Phaf1 (phagosome assembly factor 1) - Rat Genome Database

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Gene: Phaf1 (phagosome assembly factor 1) Rattus norvegicus
Analyze
Symbol: Phaf1 (Ensembl: RGD621098)
Name: phagosome assembly factor 1 (Ensembl:similar to RIKEN cDNA D230025D16Rik)
RGD ID: 621098
Description: Enables PDZ domain binding activity and glutamate receptor binding activity. Involved in Golgi to plasma membrane protein transport. Located in dendrite; synaptic vesicle membrane; and trans-Golgi network. Orthologous to human PHAF1 (phagosome assembly factor 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; acetamide; ammonium chloride.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: Lin-10; lin-10 homolog; lin-10 homolog (C. elegans); lin-10 protein homolog; lin-10 protein homolog (C. elegans); Lin10; RGD621098; similar to RIKEN cDNA D230025D16Rik; UPF0183 protein C16orf70 homolog
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
mRatBN7.21933,101,453 - 33,138,920 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1933,101,490 - 33,138,914 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1939,916,452 - 39,944,320 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01940,570,360 - 40,598,228 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01942,859,996 - 42,887,888 (+)NCBIRnor_WKY
Rnor_6.01937,179,850 - 37,207,714 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1937,179,814 - 37,215,404 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01948,045,949 - 48,074,039 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41935,038,531 - 35,066,395 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11935,043,411 - 35,071,276 (+)NCBI
Celera1932,530,706 - 32,558,571 (+)NCBICelera
Cytogenetic Map19q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Interaction of rat lin-10 with brain-enriched F-actin-binding protein, neurabin-II/spinophilin. Ide N, etal., Biochem Biophys Res Commun. 1998 Mar 6;244(1):258-62.
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. The PDZ domains of mLin-10 regulate its trans-Golgi network targeting and the surface expression of AMPA receptors. Stricker NL and Huganir RL, Neuropharmacology 2003 Nov;45(6):837-48.
Additional References at PubMed
PMID:9480860  


