Phox2b (paired like homeobox 2B) - Rat Genome Database

Name: Phox2b
Creator: Rat Genome Database
License: Creative Commons CC BY 4.0
Keywords: Rat Gene RGD Genome

Gene: Phox2b (paired like homeobox 2B) Ictidomys tridecemlineatus

Analyze

Symbol:

Phox2b

Name:

paired like homeobox 2B

RGD ID:

12480903

Description:

ENCODES a protein that exhibits DNA binding (inferred); DNA-binding transcription activator activity, RNA polymerase II-specific (inferred); DNA-binding transcription factor activity, RNA polymerase II-specific (inferred); INVOLVED IN cell development (ortholog); cell differentiation in hindbrain (ortholog); cell population proliferation (ortholog); ASSOCIATED WITH colorectal cancer (ortholog); congenital central hypoventilation syndrome (ortholog); Congenital Central Hypoventilation Syndrome 1 (ortholog); FOUND IN chromatin (inferred); nucleoplasm (inferred); nucleus (inferred)

Type:

protein-coding

RefSeq Status:

MODEL

Previously known as:

paired mesoderm homeobox protein 2B

RGD Orthologs

Alliance Genes

More Info

more info ...

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_024405285	37,322,562 - 37,326,296 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936482	8,972,433 - 8,975,284 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936482	8,972,433 - 8,975,284 (-)	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

colorectal cancer (ISO)

congenital central hypoventilation syndrome (ISO)

Congenital Central Hypoventilation Syndrome 1 (ISO)

Crohn's disease (ISO)

genetic disease (ISO)

Hereditary Neoplastic Syndromes (ISO)

Hirschsprung Disease Ganglioneuroblastoma (ISO)

Hirschsprung's disease (ISO)

Hyperglycinemia, Lactic Acidosis, and Seizures (ISO)

Hypoventilation (ISO)

neuroblastoma (ISO)

Neuroblastoma 2 (ISO)

ovarian cancer (ISO)

Gene Ontology Annotations Click to see Annotation Detail View

Biological Process

autonomic nervous system development (IEA)

brainstem development (IEA)

cell development (IEA,ISO)

cell differentiation in hindbrain (IEA,ISO)

cell population proliferation (IEA,ISO)

cellular response to BMP stimulus (IEA,ISO)

cellular response to carbon dioxide (ISO)

dopaminergic neuron differentiation (IEA)

efferent axon development in a lateral line nerve (IEA,ISO)

enteric nervous system development (IEA)

glial cell differentiation (IEA,ISO)

hindbrain tangential cell migration (IEA,ISO)

inner ear development (IEA,ISO)

medullary reticular formation development (IEA)

membrane depolarization (ISO)

motor neuron migration (IEA,ISO)

negative regulation of neuron differentiation (IEA,ISO)

negative regulation of type B pancreatic cell proliferation (IEA,ISO)

neural crest cell migration involved in autonomic nervous system development (IEA)

neuron differentiation (IEA,ISO)

noradrenergic neuron development (IEA)

noradrenergic neuron differentiation (IEA,ISO)

parasympathetic nervous system development (IEA)

positive regulation of cold-induced thermogenesis (IEA)

positive regulation of neuron differentiation (IEA,ISO)

positive regulation of transcription by RNA polymerase II (IEA)

regulation of DNA-templated transcription (IEA)

regulation of gene expression (IEA)

regulation of respiratory gaseous exchange by nervous system process (IEA)

regulation of transcription by RNA polymerase II (IEA,ISO)

respiratory system development (IEA)

response to activity (ISO)

retrotrapezoid nucleus neuron differentiation (IEA)

skeletal muscle cell differentiation (IEA,ISO)

sympathetic ganglion development (IEA)

sympathetic nervous system development (IEA)

type B pancreatic cell proliferation (IEA,ISO)

Cellular Component

chromatin (IEA)

nucleoplasm (IEA)

nucleus (IEA)

Molecular Function

DNA binding (IEA)

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

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

protein binding (ISO)

RNA polymerase II cis-regulatory region sequence-specific DNA binding (IEA)

RNA polymerase II transcription regulatory region sequence-specific DNA binding (IEA)

sequence-specific double-stranded DNA binding (IEA)

References

Additional References at PubMed

PMID:22301074	PMID:30032202

Genomics

Comparative Map Data

Phox2b
(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_024405285	37,322,562 - 37,326,296 (+)	NCBI		HiC_Itri_2
SpeTri2.0 Ensembl	NW_004936482	8,972,433 - 8,975,284 (-)	Ensembl	SpeTri2.0	SpeTri2.0 Ensembl
SpeTri2.0	NW_004936482	8,972,433 - 8,975,284 (-)	NCBI	SpeTri2.0	SpeTri2.0		SpeTri2.0

PHOX2B
(Homo sapiens - human)

Human Assembly	Chr	Position (strand)	Source	Genome Browsers
Human Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCh38	4	41,744,082 - 41,748,725 (-)	NCBI	GRCh38	GRCh38	hg38	GRCh38
GRCh38.p14 Ensembl	4	41,744,082 - 41,748,725 (-)	Ensembl	GRCh38		hg38	GRCh38
GRCh37	4	41,746,099 - 41,750,742 (-)	NCBI	GRCh37	GRCh37	hg19	GRCh37
Build 36	4	41,440,857 - 41,445,744 (-)	NCBI	NCBI36	Build 36	hg18	NCBI36
Build 34	4	41,587,027 - 41,591,915	NCBI
Celera	4	42,190,119 - 42,195,007 (-)	NCBI		Celera
Cytogenetic Map	4	p13	NCBI
HuRef	4	41,068,497 - 41,073,385 (-)	NCBI		HuRef
CHM1_1	4	41,746,637 - 41,751,525 (-)	NCBI		CHM1_1
T2T-CHM13v2.0	4	41,717,855 - 41,722,498 (-)	NCBI		T2T-CHM13v2.0

Phox2b
(Mus musculus - house mouse)

Mouse Assembly	Chr	Position (strand)	Source	Genome Browsers
Mouse Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCm39	5	67,251,751 - 67,256,399 (-)	NCBI	GRCm39	GRCm39	mm39
GRCm39 Ensembl	5	67,251,742 - 67,256,644 (-)	Ensembl		GRCm39 Ensembl
GRCm38	5	67,094,397 - 67,099,126 (-)	NCBI	GRCm38	GRCm38	mm10	GRCm38
GRCm38.p6 Ensembl	5	67,094,399 - 67,099,301 (-)	Ensembl	GRCm38		mm10	GRCm38
MGSCv37	5	67,485,636 - 67,490,365 (-)	NCBI	GRCm37	MGSCv37	mm9	NCBIm37
MGSCv36	5	67,373,532 - 67,378,261 (-)	NCBI		MGSCv36	mm8
Celera	5	64,399,184 - 64,403,936 (-)	NCBI		Celera
Cytogenetic Map	5	C3.1	NCBI
cM Map	5	35.95	NCBI

Phox2b
(Rattus norvegicus - Norway rat)

Rat Assembly	Chr	Position (strand)	Source	Genome Browsers
Rat Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
GRCr8	14	41,420,011 - 41,424,527 (+)	NCBI		GRCr8
mRatBN7.2	14	41,066,012 - 41,069,202 (+)	NCBI	mRatBN7.2	mRatBN7.2
mRatBN7.2 Ensembl	14	41,066,264 - 41,068,978 (+)	Ensembl		mRatBN7.2 Ensembl
Rnor_6.0	14	42,711,169 - 42,718,707 (+)	NCBI	Rnor6.0	Rnor_6.0	rn6	Rnor6.0
Rnor_6.0 Ensembl	14	42,714,315 - 42,717,010 (+)	Ensembl	Rnor6.0		rn6	Rnor6.0
Rnor_5.0	14	42,510,540 - 42,514,526 (+)	NCBI	Rnor5.0	Rnor_5.0	rn5	Rnor5.0
RGSC_v3.4	14	43,675,180 - 43,677,970 (+)	NCBI	RGSC3.4	RGSC_v3.4	rn4	RGSC3.4
Celera	14	40,218,744 - 40,226,258 (+)	NCBI		Celera
Cytogenetic Map	14	p11	NCBI

Phox2b
(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_004955443	5,935,975 - 5,938,747 (+)	Ensembl	ChiLan1.0
ChiLan1.0	NW_004955443	5,935,975 - 5,938,747 (+)	NCBI	ChiLan1.0	ChiLan1.0

