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

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Gene: Phox2b (paired-like homeobox 2b) Rattus norvegicus
Analyze
Symbol: Phox2b
Name: paired-like homeobox 2b
RGD ID: 1560582
Description: Predicted to enable DNA-binding transcription activator activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Involved in cellular response to carbon dioxide; membrane depolarization; and response to activity. Located in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in colorectal cancer; congenital central hypoventilation syndrome; and neuroblastoma. Orthologous to human PHOX2B (paired like homeobox 2B); INTERACTS WITH bisphenol A; copper atom; copper(0).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: NBPhox; neuroblastoma Phox; paired mesoderm homeobox protein 2B
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21441,066,012 - 41,069,202 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1441,066,264 - 41,068,978 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01442,711,169 - 42,718,707 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1442,714,315 - 42,717,010 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01442,510,540 - 42,514,526 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41443,675,180 - 43,677,970 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1440,218,744 - 40,226,258 (+)NCBICelera
Cytogenetic Map14p11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
autonomic nervous system development  (ISO)
brainstem development  (ISO)
cell development  (ISO)
cell differentiation in hindbrain  (ISO)
cell population proliferation  (ISO)
cellular response to BMP stimulus  (ISO)
cellular response to carbon dioxide  (IEP)
dopaminergic neuron differentiation  (ISO)
efferent axon development in a lateral line nerve  (ISO)
enteric nervous system development  (IBA,ISO)
glial cell differentiation  (ISO)
hindbrain tangential cell migration  (ISO)
inner ear development  (ISO)
medullary reticular formation development  (ISO)
membrane depolarization  (IEP)
motor neuron migration  (ISO)
negative regulation of cell population proliferation  (ISO)
negative regulation of neuron differentiation  (ISO)
negative regulation of type B pancreatic cell proliferation  (ISO)
neural crest cell migration involved in autonomic nervous system development  (ISO)
neuron differentiation  (ISO)
neuron migration  (ISO)
noradrenergic neuron development  (ISO)
noradrenergic neuron differentiation  (ISO)
parasympathetic nervous system development  (ISO)
positive regulation of cold-induced thermogenesis  (ISO,ISS)
positive regulation of neuron differentiation  (ISO)
positive regulation of transcription by RNA polymerase II  (ISO)
regulation of gene expression  (ISO)
regulation of respiratory gaseous exchange by nervous system process  (ISO)
regulation of transcription by RNA polymerase II  (IBA,ISO)
respiratory system development  (ISO)
response to activity  (IEP)
retrotrapezoid nucleus neuron differentiation  (ISO)
skeletal muscle cell differentiation  (ISO)
sympathetic ganglion development  (ISO)
sympathetic nervous system development  (ISO)
type B pancreatic cell proliferation  (ISO)

Cellular Component
chromatin  (ISO)
cytoplasm  (IDA)
nucleoplasm  (IEA,ISO)
nucleus  (IDA,ISO)

References

References - curated
# Reference Title Reference Citation
1. Polyalanine expansion and frameshift mutations of the paired-like homeobox gene PHOX2B in congenital central hypoventilation syndrome. Amiel J, etal., Nat Genet. 2003 Apr;33(4):459-61. Epub 2003 Mar 17.
2. Acute exercise-induced activation of Phox2b-expressing neurons of the retrotrapezoid nucleus in rats may involve the hypothalamus. Barna BF, etal., Neuroscience. 2014 Jan 31;258:355-63. doi: 10.1016/j.neuroscience.2013.11.031. Epub 2013 Nov 26.
3. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
4. Phox2b expression in the aldosterone-sensitive HSD2 neurons of the NTS. Geerling JC, etal., Brain Res. 2008 Aug 21;1226:82-8. doi: 10.1016/j.brainres.2008.05.072. Epub 2008 Jun 7.
5. Central nervous system distribution of the transcription factor Phox2b in the adult rat. Kang BJ, etal., J Comp Neurol. 2007 Aug 10;503(5):627-41.
6. PHOX2B mutation-confirmed congenital central hypoventilation syndrome in a Chinese family: presentation from newborn to adulthood. Lee P, etal., Chest. 2009 Feb;135(2):537-544. doi: 10.1378/chest.08-1664.
7. A novel PITX2 mutation in a Chinese family with Axenfeld-Rieger syndrome. Li D, etal., Mol Vis. 2008;14:2205-10. Epub 2008 Dec 5.
8. Identification of novel DNA methylation markers in colorectal cancer using MIRA-based microarrays. Li H, etal., Oncol Rep. 2012 Jul;28(1):99-104. doi: 10.3892/or.2012.1779. Epub 2012 Apr 23.
9. A case of congenital central hypoventilation syndrome in a three-generation family with non-polyalanine repeat PHOX2B mutation. Low KJ, etal., Pediatr Pulmonol. 2014 Oct;49(10):E140-3. doi: 10.1002/ppul.23051. Epub 2014 May 5.
10. PHOX2B is a suppressor of neuroblastoma metastasis. Naftali O, etal., Oncotarget. 2016 Mar 1;7(9):10627-37. doi: 10.18632/oncotarget.7056.
11. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
12. CO2-sensitive preinspiratory neurons of the parafacial respiratory group express Phox2b in the neonatal rat. Onimaru H, etal., J Neurosci. 2008 Nov 26;28(48):12845-50. doi: 10.1523/JNEUROSCI.3625-08.2008.
13. Impaired ventilatory and thermoregulatory responses to hypoxic stress in newborn phox2b heterozygous knock-out mice. Ramanantsoa N, etal., Front Physiol. 2011 Sep 23;2:61. doi: 10.3389/fphys.2011.00061. eCollection 2011.
14. GOA pipeline RGD automated data pipeline
15. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
16. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
17. Comprehensive gene review and curation RGD comprehensive gene curation
18. Molecular analysis of congenital central hypoventilation syndrome. Sasaki A, etal., Hum Genet. 2003 Dec;114(1):22-6. Epub 2003 Oct 18.
Additional References at PubMed
PMID:9374403   PMID:9758704   PMID:10360575   PMID:10395798   PMID:10536054   PMID:12885554   PMID:15580626   PMID:15733675   PMID:16033425   PMID:16144830   PMID:16280598   PMID:16319924  
PMID:16854219   PMID:17021186   PMID:17922007   PMID:18094025   PMID:18440993   PMID:18506029   PMID:19573018   PMID:19793887   PMID:19940179   PMID:20217327   PMID:20844141   PMID:21068058  
PMID:22147266   PMID:22521817   PMID:24363384   PMID:26147470   PMID:28673717   PMID:30448454   PMID:34973291  


Genomics

Comparative Map Data
Phox2b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21441,066,012 - 41,069,202 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1441,066,264 - 41,068,978 (+)EnsemblmRatBN7.2 Ensembl
Rnor_6.01442,711,169 - 42,718,707 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1442,714,315 - 42,717,010 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01442,510,540 - 42,514,526 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41443,675,180 - 43,677,970 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1440,218,744 - 40,226,258 (+)NCBICelera
Cytogenetic Map14p11NCBI
PHOX2B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38441,744,082 - 41,748,725 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl441,744,082 - 41,748,725 (-)EnsemblGRCh38hg38GRCh38
GRCh37441,746,099 - 41,750,742 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36441,440,857 - 41,445,744 (-)NCBINCBI36Build 36hg18NCBI36
Build 34441,587,027 - 41,591,915NCBI
Celera442,190,119 - 42,195,007 (-)NCBICelera
Cytogenetic Map4p13NCBI
HuRef441,068,497 - 41,073,385 (-)NCBIHuRef
CHM1_1441,746,637 - 41,751,525 (-)NCBICHM1_1
T2T-CHM13v2.0441,717,855 - 41,722,498 (-)NCBIT2T-CHM13v2.0
Phox2b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39567,251,740 - 67,256,469 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl567,251,742 - 67,256,644 (-)EnsemblGRCm39 Ensembl
GRCm38567,094,397 - 67,099,126 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl567,094,399 - 67,099,301 (-)EnsemblGRCm38mm10GRCm38
MGSCv37567,485,636 - 67,490,365 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36567,373,532 - 67,378,261 (-)NCBIMGSCv36mm8
Celera564,399,184 - 64,403,936 (-)NCBICelera
Cytogenetic Map5C3.1NCBI
cM Map535.95NCBI
Phox2b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554435,935,975 - 5,938,747 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554435,935,975 - 5,938,747 (+)NCBIChiLan1.0ChiLan1.0
PHOX2B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1441,918,047 - 41,922,449 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl441,919,742 - 41,922,449 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0436,070,924 - 36,074,532 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PHOX2B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11338,865,963 - 38,869,912 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1338,865,995 - 38,869,854 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1338,841,873 - 38,845,270 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01339,356,028 - 39,359,380 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.11339,045,848 - 39,049,183 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01339,156,421 - 39,159,820 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01339,631,094 - 39,634,496 (-)NCBIUU_Cfam_GSD_1.0
Phox2b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440528537,322,562 - 37,326,296 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049364828,972,433 - 8,975,284 (-)EnsemblSpeTri2.0
SpeTri2.0NW_0049364828,972,433 - 8,975,284 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PHOX2B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl832,842,145 - 32,846,127 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1832,841,425 - 32,846,133 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PHOX2B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1278,602,764 - 8,608,052 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl278,603,484 - 8,606,299 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604754,920,668 - 54,926,074 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Phox2b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462476125,234,372 - 25,237,102 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462476125,234,048 - 25,238,725 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Phox2b
3 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:172
Count of miRNA genes:127
Interacting mature miRNAs:140
Transcripts:ENSRNOT00000003136, ENSRNOT00000071497
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634352Apr6Acute phase response QTL 63.7blood interleukin-6 amount (VT:0008595)plasma interleukin-6 level (CMO:0001927)14141131407Rat
1581500Renag1Renal agenesis QTL 1kidney development trait (VT:0000527)percentage of study population developing unilateral renal agenesis during a period of time (CMO:0000940)14817066868298175Rat
1358296Ael3Aortic elastin QTL 33.70.00051aorta elastin amount (VT:0003905)aortic elastin14826709053267090Rat
2302045Pia39Pristane induced arthritis QTL 394.90.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G2a level (CMO:0002116)14826709053267090Rat
631839Niddm37Non-insulin dependent diabetes mellitus QTL 373.37blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)141103062295876975Rat
71117Niddm17Non-insulin dependent diabetes mellitus QTL 172.35blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)141759376142336881Rat
631262Tcas4Tongue tumor susceptibility QTL 47.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)141762256142337007Rat
2313397Coatc1Coat color QTL1coat/hair pigmentation trait (VT:0010463)coat/hair color measurement (CMO:0001808)141854133263541332Rat
61420Pia6Pristane induced arthritis QTL 64.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)141863134542337007Rat
10755459Coatc15Coat color QTL 150.01681coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)141983694464836944Rat
70187Pancm5Pancreatic morphology QTL 516.7pancreas mass (VT:0010144)pancreas weight to body weight ratio (CMO:0000630)143032009280829842Rat
1300154Bp189Blood pressure QTL 1893.04arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)143088377768757901Rat
2313048Bss84Bone structure and strength QTL 843.10.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143766971982669719Rat
2313084Bss83Bone structure and strength QTL 832.90.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143766971982669719Rat
2313089Bss81Bone structure and strength QTL 813.40.0001body length (VT:0001256)body length, nose to rump (CMO:0000079)143766971982669719Rat
2313100Bss82Bone structure and strength QTL 8230.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143766971982669719Rat
738037Hcas6Hepatocarcinoma susceptibility QTL 62.93liver integrity trait (VT:0010547)liver nonremodeling tumorous lesion volume to total liver volume ratio (CMO:0001464)143905723783368335Rat
70214Niddm28Non-insulin dependent diabetes mellitus QTL 284.06blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)143999825175582726Rat
631523Pia13Pristane induced arthritis QTL 133.3joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)144079346098037301Rat

Markers in Region
MARC_17835-17836:1025010330:1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21441,065,882 - 41,066,372 (+)MAPPERmRatBN7.2
Rnor_6.01442,713,934 - 42,714,423NCBIRnor6.0
Rnor_5.01442,510,394 - 42,510,883UniSTSRnor5.0
RGSC_v3.41443,674,799 - 43,675,288UniSTSRGSC3.4
Celera1440,221,509 - 40,221,998UniSTS
Cytogenetic Map14p11UniSTS


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 1 2
Low 3 6 10 2 2 32 2 9
Below cutoff 14 4 4 1 4 1 3 11 7 11 2 1

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000084095   ⟹   ENSRNOP00000075383
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1442,714,315 - 42,715,718 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000091449   ⟹   ENSRNOP00000070623
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1441,066,264 - 41,068,978 (+)Ensembl
Rnor_6.0 Ensembl1442,714,315 - 42,717,010 (+)Ensembl
RefSeq Acc Id: XM_008770167   ⟹   XP_008768389
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21441,066,012 - 41,069,202 (+)NCBI
Rnor_6.01442,711,169 - 42,718,707 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs XP_008768389 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein BAD83365 (Get FASTA)   NCBI Sequence Viewer  
  EDL90031 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: XP_008768389   ⟸   XM_008770167
- UniProtKB: A0A0G2JYE6 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070623   ⟸   ENSRNOT00000091449
RefSeq Acc Id: ENSRNOP00000075383   ⟸   ENSRNOT00000084095
Protein Domains
Homeobox

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JYE6-F1-model_v2 AlphaFold A0A0G2JYE6 1-307 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1560582 AgrOrtholog
BioCyc Gene G2FUF-15773 BioCyc
Ensembl Genes ENSRNOG00000051929 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000070623 ENTREZGENE
  ENSRNOP00000070623.2 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000091449 ENTREZGENE
  ENSRNOT00000091449.2 UniProtKB/TrEMBL
InterPro Homeobox_CS UniProtKB/TrEMBL
  Homeodomain UniProtKB/TrEMBL
  Homeodomain-like UniProtKB/TrEMBL
NCBI Gene 364152 ENTREZGENE
Pfam Homeobox UniProtKB/TrEMBL
PhenoGen Phox2b PhenoGen
PROSITE HOMEOBOX_1 UniProtKB/TrEMBL
  HOMEOBOX_2 UniProtKB/TrEMBL
SMART HOX UniProtKB/TrEMBL
Superfamily-SCOP Homeodomain_like UniProtKB/TrEMBL
UniProt A0A0G2JYE6 ENTREZGENE, UniProtKB/TrEMBL
  Q5NSW4_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Phox2b  paired-like homeobox 2b   Phox2b_predicted  paired-like homeobox 2b (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 Phox2b_predicted  paired-like homeobox 2b (predicted)  Phox2b  paired-like homeobox 2b  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 Phox2b  paired-like homeobox 2b      Symbol and Name status set to provisional 70820 PROVISIONAL