Phf21b (PHD finger protein 21B) - Rat Genome Database

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Gene: Phf21b (PHD finger protein 21B) Rattus norvegicus
Analyze
Symbol: Phf21b
Name: PHD finger protein 21B
RGD ID: 1308739
Description: Orthologous to human PHF21B (PHD finger protein 21B); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamiprid; bisphenol A.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: LOC300117; RGD1308739; similar to hypothetical protein BC012187
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87117,793,643 - 117,864,141 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7117,794,046 - 117,864,141 (-)EnsemblGRCr8
mRatBN7.27115,913,704 - 115,984,215 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7115,915,412 - 115,984,215 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7117,665,985 - 117,734,741 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07119,891,709 - 119,960,466 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07119,861,154 - 119,929,908 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07125,649,688 - 125,720,694 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7125,649,688 - 125,718,986 (+)Ensemblrn6Rnor6.0
Rnor_5.07125,370,846 - 125,438,318 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47122,808,454 - 122,879,651 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7112,213,870 - 112,282,352 (-)NCBICelera
RGSC_v3.17122,839,964 - 122,912,933 (-)NCBI
Cytogenetic Map7q34NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
2. GOA pipeline RGD automated data pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:15632090  


Genomics

Comparative Map Data
Phf21b
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr87117,793,643 - 117,864,141 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl7117,794,046 - 117,864,141 (-)EnsemblGRCr8
mRatBN7.27115,913,704 - 115,984,215 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl7115,915,412 - 115,984,215 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx7117,665,985 - 117,734,741 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.07119,891,709 - 119,960,466 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.07119,861,154 - 119,929,908 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.07125,649,688 - 125,720,694 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl7125,649,688 - 125,718,986 (+)Ensemblrn6Rnor6.0
Rnor_5.07125,370,846 - 125,438,318 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.47122,808,454 - 122,879,651 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera7112,213,870 - 112,282,352 (-)NCBICelera
RGSC_v3.17122,839,964 - 122,912,933 (-)NCBI
Cytogenetic Map7q34NCBI
PHF21B
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382244,881,162 - 45,010,005 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2244,881,162 - 45,010,022 (-)Ensemblhg38GRCh38
GRCh372245,277,042 - 45,405,886 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362243,655,706 - 43,784,245 (-)NCBIBuild 36Build 36hg18NCBI36
Build 342243,597,578 - 43,726,118NCBI
Celera2229,188,973 - 29,317,403 (-)NCBICelera
Cytogenetic Map22q13.31NCBI
HuRef2228,224,326 - 28,376,232 (-)NCBIHuRef
CHM1_12245,235,760 - 45,364,535 (-)NCBICHM1_1
T2T-CHM13v2.02245,364,687 - 45,493,893 (-)NCBIT2T-CHM13v2.0
Phf21b
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391584,669,577 - 84,740,330 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1584,669,582 - 84,740,250 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm381584,785,376 - 84,856,129 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1584,785,381 - 84,856,049 (-)Ensemblmm10GRCm38
MGSCv371584,615,806 - 84,686,559 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361584,613,150 - 84,683,815 (-)NCBIMGSCv36mm8
Celera1586,917,054 - 86,987,956 (-)NCBICelera
Cytogenetic Map15E2NCBI
cM Map1540.08NCBI
Phf21b
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541329,442,357 - 29,507,060 (-)Ensembl
ChiLan1.0NW_00495541329,442,357 - 29,507,060 (-)NCBIChiLan1.0ChiLan1.0
PHF21B
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22354,714,505 - 54,845,937 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12257,406,964 - 57,540,892 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02225,773,965 - 25,907,113 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12243,959,758 - 44,006,406 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2243,959,758 - 44,088,445 (-)EnsemblpanPan2panpan1.1
PHF21B