Genomics

Comparative Map Data
Phaf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21933,101,453 - 33,138,920 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1933,101,490 - 33,138,914 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1939,916,452 - 39,944,320 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.01940,570,360 - 40,598,228 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.01942,859,996 - 42,887,888 (+)NCBIRnor_WKY
Rnor_6.01937,179,850 - 37,207,714 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1937,179,814 - 37,215,404 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01948,045,949 - 48,074,039 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41935,038,531 - 35,066,395 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11935,043,411 - 35,071,276 (+)NCBI
Celera1932,530,706 - 32,558,571 (+)NCBICelera
Cytogenetic Map19q11NCBI
PHAF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381667,109,941 - 67,148,544 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1667,109,941 - 67,148,544 (+)EnsemblGRCh38hg38GRCh38
GRCh371667,143,844 - 67,182,447 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361665,701,416 - 65,739,943 (+)NCBINCBI36Build 36hg18NCBI36
Celera1651,652,166 - 51,690,685 (+)NCBICelera
Cytogenetic Map16q22.1NCBI
HuRef1653,017,619 - 53,055,959 (+)NCBIHuRef
CHM1_11668,551,219 - 68,589,761 (+)NCBICHM1_1
T2T-CHM13v2.01672,904,233 - 72,942,836 (+)NCBIT2T-CHM13v2.0
Phaf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398105,951,779 - 105,979,685 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8105,951,777 - 105,979,685 (+)EnsemblGRCm39 Ensembl
GRCm388105,225,146 - 105,253,053 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8105,225,145 - 105,253,053 (+)EnsemblGRCm38mm10GRCm38
MGSCv378107,749,088 - 107,776,953 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368108,114,434 - 108,142,182 (+)NCBIMGSCv36mm8
Celera8109,447,942 - 109,475,836 (+)NCBICelera
Cytogenetic Map8D3NCBI
Phaf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554849,466,880 - 9,491,182 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554849,466,880 - 9,491,176 (-)NCBIChiLan1.0ChiLan1.0
PHAF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11666,845,175 - 66,883,222 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1666,845,181 - 66,883,213 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01647,455,363 - 47,494,241 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PHAF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1582,215,511 - 82,244,216 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl582,216,897 - 82,244,362 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha582,204,381 - 82,232,597 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0582,650,083 - 82,680,720 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl582,649,851 - 82,680,551 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1582,476,150 - 82,504,581 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0582,161,482 - 82,189,912 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0582,800,984 - 82,829,418 (-)NCBIUU_Cfam_GSD_1.0
Phaf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934941,965,030 - 41,992,478 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493647517,596,671 - 17,626,758 (+)EnsemblSpeTri2.0
SpeTri2.0NW_00493647517,596,703 - 17,624,084 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PHAF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl627,757,582 - 27,792,565 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1627,757,576 - 27,792,564 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
PHAF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1560,308,832 - 60,346,599 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl560,306,538 - 60,345,714 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604723,060,960 - 23,096,717 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Phaf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474619,170,115 - 19,197,608 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Phaf1
132 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:112
Count of miRNA genes:83
Interacting mature miRNAs:106
Transcripts:ENSRNOT00000020003
Prediction methods: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
9590298Uminl5Urine mineral level QTL 53.590.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)19136824771Rat
8552935Pigfal10Plasma insulin-like growth factor 1 level QTL 105.7blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)19136824771Rat
9590250Scort11Serum corticosterone level QTL 1123.450.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)19136824771Rat
9590090Insglur8Insulin/glucose ratio QTL 810.810.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)19136824771Rat
9589102Slep13Serum leptin concentration QTL 134.630.001blood leptin amount (VT:0005667)plasma leptin level (CMO:0000781)1956937445569374Rat
8694186Bw152Body weight QTL 1523.340.001body mass (VT:0001259)body weight gain (CMO:0000420)1956937445569374Rat
7247442Uae39Urinary albumin excretion QTL 39urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19218792746708701Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
61447Tcas1Tongue tumor susceptibility QTL 16.08tongue integrity trait (VT:0010553)squamous cell carcinoma of the tongue maximum tumor diameter (CMO:0001875)19231612147316121Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
724518Uae19Urinary albumin excretion QTL 195.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)19745724942983518Rat
724565Tcas5Tongue tumor susceptibility QTL 510.04tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)19997775339654489Rat
61423Cia14Collagen induced arthritis QTL 143joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)191082797043544039Rat
1558656Prcs1Prostate cancer susceptibility QTL 15prostate integrity trait (VT:0010571)percentage of study population developing ventral prostate tumorous lesions during a period of time (CMO:0000943)191511459834521833Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1331788Rf45Renal function QTL 452.818kidney blood vessel physiology trait (VT:0100012)absolute change in renal blood flow rate (CMO:0001168)191560502346559041Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
1549835Tcas7Tongue tumor susceptibility QTL 70.001tongue integrity trait (VT:0010553)squamous cell carcinoma of the head and neck tumor number (CMO:0001876)192481797839654489Rat
1354600Salc2Saline consumption QTL 29.910.001drinking behavior trait (VT:0001422)saline drink intake rate (CMO:0001627)192753020737947399Rat
1354607Gmadr1Adrenal mass QTL 15.83adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)192753020737947399Rat
1354633Bw28Body weight QTL 286.04body mass (VT:0001259)body weight (CMO:0000012)192753020737947399Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat


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 3 31 39 23 19 23 8 11 74 35 35 11 8
Low 12 18 18 18 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000020003   ⟹   ENSRNOP00000020003
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1933,101,544 - 33,130,136 (+)Ensembl
Rnor_6.0 Ensembl1937,179,846 - 37,207,714 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000085891   ⟹   ENSRNOP00000069827
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1933,101,490 - 33,138,914 (+)Ensembl
Rnor_6.0 Ensembl1937,179,814 - 37,215,404 (+)Ensembl
RefSeq Acc Id: NM_139040   ⟹   NP_620609
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21933,101,529 - 33,129,393 (+)NCBI
Rnor_6.01937,179,850 - 37,207,714 (+)NCBI
Rnor_5.01948,045,949 - 48,074,039 (+)NCBI
RGSC_v3.41935,038,531 - 35,066,395 (+)RGD
Celera1932,530,706 - 32,558,571 (+)RGD
Sequence:
RefSeq Acc Id: XM_039097463   ⟹   XP_038953391
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21933,101,454 - 33,138,920 (+)NCBI
RefSeq Acc Id: XM_039097464   ⟹   XP_038953392
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21933,101,453 - 33,127,886 (+)NCBI
RefSeq Acc Id: XM_039097465   ⟹   XP_038953393
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21933,101,454 - 33,127,769 (+)NCBI
RefSeq Acc Id: XR_005496611
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21933,101,454 - 33,138,920 (+)NCBI
RefSeq Acc Id: XR_005496612
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21933,101,454 - 33,138,917 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_620609   ⟸   NM_139040
- UniProtKB: G3V7W8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000069827   ⟸   ENSRNOT00000085891
RefSeq Acc Id: ENSRNOP00000020003   ⟸   ENSRNOT00000020003
RefSeq Acc Id: XP_038953392   ⟸   XM_039097464
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038953391   ⟸   XM_039097463
- Peptide Label: isoform X1
- UniProtKB: A0A0G2JWC6 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038953393   ⟸   XM_039097465
- Peptide Label: isoform X3

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-O08654-F1-model_v2 AlphaFold O08654 1-422 view protein structure

Transcriptome

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

Promoters
RGD ID:13701077
Promoter ID:EPDNEW_R11590
Type:multiple initiation site
Name:RGD621098_1
Description:similar to RIKEN cDNA D230025D16Rik
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01937,179,811 - 37,179,871EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:621098 AgrOrtholog
BioCyc Gene G2FUF-5854 BioCyc
Ensembl Genes ENSRNOG00000014668 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000020003 ENTREZGENE
  ENSRNOP00000020003.2 UniProtKB/TrEMBL
  ENSRNOP00000069827 ENTREZGENE
  ENSRNOP00000069827.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020003 ENTREZGENE
  ENSRNOT00000020003.3 UniProtKB/TrEMBL
  ENSRNOT00000085891 ENTREZGENE
  ENSRNOT00000085891.2 UniProtKB/TrEMBL
InterPro UPF0183 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  UPF0183/BROMI UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:207123 UniProtKB/Swiss-Prot
NCBI Gene 207123 ENTREZGENE
PANTHER PTHR13465 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR13465:SF2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam UPF0183 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Phaf1 PhenoGen
UniProt A0A0G2JWC6 ENTREZGENE, UniProtKB/TrEMBL
  CP070_RAT UniProtKB/Swiss-Prot
  G3V7W8 ENTREZGENE, UniProtKB/TrEMBL
  O08654 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Phaf1  phagosome assembly factor 1  RGD621098  similar to RIKEN cDNA D230025D16Rik  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-31 RGD621098  similar to RIKEN cDNA D230025D16Rik  Lin10  lin-10 homolog (C. elegans)  symbol and name updated in response to new information regarding the homologous C. elegans protein (P34692) 1299863 APPROVED
2006-03-30 Lin10  lin-10 homolog (C. elegans)    lin-10 protein homolog (C. elegans)  Name updated 1299863 APPROVED
2005-01-20 Lin10  lin-10 protein homolog (C. elegans)    lin-10 protein homolog  Name updated 1299863 APPROVED
2002-08-07 Lin10  lin-10 protein homolog      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_other This gene was originally thought to be homologous to C. elegans Lin-10 (PMID:2159938) but that has since been shown to be untrue. The nucleotide and amino acid sequences have little similarity to Lin-10. 1578523
gene_physical_interaction interaction with glutamate receptors occurs via the Lin10 PDZ domain 1302287
gene_product member of the UPF0183 family of uncharacterized proteins 1578523