeletal 39

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):	KRT39 (keratin 39)	NCBI	Ortholog
Mus musculus (house mouse):	Krt39 (keratin 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Rattus norvegicus (Norway rat):	Krt39 (keratin 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chinchilla lanigera (long-tailed chinchilla):	Krt39 (keratin 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Pan paniscus (bonobo/pygmy chimpanzee):	KRT39 (keratin 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Canis lupus familiaris (dog):	KRT39 (keratin 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Sus scrofa (pig):	KRT39 (keratin 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Chlorocebus sabaeus (green monkey):	KRT39 (keratin 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline
Heterocephalus glaber (naked mole-rat):	Krt39 (keratin 39)	Transitive Ortholog Pipeline	Transitive Ortholog Pipeline

Latest Assembly:

SpeTri2.0 - Squirrel SpeTri2.0 Assembly

Position:

Squirrel Assembly	Chr	Position (strand)	Source	Genome Browsers
Squirrel Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
HiC_Itri_2	NW_024405602	21,153,809 - 21,162,391 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936490	15,914,243 - 15,938,516 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936490	15,914,243 - 15,943,139 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

JBrowse:

View Region in Genome Browser (JBrowse)

Model

Annotation Click to see Annotation Detail View

Disease Annotations Click to see Annotation Detail View

genetic disease (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

epithelial cell differentiation (IEA)

intermediate filament organization (IEA)

Cellular Component

cytoskeleton (IEA)

intermediate filament (IEA)

Molecular Function

protein binding (ISO)

structural molecule activity (IEA)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Krt39
(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_024405602	21,153,809 - 21,162,391 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936490	15,914,243 - 15,938,516 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936490	15,914,243 - 15,943,139 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

KRT39
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	17	40,958,417 - 40,966,948 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	17	40,958,417 - 40,966,948 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	17	39,114,669 - 39,123,200 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	17	36,368,195 - 36,376,670 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Celera	17	35,776,241 - 35,784,715 (-)	NCBI		Celera
Cytogenetic Map	17	q21.2	NCBI
HuRef	17	34,909,527 - 34,918,004 (-)	NCBI		HuRef
CHM1_1	17	39,350,411 - 39,358,891 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	17	41,822,878 - 41,831,409 (-)	NCBI		T2T-CHM13v2.0

Krt39
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	11	99,403,786 - 99,412,164 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	11	99,404,940 - 99,412,164 (-)	Ensembl		GRCm39 Ensembl
GRCm38	11	99,512,960 - 99,521,338 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	11	99,514,114 - 99,521,338 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	11	99,375,938 - 99,382,572 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	11	99,330,714 - 99,337,348 (-)	NCBI		MGSCv36	mm8
MGSCv36	11	100,294,179 - 100,300,813 (-)	NCBI		MGSCv36	mm8
Cytogenetic Map	11	D	NCBI
cM Map	11	62.92	NCBI

Krt39
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	10	84,970,096 - 84,976,701 (-)	NCBI		GRCr8
mRatBN7.2	10	84,473,946 - 84,480,552 (-)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	10	84,473,946 - 84,480,552 (-)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	10	89,423,864 - 89,430,457 (-)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	10	88,921,993 - 88,928,586 (-)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	10	84,313,966 - 84,320,559 (-)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	10	87,430,850 - 87,437,455 (-)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	10	87,430,850 - 87,437,455 (-)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	10	87,227,067 - 87,233,672 (-)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	10	88,460,258 - 88,466,863 (-)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	10	88,474,627 - 88,481,233 (-)	NCBI
Celera	10	83,213,779 - 83,220,384 (-)	NCBI		Celera
Cytogenetic Map	10	q31	NCBI

Krt39
(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_004955451	15,384,758 - 15,390,868 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955451	15,383,334 - 15,391,573 (-)	NCBI	ChiLan1.0	ChiLan1.0

KRT39
(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	19	23,984,641 - 23,993,815 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	17	25,875,124 - 25,884,231 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	17	16,316,268 - 16,326,720 (+)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	17	16,541,932 - 16,550,990 (+)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	17	16,541,932 - 16,550,990 (+)	Ensembl	panpan1.1		panPan2

KRT39
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	9	21,722,514 - 21,730,762 (+)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	9	21,722,644 - 21,729,388 (+)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	9	21,195,702 - 21,207,233 (+)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	9	22,509,299 - 22,520,831 (+)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	9	22,509,364 - 22,516,107 (+)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	9	21,290,197 - 21,301,726 (+)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	9	21,548,924 - 21,560,456 (+)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	9	21,672,700 - 21,684,236 (+)	NCBI		UU_Cfam_GSD_1.0