PHOX2B
(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	3	41,930,596 - 41,933,522 (-)	NCBI		NHGRI_mPanPan1-v2
NHGRI_mPanPan1	4	42,123,959 - 42,126,885 (-)	NCBI		NHGRI_mPanPan1
Mhudiblu_PPA_v0	4	36,070,924 - 36,074,532 (-)	NCBI	Mhudiblu_PPA_v0	Mhudiblu_PPA_v0	panPan3
PanPan1.1	4	41,918,047 - 41,922,449 (-)	NCBI	panpan1.1	PanPan1.1	panPan2
PanPan1.1 Ensembl	4	41,919,742 - 41,922,449 (-)	Ensembl	panpan1.1		panPan2

PHOX2B
(Canis lupus familiaris - dog)

Dog Assembly	Chr	Position (strand)	Source	Genome Browsers
Dog Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
CanFam3.1	13	38,865,963 - 38,869,912 (-)	NCBI	CanFam3.1	CanFam3.1	canFam3	CanFam3.1
CanFam3.1 Ensembl	13	38,865,995 - 38,869,854 (-)	Ensembl	CanFam3.1		canFam3	CanFam3.1
Dog10K_Boxer_Tasha	13	38,841,873 - 38,845,270 (-)	NCBI		Dog10K_Boxer_Tasha
ROS_Cfam_1.0	13	39,356,028 - 39,359,380 (-)	NCBI		ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl	13	39,356,056 - 39,359,022 (-)	Ensembl		ROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1	13	39,045,848 - 39,049,183 (-)	NCBI		UMICH_Zoey_3.1
UNSW_CanFamBas_1.0	13	39,156,421 - 39,159,820 (-)	NCBI		UNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0	13	39,631,094 - 39,634,496 (-)	NCBI		UU_Cfam_GSD_1.0

PHOX2B
(Sus scrofa - pig)

Pig Assembly	Chr	Position (strand)	Source	Genome Browsers
Pig Assembly	Chr	Position (strand)	Source	JBrowse	NCBI	UCSC	Ensembl
Sscrofa11.1 Ensembl	8	32,842,145 - 32,846,127 (-)	Ensembl	Sscrofa11.1		susScr11	Sscrofa11.1
Sscrofa11.1	8	32,841,425 - 32,846,133 (-)	NCBI	Sscrofa11.1	Sscrofa11.1	susScr11	Sscrofa11.1

PHOX2B
(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	27	8,602,764 - 8,608,052 (+)	NCBI	ChlSab1.1	ChlSab1.1	chlSab2
ChlSab1.1 Ensembl	27	8,603,484 - 8,606,299 (+)	Ensembl	ChlSab1.1	ChlSab1.1 Ensembl	chlSab2
Vero_WHO_p1.0	NW_023666047	54,920,668 - 54,926,074 (+)	NCBI	Vero_WHO_p1.0	Vero_WHO_p1.0

Phox2b
(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_004624761	25,234,372 - 25,237,102 (+)	Ensembl	HetGla_female_1.0	HetGla_female_1.0 Ensembl	hetGla2
HetGla 1.0	NW_004624761	25,234,048 - 25,238,725 (+)	NCBI	HetGla_female_1.0	HetGla 1.0	hetGla2

Expression

Sequence

Nucleotide Sequences


RefSeq Transcripts	XM_021722709	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles
GenBank Nucleotide	JAESOR010000344	(Get FASTA)	NCBI Sequence Viewer	Search GEO for Microarray Profiles

RefSeq Acc Id:

ENSSTOT00000029087 ⟹ ENSSTOP00000019806

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
SpeTri2.0 Ensembl	NW_004936482	8,972,433 - 8,975,284 (-)	Ensembl

RefSeq Acc Id:

XM_021722709 ⟹ XP_021578384

Type:

CODING

Position:

Squirrel Assembly	Chr	Position (strand)	Source
HiC_Itri_2	NW_024405285	37,322,562 - 37,326,296 (+)	NCBI
SpeTri2.0	NW_004936482	8,972,433 - 8,975,284 (-)	NCBI

