Odc1 (ornithine decarboxylase 1) - Rat Genome Database

Name: Odc1
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Odc1 (ornithine decarboxylase 1) Chinchilla lanigera

Analyze

Symbol:

Odc1

Name:

ornithine decarboxylase 1

RGD ID:

9010740

Description:

ENCODES a protein that exhibits ornithine decarboxylase activity (ortholog); protein homodimerization activity (ortholog); INVOLVED IN cell population proliferation (ortholog); kidney development (ortholog); polyamine metabolic process (ortholog); PARTICIPATES IN polyamine metabolic pathway; putrescine metabolic pathway; spermidine metabolic pathway; ASSOCIATED WITH Colonic Neoplasms (ortholog); Colorectal Neoplasms (ortholog); genetic disease (ortholog); FOUND IN cytoplasm (ortholog); cytosol (ortholog); perinuclear region of cytoplasm (ortholog)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

ornithine decarboxylase

RGD Orthologs

Alliance Genes

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_004955487	5,603,722 - 5,608,386 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955487	5,603,722 - 5,608,386 (-)	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

Colonic Neoplasms (ISO)

Colorectal Neoplasms (ISO)

genetic disease (ISO)

human immunodeficiency virus infectious disease (ISO)

Neurodevelopmental Disorder with Alopecia and Brain Abnormalities (ISO)

papilloma (ISO)

Skin Neoplasms (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

cell population proliferation (ISO)

kidney development (ISO)

polyamine metabolic process (ISO)

positive regulation of cell population proliferation (ISO)

putrescine biosynthetic process (ISO)

putrescine biosynthetic process from ornithine (ISO)

regulation of protein catabolic process (ISO)

response to virus (ISO)

Cellular Component

cytoplasm (ISO)

cytosol (ISO)

perinuclear region of cytoplasm (ISO)

Molecular Function

ornithine decarboxylase activity (ISO)

protein binding (ISO)

protein homodimerization activity (ISO)

Molecular Pathway Annotations Click to see Annotation Detail View

polyamine metabolic pathway (ISO)

putrescine metabolic pathway (ISO)

spermidine metabolic pathway (ISO)

spermine metabolic pathway (ISO)

References

References - curated

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

Additional References at PubMed

PMID:30032202

Genomics

Comparative Map Data

Odc1
(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_004955487	5,603,722 - 5,608,386 (-)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955487	5,603,722 - 5,608,386 (-)	NCBI	ChiLan1.0	ChiLan1.0

ODC1
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	2	10,439,968 - 10,448,327 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	2	10,439,968 - 10,448,327 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	2	10,580,094 - 10,588,453 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	2	10,497,959 - 10,505,904 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	2	10,531,105 - 10,539,051	NCBI
Celera	2	10,496,293 - 10,504,232 (-)	NCBI		Celera
Cytogenetic Map	2	p25.1	NCBI
HuRef	2	10,432,740 - 10,440,685 (-)	NCBI		HuRef
CHM1_1	2	10,509,903 - 10,517,848 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	2	10,469,577 - 10,477,937 (-)	NCBI		T2T-CHM13v2.0

Odc1
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	12	17,594,906 - 17,601,503 (+)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	12	17,594,795 - 17,601,506 (+)	Ensembl		GRCm39 Ensembl
GRCm38	12	17,544,808 - 17,551,502 (+)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	12	17,544,794 - 17,551,505 (+)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	12	17,551,679 - 17,558,308 (+)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	12	17,570,570 - 17,576,557 (+)	NCBI		MGSCv36	mm8
Celera	12	17,867,446 - 17,874,062 (+)	NCBI		Celera
Cytogenetic Map	12	A1.1- A1.2	NCBI
cM Map	12	8.11	NCBI

Odc1
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	6	46,058,439 - 46,065,148 (+)	NCBI		GRCr8
mRatBN7.2	6	40,329,831 - 40,336,444 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	6	40,329,964 - 40,336,440 (+)	Ensembl		mRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx	6	40,657,182 - 40,663,666 (+)	NCBI	Rnor_SHR	UTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0	6	40,971,864 - 40,978,348 (+)	NCBI	Rnor_SHRSP	UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0	6	40,405,122 - 40,411,607 (+)	NCBI	Rnor_WKY	UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0	6	42,852,529 - 42,859,142 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	6	42,852,683 - 42,859,927 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	6	52,565,188 - 52,571,773 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	6	41,309,211 - 41,315,796 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
RGSC_v3.1	6	41,312,265 - 41,318,665 (+)	NCBI
Celera	6	39,628,825 - 39,635,308 (+)	NCBI		Celera
Cytogenetic Map	6	q16	NCBI

ODC1
(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	116,062,594 - 116,072,320 (+)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	2A	116,066,565 - 116,076,289 (+)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	2A	10,443,308 - 10,451,412 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	2A	10,598,125 - 10,607,152 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	2A	10,598,125 - 10,607,152 (-)	Ensembl	panpan1.1		panPan2

ODC1
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	17	7,368,699 - 7,376,970 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	17	7,369,232 - 7,376,975 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	17	7,294,922 - 7,302,658 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	17	7,467,169 - 7,474,927 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	17	7,457,350 - 7,472,111 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	17	7,357,671 - 7,365,425 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	17	7,360,253 - 7,368,002 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	17	7,374,368 - 7,382,137 (-)	NCBI		UU_Cfam_GSD_1.0

Odc1
(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	51,826,681 - 51,831,970 (-)	NCBI		HiC_Itri_2
SpeTri2.0	NW_004936532	6,581,717 - 6,587,116 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

ODC1
(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	126,087,242 - 126,096,051 (+)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	3	126,087,013 - 126,095,644 (+)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

ODC1
(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	97,173,338 - 97,182,253 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
Vero_WHO_p1.0	NW_023666045	15,117,435 - 15,125,604 (-)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Odc1
(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_004624865	4,851,878 - 4,860,558 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624865	4,851,565 - 4,858,868 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_013504362	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	AGCD01059341	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
	GBDK01136620	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSCLAT00000003045 ⟹ ENSCLAP00000002983

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0 Ensembl	NW_004955487	5,603,722 - 5,608,386 (-)	Ensembl

RefSeq Acc Id:

XM_013504362 ⟹ XP_013359816

Type:

CODING

Position:

Chinchilla Assembly	Chr	Position (strand)	Source
ChiLan1.0	NW_004955487	5,603,722 - 5,608,386 (-)	NCBI

Sequence:

show sequence

GCGGAGGCGGCGGGCGGCCCAGCGCCGCGGCCCGGCTCGGCTCCGGCTCCGGCTCCGGCTCGGC
GCGGTCTCGGCCCGGTCCCGGCTCCGGCGCGTCTCCATGGGGCCGGCCCGCGGCGCCCGGGCGC
TCTGAGCGAGAACGTTTCCAGTGCTGCTCTGAGGACTTGGGGCTTGGAGTTCCTGGACCATCAG
CCTTGTGAGCAACCAGAAGGGTCCCTGGAATTCCATTGCCTAGTTTCCCACGTGTGGAGAAACC
ATGACCGGCGCCCGCAGTGAGGAGTTTGACTGCTGCTTCCTGGATGAAGGCTTCACAGCCAAGG
ACATCCTGGACCAGAAGATCAACGAGGTCATGTCCTCTGATGACAAGGATGCCTTCTATGTCGC
AGACCTTGGGGATGTTCTCAAGAAGCATCTGCGCTGGCGGAAAGCTCTCCCTCGAGTCACCCCC
TTCTATGCAGTCAAGTGCAATGACAGCAGAGCTATTGTGAAGACCCTCGCCGCCATCGGGACAG
GATTTGACTGCGCGAGCAAGACGGAGATCCAGCTGGTGCAGAGTCTCGGGGTACCCCCGGAAAG
GATCATCTACGCCAACCCCTGCAAGCAGGTGTCACAGATCAAGTATGCCGCCAGCAGTGGGGTC
CAGATGATGACCTTCGACAGCGAAGTCGAGCTGCTGAAAGTGGCCCGAGCACATCCGAAGGCCA
AGTTAGTCTTACGGATCGCTACTGACGACTCCAAAGCTGTCTGTCGCCTTAGTGTGAAATTCGG
TGCCACGCTGAAAACCAGCAGACTCCTTTTGGAACGGGCAAAAGAGCTACATATCGATGTCATT
GGTGTCAGCTTCCACGTGGGGAGTGGCTGCACTGACCCCGAGACCTTTGTGCAGGCTGTGGCGG
ACGCACGCTGTGTCTTTGACATGGGGGCTGAGGTCGGCTTCCACATGTATCTGCTTGATATTGG
AGGGGGCTTTCCTGGATCCGAGGATGCAAAGCTCAAGTTTGAAGAGATCACCAGTGTGATCAAC
CCTGCACTGGACAAATGCTTCCCGGTGGACTCAGGTGTGCGGATCATAGCTGAGCCTGGCAGGT
ACTACGTGGCGTCGGCGTTCACCCTTGCGGTGAACATCATAGCCAAGAAGCTGGTGCTGAAGGA
GCAGGCTGGCTCGGACGATGAGGAGGAGGCGAGCGAGCCGACCTTCATGTACTACGTGAATGAT
GGTGTGTACGGCTCGTTCAACTGCATCCTGTATGACCACGCACACGTGAGGCCGCTGCTGCAGA
AGAGACCCAAGCCCGACGAGAAGCACTACTCATCCAGCATCTGGGGCCCCACGTGCGACGGCCT
GGACCGCATTGTGGAGCGCTGCGACCTGCCCGAGCTGCATGTGGGTGACTGGATGCTTTTCGAG
AACATGGGCGCCTACACCGTTGCTGCGGCCTCCACCTTCAACGGCTTCCAGAGGCCAACCATCT
ACTATGTGATGTCGCGACCGACGTGGCAGCTTGTGCAGCGTGTCCGGAGCCACAGCTTCCCACC
CGGGGTGGAGGAGCAGGATGTCGGGCCCCTGCCTGTGCCCTGTGCCCGGGAGAGCGAGATGAAG
GGGCACACAGCGGCGCGTGCCTCCACCAGCATCAATGTGTAGCCGCCTGGAGCCACGAGCATGG
AGCTCAGCTCCATCCGCTTCGTCACTGCTAGTTCTGGGCGACTTCACAAGAGTGGGGCCGGCAC
AGCGTAGCCACATGGAGACTAGGAGACAGTCACACTTATCTGTGTTCCTATGGAAACTATTTGG
ATATTTGTTTTATATGGATTTTTATTCACTTTCACACGCTACGAAAGAGGGCCCGCAACTGCCA
AGCAAGCATTTGTAGCTTGTGCTACGGTAGTGTGGGCTGAAAGCTTAGTGTCGTGACCTGTTTT
AAAAATAAAGCCATCTTGAAAGAA

hide sequence

Protein Sequences


Protein RefSeqs	XP_013359816	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSCLAP00000002983
	ENSCLAP00000002983.1

RefSeq Acc Id:

XP_013359816 ⟸ XM_013504362

- UniProtKB:

A0A8C2UM87 (UniProtKB/TrEMBL)

- Sequence:

show sequence

MTGARSEEFDCCFLDEGFTAKDILDQKINEVMSSDDKDAFYVADLGDVLKKHLRWRKALPRVTP
FYAVKCNDSRAIVKTLAAIGTGFDCASKTEIQLVQSLGVPPERIIYANPCKQVSQIKYAASSGV
QMMTFDSEVELLKVARAHPKAKLVLRIATDDSKAVCRLSVKFGATLKTSRLLLERAKELHIDVI
GVSFHVGSGCTDPETFVQAVADARCVFDMGAEVGFHMYLLDIGGGFPGSEDAKLKFEEITSVIN
PALDKCFPVDSGVRIIAEPGRYYVASAFTLAVNIIAKKLVLKEQAGSDDEEEASEPTFMYYVND
GVYGSFNCILYDHAHVRPLLQKRPKPDEKHYSSSIWGPTCDGLDRIVERCDLPELHVGDWMLFE
NMGAYTVAAASTFNGFQRPTIYYVMSRPTWQLVQRVRSHSFPPGVEEQDVGPLPVPCARESEMK
GHTAARASTSINV

hide sequence

RefSeq Acc Id:

ENSCLAP00000002983 ⟸ ENSCLAT00000003045

Protein Domains

Orn/DAP/Arg decarboxylase 2 C-terminal Orn/DAP/Arg decarboxylase 2 N-terminal

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSCLAG00000002140	Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript	ENSCLAT00000003045	ENTREZGENE
	ENSCLAT00000003045.1	UniProtKB/TrEMBL
Gene3D-CATH	3.20.20.10	UniProtKB/TrEMBL
InterPro	Ala_racemase/Decarboxylase_C	UniProtKB/TrEMBL
	De-COase2_C	UniProtKB/TrEMBL
	De-COase2_CS	UniProtKB/TrEMBL
	De-COase2_N	UniProtKB/TrEMBL
	De-COase2_pyr-phos_BS	UniProtKB/TrEMBL
	Orn/DAP/Arg_de-COase	UniProtKB/TrEMBL
	Orn_de-COase	UniProtKB/TrEMBL
	PLP-binding_barrel	UniProtKB/TrEMBL
NCBI Gene	Odc1	ENTREZGENE
PANTHER	ORNITHINE DECARBOXYLASE	UniProtKB/TrEMBL
	PTHR11482	UniProtKB/TrEMBL
Pfam	Orn_Arg_deC_N	UniProtKB/TrEMBL
	Orn_DAP_Arg_deC	UniProtKB/TrEMBL
PRINTS	ODADCRBXLASE	UniProtKB/TrEMBL
	ORNDCRBXLASE	UniProtKB/TrEMBL
PROSITE	ODR_DC_2_1	UniProtKB/TrEMBL
	ODR_DC_2_2	UniProtKB/TrEMBL
Superfamily-SCOP	SSF50621	UniProtKB/TrEMBL
	SSF51419	UniProtKB/TrEMBL
UniProt	A0A8C2UM87	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)

Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - SMPDB

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Imported Disease Annotations - ClinVar

Imported Disease Annotations - CTD

Imported Disease Annotations - OMIM

RGD Manual Annotations

Imported Annotations - SMPDB