KRT39
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	12	21,492,253 - 21,500,375 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	12	21,491,676 - 21,500,375 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1
Sscrofa10.2	12	21,689,828 - 21,698,130 (-)	NCBI	Sscrofa10.2	Sscrofa10.2	susScr3

KRT39
(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	16	65,215,462 - 65,225,991 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	16	65,216,622 - 65,224,818 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666077	36,094,824 - 36,104,489 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Krt39
(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_female_1.0 Ensembl	NW_004624795	2,502,510 - 2,509,498 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624795	2,502,510 - 2,509,527 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_013356967	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	XR_005726963	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010000662	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSSTOT00000013186 ⟹ ENSSTOP00000011820

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936490	15,914,243 - 15,938,516 (-)	Ensembl

RefSeq Acc Id:

XM_013356967 ⟹ XP_013212421

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024405602	21,153,809 - 21,161,674 (+)	NCBI
SpeTri2.0	NW_004936490	15,914,243 - 15,943,139 (-)	NCBI

Sequence:

show sequence

ATGCCAGATTTGAGGGACCCCAATAGACCTCCAGGAGCCGAATCGGATGCAATCACACAAAAGT
ATGAGAGTGAGCTGTCTCTTCGCCAGCTGGTAGAGACGGACATCAGTGGCCTGCGTGGAATCCT
GAATGAGCTGAACCTGTGCAAATCTGATCTGGAAGCCCATGTGGAGTCTTTGAAGGAAGACCTC
CTTTGCCTTAAGAAAAGTCACGAAGAGCTCGGAGACCGACTCAATGTGGAGCTGGACACTGCCC
CCACCGTCGACCTCAACAGGGTCCTGGATGAGATGCGAAGTCAGTATGAAACGGTGCTGGCCAA
CAACCGCAGAGACGCGGAGGAATGGTTCGCCGTTCAGACAGAAGAGCTGAATCAGCAGCAGCAG
TCCAGCGTGGAGCAGCTGCAGGGCTGCCAGACGGAGATATTGGAGCTAAAACGCACGGCCAACA
CCCTGGAAATTGAGCTCCAAGCCCAGCAAAACCTGGTGCGTAAGGCAAACACAGGCTGGACACA
CGCTGTGGATACCGAGGGCTCTAGAACAACTATTTCTTCTTCAGCCTCACCCCATAACTGCTCT
GGGATTACAAATTTTAGGACCATGTCTGCTAACAACAGCTGCCAATCAACTGGCCACGAACCAA
GAACTCCCCAGAGCCGGGTCTGCCAATCCACTCATCGCCTTTGTCGCACCCCCATCTACCTCAT
AAGCAACTTCTGTGTCCATCCCTCTCTGGATGACTGCAGCTGGTTGGGTGAAGGTATCAACAGC
AACGAGAAGGAGACCATGCAGATCTTGAACGACCGCCTTGCTAACTTCCTGGAAAAGGTGCGAA
TGCTGGAACGAGAGAACGCTGAACTGGAGTGCAGAATCCAGGAAGAGCGTAACAAAGAGCTCCC
TGTCCTGTGTCCTAATTACCTGTCCTACTACACCACCATCGAGGAGCTCCAGCAGAAGATCTTG
TGTACCAAGGCTGAGAATTCCAGGCTGGTCTCACAAATTGACAACACCAAACTGGCTGCAGATG
ACTTGAGAGCCAACTATGAAGCTGAGGTGTCCCTACGCCAGCTCGTGGAGGCCGACGCCAACAG
CCTACGGAAGATCCTGGATGCACTGACCCTGAGTAAGGCTGACCTGGAGGCACGAGTGCAGTCT
CTGAAGGAGGAGCTCCTCTGCCTCAAAAACAGTCACCAAGAGGATATCAACTCCTTATGGGGGC
AGCTTGGGGACAGACTCAACATTGAAGTAACCGCAGCCCCTTCTGTGGACATAAACCAGATTCT
ACAAGAAATGAGATGTCAGTATGAGTCCATCATGGAGACAAACCGTAAAGATGTGGAACAATGG
TTCAACACCCAGATGTTGGAGCTGAATCAACAAGTGGTGACCAGCTCTCAACAGCAGCAGTGCT
CCCAGAAGGAAATCGCAGAACTGAGACGTACCGTGAATGCTCTGGAGGTGGAACTACAGGCCCA
GCACCGAATGAGAGATTCGCAGGAATGCATCCTGACAGAGACTGAGGCCCGCTACACGACCCTG
CTGGCCCAGATCCAAAGTCTGGTCCATAACCTGGAGGCTCAGCTGGCGGAGATCCGCAGTGCCC
TGGAAAGACAGAACCAGGAATGTGACATTCTGCTGGATATTAAGTCCCGGCTGGAGTGTGAGAT
TGCCACATACCGCAGCCTTCTGGAGAGCTCAGACTGCAAGCTTCCCTGTAACCCGTGTGCCACC
CGATGCAAGCCTTCCACTTGCACACCCTCCAAGCCCAGCACCGTGGAATGCACCGCCCCGGTTT
TCACATCCTCAGCCCCCAATGGGATTCTCAAGCGGTACAACGTCTGTGGACCCCCATCCCGGAT
ACTGGTTAAAATATGCACCATCACCAAGGAGATTCAGGACGGGAAGGTCATTTCTTCTCATGAA
CATGTGCAGCCTTGCTTCATCCCCAGACTTGCCAAAGTCTAA