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11021,042,151 - 21,068,180 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1020,986,924 - 21,066,392 (+)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha1020,915,777 - 20,998,844 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.01021,722,328 - 21,805,422 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1021,721,607 - 21,806,414 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11021,442,069 - 21,525,097 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01021,762,329 - 21,845,707 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01021,936,652 - 22,019,622 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Phf21b
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049454,759,457 - 4,767,422 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049367182,212,741 - 2,240,530 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PHF21B
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl54,291,396 - 4,386,247 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.154,290,962 - 4,387,112 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.251,661,338 - 1,697,485 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PHF21B
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11927,353,586 - 27,501,080 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366604597,845,948 - 97,977,833 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Phf21b
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247524,544,003 - 4,605,501 (+)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_0046247524,543,998 - 4,605,501 (+)NCBIHetGla 1.0HetGla 1.0hetGla2
Phf21b
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11254,172,699 - 254,243,634 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Phf21b
262 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:79
Count of miRNA genes:70
Interacting mature miRNAs:72
Transcripts:ENSRNOT00000017906
Prediction methods:Microtar, Miranda, Rnahybrid
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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)792388565119280177Rat
1331728Bp214Blood pressure QTL 2142.825arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)782111245123048330Rat
1331731Bp216Blood pressure QTL 2162.851arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7104186212135371468Rat
70159Bp61Blood pressure QTL 610.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)773618702118618702Rat
631687Hcas1Hepatocarcinoma susceptibility QTL 13.90.001liver integrity trait (VT:0010547)liver tumorous lesion volume to total liver volume ratio (CMO:0001082)793302009131686183Rat
61397Bw17Body weight QTL 176.3body mass (VT:0001259)body weight (CMO:0000012)795485047137014596Rat
1358914Bp266Blood pressure QTL 266arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7115313999136544683Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)746307490127866166Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)785043242130043242Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)785497398130497398Rat
1549899Stresp8Stress response QTL 84.370.0008stress-related behavior trait (VT:0010451)defensive burying duration (CMO:0001961)792362341137014596Rat
2317052Aia17Adjuvant induced arthritis QTL 172.13joint integrity trait (VT:0010548)left rear ankle joint diameter (CMO:0002149)783626689128626689Rat
631529Tls2T-lymphoma susceptibility QTL 200.001thymus integrity trait (VT:0010555)percentage of study population developing T-cell lymphomas during a period of time (CMO:0001911)782111382132099989Rat
731176Glom5Glomerulus QTL 52.50.0035kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)798549867137014596Rat
7411607Foco15Food consumption QTL 150.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
631201Panci1Pancreas inflammation QTL 100.001pancreas integrity trait (VT:0010560)percentage of study population displaying chronic pancreatitis at a point in time (CMO:0001214)773557047118557047Rat
1331768Kidm10Kidney mass QTL 104.62096kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)782111245123048330Rat
2313102Bmd79Bone mineral density QTL 792.30.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)796700404118618702Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)740540077123682549Rat
1331748Bp215Blood pressure QTL 2154.043arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)7110725024135371468Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)7100548246137014596Rat
1331746Kidm9Kidney mass QTL 93.934kidney mass (VT:0002707)right kidney wet weight (CMO:0000082)782111245134948181Rat
7411654Foco25Food consumption QTL 259.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)777807807122807807Rat