Sequence:

show sequence

ATGTATAAAATGGAATATTCTTACCTCAATTCCTCTGCCTACGAGTCCTGTATGGCTGGGATGG
ACACCTCGAGCCTGGCTTCAGCCTATGCTGACTTCAGTTCCTGCAGCCAGGCCAGTGGCTTCCA
GTATAACCCGATAAGGACCACTTTTGGGGCCACGTCCGGCTGCCCGTCCCTCACACCGGGATCC
TGCAGCCTCGGCACCCTCAGGGACCACCAGAGCAGTCCGTACGCCGCAGTTCCTTACAAACTCT
TCACCGACCACGGCGGCCTCAACGAGAAACGCAAGCAGCGGCGCATCCGCACCACTTTCACAAG
TGCGCAGCTCAAAGAGCTGGAGAGGGTCTTCGCTGAGACTCACTACCCGGACATCTACACCCGG
GAGGAGTTAGCCCTGAAGATCGACCTCACAGAGGCGCGAGTCCAGGTGTGGTTCCAGAACCGCC
GCGCCAAGTTTCGCAAGCAGGAGCGCGCAGCAGCTGCTGCAGCGGCCGCAGCCAAGAACGGCTC
CTCGGGAAAAAAGTCTGATTCCTCCCGGGACGACGAGAGCAAAGAGGCCAAGAGCACCGACCCG
GACAGCACTGNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNNN
NNNNNNNNNNCGGCGGCGGGAGGCCTGGCTGCGGCTGGGGGTCCTGGACAAGGCTGGGCTCCCG
GCCCCGGCCCCATCACCTCCATCCCAGATTCGCTCGGTGGCCCCTTCGCCAGCGTCCTATCTTC
ACTCCAAAGACCCAACGGTGCCAAAGCCGCCTTAGTGAAGAGCAGTATGTTCTGA

hide sequence

Protein Sequences


Protein RefSeqs	XP_021578384	(Get FASTA)	NCBI Sequence Viewer
Ensembl Protein	ENSSTOP00000019806.2

RefSeq Acc Id:

XP_021578384 ⟸ XM_021722709

- Sequence:

show sequence

MYKMEYSYLNSSAYESCMAGMDTSSLASAYADFSSCSQASGFQYNPIRTTFGATSGCPSLTPGS
CSLGTLRDHQSSPYAAVPYKLFTDHGGLNEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTR
EELALKIDLTEARVQVWFQNRRAKFRKQERAAAAAAAAAKNGSSGKKSDSSRDDESKEAKSTDP
DSTXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXXX
XXXXAAGGLAAAGGPGQGWAPGPGPITSIPDSLGGPFASVLSSLQRPNGAKAALVKSSMF

hide sequence

RefSeq Acc Id:

ENSSTOP00000019806 ⟸ ENSSTOT00000029087

Protein Domains

Homeobox

Additional Information

External Database Links

Database	Acc Id	Source(s)
Ensembl Genes	ENSSTOG00000022720	Ensembl, UniProtKB/TrEMBL
Ensembl Transcript	ENSSTOT00000029087.2	UniProtKB/TrEMBL
Gene3D-CATH	Homeodomain-like	UniProtKB/TrEMBL
InterPro	Homeobox-like_sf	UniProtKB/TrEMBL
	Homeobox_CS	UniProtKB/TrEMBL
	Homeobox_dom	UniProtKB/TrEMBL
NCBI Gene	Phox2b	ENTREZGENE
PANTHER	HOMEOBOX PROTEIN ARISTALESS	UniProtKB/TrEMBL
	PAIRED MESODERM HOMEOBOX PROTEIN 2B	UniProtKB/TrEMBL
Pfam	Homeodomain	UniProtKB/TrEMBL
PROSITE	HOMEOBOX_1	UniProtKB/TrEMBL
	HOMEOBOX_2	UniProtKB/TrEMBL
SMART	HOX	UniProtKB/TrEMBL
Superfamily-SCOP	SSF46689	UniProtKB/TrEMBL
UniProt	I3N610_ICTTR	UniProtKB/TrEMBL

Nomenclature History

Date	Current Symbol	Current Name	Previous Symbol	Previous Name	Description	Reference	Status
2018-07-24	Phox2b	paired like homeobox 2B		paired like homeobox 2b	Symbol and/or name change	5135510	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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