hide sequence

RefSeq Acc Id:

XR_005726963

Type:

NON-CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024405602	21,153,809 - 21,162,391 (+)	NCBI

Protein Sequences


Protein RefSeqs	XP_013212421	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000011820.3
GenBank Protein	KAG3269013	(Get FASTA)	NCBI Sequence Viewer

RefSeq Acc Id:

XP_013212421 ⟸ XM_013356967

- UniProtKB:

I3MKJ0 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MPDLRDPNRPPGAESDAITQKYESELSLRQLVETDISGLRGILNELNLCKSDLEAHVESLKEDL
LCLKKSHEELGDRLNVELDTAPTVDLNRVLDEMRSQYETVLANNRRDAEEWFAVQTEELNQQQQ
SSVEQLQGCQTEILELKRTANTLEIELQAQQNLVRKANTGWTHAVDTEGSRTTISSSASPHNCS
GITNFRTMSANNSCQSTGHEPRTPQSRVCQSTHRLCRTPIYLISNFCVHPSLDDCSWLGEGINS
NEKETMQILNDRLANFLEKVRMLERENAELECRIQEERNKELPVLCPNYLSYYTTIEELQQKIL
CTKAENSRLVSQIDNTKLAADDLRANYEAEVSLRQLVEADANSLRKILDALTLSKADLEARVQS
LKEELLCLKNSHQEDINSLWGQLGDRLNIEVTAAPSVDINQILQEMRCQYESIMETNRKDVEQW
FNTQMLELNQQVVTSSQQQQCSQKEIAELRRTVNALEVELQAQHRMRDSQECILTETEARYTTL
LAQIQSLVHNLEAQLAEIRSALERQNQECDILLDIKSRLECEIATYRSLLESSDCKLPCNPCAT
RCKPSTCTPSKPSTVECTAPVFTSSAPNGILKRYNVCGPPSRILVKICTITKEIQDGKVISSHE
HVQPCFIPRLAKV

hide sequence

RefSeq Acc Id:

ENSSTOP00000011820 ⟸ ENSSTOT00000013186

Protein Domains

IF rod

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000013190	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000013186.3	UniProtKB/TrEMBL
Gene3D-CATH	1.20.5.170	UniProtKB/TrEMBL
	Single helix bin	UniProtKB/TrEMBL
	Vasodilator-stimulated phosphoprotein	UniProtKB/TrEMBL
InterPro	IF_conserved	UniProtKB/TrEMBL
	IF_rod_dom	UniProtKB/TrEMBL
	Keratin_I	UniProtKB/TrEMBL
NCBI Gene	Krt39	ENTREZGENE
PANTHER	KERATIN, TYPE I CYTOSKELETAL 39	UniProtKB/TrEMBL
	PTHR23239	UniProtKB/TrEMBL
Pfam	Filament	UniProtKB/TrEMBL
PRINTS	TYPE1KERATIN	UniProtKB/TrEMBL
PROSITE	IF_ROD_1	UniProtKB/TrEMBL
	IF_ROD_2	UniProtKB/TrEMBL
SMART	Filament	UniProtKB/TrEMBL
Superfamily-SCOP	Intermediate filament protein, coiled coil region	UniProtKB/TrEMBL
UniProt	I3MKJ0	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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