2299163Iddm34Insulin dependent diabetes mellitus QTL 342.71blood glucose amount (VT:0000188)age at onset/diagnosis of type 1 diabetes mellitus (CMO:0001140)7116269196132020414Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)778682549123682549Rat
631540Bw9Body weight QTL 94.5body mass (VT:0001259)body weight (CMO:0000012)771621154119349044Rat
1358891Bp265Blood pressure QTL 2652.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)771827901136544683Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 11 66 161 91 90 59 91 59 6 352 190 11 140 80 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000017906   ⟹   ENSRNOP00000017906
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7117,795,475 - 117,864,141 (-)Ensembl
mRatBN7.2 Ensembl7115,915,412 - 115,984,215 (-)Ensembl
Rnor_6.0 Ensembl7125,649,688 - 125,718,986 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000125356   ⟹   ENSRNOP00000101108
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7117,794,046 - 117,864,141 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000129997   ⟹   ENSRNOP00000104335
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl7117,795,348 - 117,863,392 (-)Ensembl
RefSeq Acc Id: NM_001130680   ⟹   NP_001124152
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87117,795,348 - 117,864,141 (-)NCBI
mRatBN7.27115,915,412 - 115,984,215 (-)NCBI
Rnor_6.07125,649,688 - 125,718,986 (+)NCBI
Rnor_5.07125,370,846 - 125,438,318 (+)NCBI
RGSC_v3.47122,808,454 - 122,879,651 (-)RGD
Celera7112,213,870 - 112,282,352 (-)RGD
Sequence:
RefSeq Acc Id: XM_008765685   ⟹   XP_008763907
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87117,793,643 - 117,863,574 (-)NCBI
mRatBN7.27115,913,704 - 115,983,508 (-)NCBI
Rnor_6.07125,650,469 - 125,720,694 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039078846   ⟹   XP_038934774
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr87117,797,309 - 117,863,571 (-)NCBI
mRatBN7.27115,917,399 - 115,983,506 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001124152 (Get FASTA)   NCBI Sequence Viewer  
  XP_008763907 (Get FASTA)   NCBI Sequence Viewer  
  XP_038934774 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM15598 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000017906
  ENSRNOP00000017906.5
  ENSRNOP00000101108.1
  ENSRNOP00000104335
  ENSRNOP00000104335.1
RefSeq Acc Id: NP_001124152   ⟸   NM_001130680
- UniProtKB: D4A9U0 (UniProtKB/TrEMBL),   A6HTC4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008763907   ⟸   XM_008765685
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000017906   ⟸   ENSRNOT00000017906
RefSeq Acc Id: XP_038934774   ⟸   XM_039078846
- Peptide Label: isoform X2
Ensembl Acc Id: ENSRNOP00000101108   ⟸   ENSRNOT00000125356
Ensembl Acc Id: ENSRNOP00000104335   ⟸   ENSRNOT00000129997
Protein Domains
PHD-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A9U0-F1-model_v2 AlphaFold D4A9U0 1-494 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:1308739 AgrOrtholog
BioCyc Gene G2FUF-32569 BioCyc
Ensembl Genes ENSRNOG00000013067 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000017906 ENTREZGENE
  ENSRNOT00000017906.8 UniProtKB/TrEMBL
  ENSRNOT00000125356.1 UniProtKB/TrEMBL
  ENSRNOT00000129997 ENTREZGENE
  ENSRNOT00000129997.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/TrEMBL
InterPro Znf_FYVE_PHD UniProtKB/TrEMBL
  Znf_PHD UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/TrEMBL
KEGG Report rno:300117 UniProtKB/TrEMBL
NCBI Gene 300117 ENTREZGENE
PANTHER PHD FINGER PROTEIN UniProtKB/TrEMBL
  PHD FINGER PROTEIN 21B UniProtKB/TrEMBL
Pfam PHD UniProtKB/TrEMBL
PhenoGen Phf21b PhenoGen
PROSITE ZF_PHD_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000013067 RatGTEx
SMART PHD UniProtKB/TrEMBL
Superfamily-SCOP FYVE_PHD_ZnF UniProtKB/TrEMBL
UniProt A0ABK0L8P0_RAT UniProtKB/TrEMBL
  A0ABK0LLJ6_RAT UniProtKB/TrEMBL
  A6HTC4 ENTREZGENE, UniProtKB/TrEMBL
  D4A9U0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Phf21b  PHD finger protein 21B   Phf21b_predicted  PHD finger protein 21B (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Phf21b_predicted  PHD finger protein 21B (predicted)  RGD1308739_predicted  similar to hypothetical protein BC012187 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1308739_predicted  similar to hypothetical protein BC012187 (predicted)  LOC300117_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC300117_predicted  similar to hypothetical protein BC012187 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL