C1orf52 (chromosome 1 open reading frame 52) - Rat Genome Database

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Gene: C1orf52 (chromosome 1 open reading frame 52) Homo sapiens
Analyze
Symbol: C1orf52
Name: chromosome 1 open reading frame 52
RGD ID: 1346419
HGNC Page HGNC:24871
Description: Enables RNA binding activity. Located in nucleoplasm.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: BCL10-associated gene protein; FLJ44982; gm117; hypothetical protein LOC148423; RP11-234D19.1; UPF0690 protein C1orf52
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38185,249,953 - 85,259,662 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl185,249,953 - 85,259,672 (-)EnsemblGRCh38hg38GRCh38
GRCh37185,715,636 - 85,725,345 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36185,490,244 - 85,497,913 (-)NCBINCBI36Build 36hg18NCBI36
Build 34185,429,676 - 85,437,346NCBI
Celera183,960,049 - 83,969,784 (-)NCBICelera
Cytogenetic Map1p22.3NCBI
HuRef183,826,606 - 83,836,344 (-)NCBIHuRef
CHM1_1185,831,237 - 85,840,978 (-)NCBICHM1_1
T2T-CHM13v2.0185,091,053 - 85,100,781 (-)NCBIT2T-CHM13v2.0
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

Cellular Component
nucleoplasm  (IDA)

Molecular Function
RNA binding  (HDA)

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
2. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:11891061   PMID:15489334   PMID:15592455   PMID:16344560   PMID:16710414   PMID:17081983   PMID:19773279   PMID:20360068   PMID:22658674   PMID:24999758   PMID:26186194   PMID:26496610  
PMID:27609421   PMID:28514442   PMID:29395067   PMID:29568061   PMID:30021884   PMID:33916271   PMID:33957083   PMID:33961781   PMID:34079125   PMID:34189442   PMID:34597346   PMID:34672954  
PMID:35439318   PMID:35944360   PMID:37827155  


Genomics

Comparative Map Data
C1orf52
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38185,249,953 - 85,259,662 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl185,249,953 - 85,259,672 (-)EnsemblGRCh38hg38GRCh38
GRCh37185,715,636 - 85,725,345 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36185,490,244 - 85,497,913 (-)NCBINCBI36Build 36hg18NCBI36
Build 34185,429,676 - 85,437,346NCBI
Celera183,960,049 - 83,969,784 (-)NCBICelera
Cytogenetic Map1p22.3NCBI
HuRef183,826,606 - 83,836,344 (-)NCBIHuRef
CHM1_1185,831,237 - 85,840,978 (-)NCBICHM1_1
T2T-CHM13v2.0185,091,053 - 85,100,781 (-)NCBIT2T-CHM13v2.0
2410004B18Rik
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm393145,643,769 - 145,650,584 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl3145,643,769 - 145,650,584 (+)EnsemblGRCm39 Ensembl
GRCm383145,938,014 - 145,944,829 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl3145,938,014 - 145,944,829 (+)EnsemblGRCm38mm10GRCm38
MGSCv373145,600,996 - 145,607,239 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv363145,875,418 - 145,881,661 (+)NCBIMGSCv36mm8
Celera3152,391,563 - 152,397,806 (+)NCBICelera
Cytogenetic Map3H2NCBI
cM Map371.03NCBI
C2h1orf52
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82237,510,974 - 237,520,346 (+)NCBIGRCr8
mRatBN7.22234,853,378 - 234,860,045 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2234,853,410 - 234,860,040 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2242,645,681 - 242,652,348 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02240,535,997 - 240,542,623 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02235,403,300 - 235,409,967 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02251,817,862 - 251,824,784 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2251,817,694 - 251,824,784 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02270,342,994 - 270,349,932 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42244,129,298 - 244,135,911 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera2226,835,470 - 226,841,562 (+)NCBICelera
Cytogenetic Map2q44NCBI
CUNH1orf52
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554238,728,750 - 8,736,738 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554238,728,976 - 8,735,511 (+)NCBIChiLan1.0ChiLan1.0
C1H1orf52
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21141,673,468 - 141,683,223 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11140,828,808 - 140,838,566 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01117,809,571 - 117,817,306 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1186,663,906 - 86,673,613 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl186,663,906 - 86,673,613 (-)Ensemblpanpan1.1panPan2
C6H1orf52
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1662,729,128 - 62,740,386 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl662,729,136 - 62,736,975 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha665,377,807 - 65,388,879 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0663,269,031 - 63,280,310 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl663,269,056 - 63,280,310 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1662,796,221 - 62,807,491 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0662,766,527 - 62,777,560 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0663,273,995 - 63,285,453 (+)NCBIUU_Cfam_GSD_1.0
CUNH1orf52
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440505895,843,813 - 95,851,686 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936608454,393 - 462,222 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936608454,354 - 462,222 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
C4H1orf52
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl4130,659,924 - 130,662,089 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.14130,659,924 - 130,690,095 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.24143,251,502 - 143,259,391 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CUNH1orf52
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12048,090,667 - 48,097,968 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603369,709,225 - 69,718,675 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
CUNH1orf52
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462474212,230,420 - 12,236,711 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462474212,230,391 - 12,236,743 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2


Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 1p31.1-13.3(chr1:72661709-107456880)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051825]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051825]|See cases [RCV000051825] Chr1:72661709..107456880 [GRCh38]
Chr1:73127392..107999502 [GRCh37]
Chr1:72899980..107801025 [NCBI36]
Chr1:1p31.1-13.3		 pathogenic
GRCh38/hg38 1p31.1-21.1(chr1:83457325-104273917)x3 copy number gain See cases [RCV000135654] Chr1:83457325..104273917 [GRCh38]
Chr1:83923008..104816539 [GRCh37]
Chr1:83695596..104618062 [NCBI36]
Chr1:1p31.1-21.1		 pathogenic
GRCh38/hg38 1p32.1-22.3(chr1:58819605-86098611)x1 copy number loss See cases [RCV000136913] Chr1:58819605..86098611 [GRCh38]
Chr1:59285277..86564294 [GRCh37]
Chr1:59057865..86336882 [NCBI36]
Chr1:1p32.1-22.3		 pathogenic
GRCh38/hg38 1p31.1-22.2(chr1:76419302-88628464)x1 copy number loss See cases [RCV000138957] Chr1:76419302..88628464 [GRCh38]
Chr1:76884987..89094147 [GRCh37]
Chr1:76657575..88866735 [NCBI36]
Chr1:1p31.1-22.2		 pathogenic
GRCh37/hg19 1p36.12-12(chr1:20608823-120546301)x3 copy number loss not provided [RCV000762767] Chr1:20608823..120546301 [GRCh37]
Chr1:1p36.12-12		 likely benign
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684)x3 copy number gain See cases [RCV000510383] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p31.1-22.1(chr1:72044544-92505091)x1 copy number loss See cases [RCV000510161] Chr1:72044544..92505091 [GRCh37]
Chr1:1p31.1-22.1		 pathogenic
GRCh37/hg19 1p31.3-22.3(chr1:64321264-88153669)x1 copy number loss See cases [RCV000511392] Chr1:64321264..88153669 [GRCh37]
Chr1:1p31.3-22.3		 pathogenic|uncertain significance
GRCh37/hg19 1p36.33-q44(chr1:849467-249224684) copy number gain See cases [RCV000510926] Chr1:849467..249224684 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:47851-249228449)x3 copy number gain not provided [RCV000736295] Chr1:47851..249228449 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p36.33-q44(chr1:82154-249218992)x3 copy number gain not provided [RCV000736305] Chr1:82154..249218992 [GRCh37]
Chr1:1p36.33-q44		 pathogenic
GRCh37/hg19 1p22.3(chr1:85679397-85786233)x3 copy number gain not provided [RCV000749055] Chr1:85679397..85786233 [GRCh37]
Chr1:1p22.3		 benign
GRCh37/hg19 1p36.22-21.1(chr1:103343285-103455144)x3 copy number gain Global developmental delay [RCV000787285] Chr1:103343285..103455144 [GRCh37]
Chr1:1p36.22-21.1		 uncertain significance
Single allele deletion not provided [RCV000844927] Chr1:66085524..88429789 [GRCh37]
Chr1:1p31.3-22.2		 not provided
GRCh37/hg19 1p31.3-22.3(chr1:67851233-86101340)x1 copy number loss not provided [RCV000846441] Chr1:67851233..86101340 [GRCh37]
Chr1:1p31.3-22.3		 pathogenic
GRCh37/hg19 1p31.1-22.2(chr1:80804502-89490384)x3 copy number gain not provided [RCV001259073] Chr1:80804502..89490384 [GRCh37]
Chr1:1p31.1-22.2		 likely pathogenic
GRCh37/hg19 1p31.3-22.1(chr1:68180293-92731957) copy number loss not specified [RCV002053392] Chr1:68180293..92731957 [GRCh37]
Chr1:1p31.3-22.1		 pathogenic
GRCh37/hg19 1p22.3(chr1:85667594-85875622)x3 copy number gain not provided [RCV002472538] Chr1:85667594..85875622 [GRCh37]
Chr1:1p22.3		 likely pathogenic
GRCh37/hg19 1p22.3(chr1:85513068-86105378)x3 copy number gain not specified [RCV003986340] Chr1:85513068..86105378 [GRCh37]
Chr1:1p22.3		 uncertain significance
GRCh37/hg19 1p31.1-22.3(chr1:73616197-87012961)x1 copy number loss not provided [RCV003885448] Chr1:73616197..87012961 [GRCh37]
Chr1:1p31.1-22.3		 likely pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:597
Count of miRNA genes:377
Interacting mature miRNAs:416
Transcripts:ENST00000294661, ENST00000344356, ENST00000471115, ENST00000493514
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.

Markers in Region
SHGC-75084  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh37185,717,652 - 85,717,780UniSTSGRCh37
Build 36185,490,240 - 85,490,368RGDNCBI36
Celera183,962,065 - 83,962,193RGD
Cytogenetic Map1p22.3UniSTS
HuRef183,828,622 - 83,828,750UniSTS
TNG Radiation Hybrid Map148649.0UniSTS
GeneMap99-GB4 RH Map1240.96UniSTS
Whitehead-RH Map1243.7UniSTS
NCBI RH Map1566.2UniSTS


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 sensory system visual system adipose tissue appendage entire extraembryonic component pharyngeal arch
High
Medium 1719 1272 1050 128 1094 93 3118 860 2987 208 1370 1520 51 1 1044 1720 5 2
Low 720 1714 676 496 852 372 1239 1337 747 211 90 93 124 160 1068 1
Below cutoff 5 5

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000294661
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl185,249,953 - 85,259,672 (-)Ensembl
RefSeq Acc Id: ENST00000344356   ⟹   ENSP00000345092
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl185,257,443 - 85,259,633 (-)Ensembl
RefSeq Acc Id: ENST00000471115   ⟹   ENSP00000419417
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl185,249,953 - 85,259,662 (-)Ensembl
RefSeq Acc Id: ENST00000493514
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl185,257,443 - 85,259,633 (-)Ensembl
RefSeq Acc Id: NM_198077   ⟹   NP_932343
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38185,249,953 - 85,259,662 (-)NCBI
GRCh37185,715,636 - 85,725,355 (-)RGD
Build 36185,490,244 - 85,497,913 (-)NCBI Archive
Celera183,960,049 - 83,969,784 (-)RGD
HuRef183,826,606 - 83,836,344 (-)ENTREZGENE
CHM1_1185,831,237 - 85,840,978 (-)NCBI
T2T-CHM13v2.0185,091,053 - 85,100,781 (-)NCBI
Sequence:
RefSeq Acc Id: NR_024113
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38185,249,953 - 85,259,662 (-)NCBI
GRCh37185,715,636 - 85,725,355 (-)RGD
Celera183,960,049 - 83,969,784 (-)RGD
HuRef183,826,606 - 83,836,344 (-)ENTREZGENE
CHM1_1185,831,237 - 85,840,978 (-)NCBI
T2T-CHM13v2.0185,091,053 - 85,100,781 (-)NCBI
Sequence:
RefSeq Acc Id: XR_008485932
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.0185,096,741 - 85,100,781 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_932343   ⟸   NM_198077
- UniProtKB: Q8TDK5 (UniProtKB/Swiss-Prot),   B3KX89 (UniProtKB/Swiss-Prot),   Q8TDK6 (UniProtKB/Swiss-Prot),   Q8N6N3 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSP00000419417   ⟸   ENST00000471115
RefSeq Acc Id: ENSP00000345092   ⟸   ENST00000344356

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8N6N3-F1-model_v2 AlphaFold Q8N6N3 1-182 view protein structure

Promoters
RGD ID:6856060
Promoter ID:EPDNEW_H1194
Type:initiation region
Name:C1orf52_1
Description:chromosome 1 open reading frame 52
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh38185,259,654 - 85,259,714EPDNEW
RGD ID:6784802
Promoter ID:HG_KWN:3472
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:NM_198077,   NR_024113,   UC001DKX.2,   UC009WCN.1
Position:
Human AssemblyChrPosition (strand)Source
Build 36185,497,634 - 85,498,134 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:24871 AgrOrtholog
COSMIC C1orf52 COSMIC
Ensembl Genes ENSG00000162642 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENST00000294661 ENTREZGENE
  ENST00000344356.5 UniProtKB/Swiss-Prot
  ENST00000471115 ENTREZGENE
  ENST00000471115.6 UniProtKB/Swiss-Prot
GTEx ENSG00000162642 GTEx
HGNC ID HGNC:24871 ENTREZGENE
Human Proteome Map C1orf52 Human Proteome Map
InterPro DUF4660 UniProtKB/Swiss-Prot
KEGG Report hsa:148423 UniProtKB/Swiss-Prot
NCBI Gene 148423 ENTREZGENE
PANTHER UPF0690 PROTEIN C1ORF52 UniProtKB/Swiss-Prot
  UPF0690 PROTEIN C1ORF52 UniProtKB/Swiss-Prot
Pfam DUF4660 UniProtKB/Swiss-Prot
PharmGKB PA142672503 PharmGKB
UniProt B3KX89 ENTREZGENE
  CA052_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE
  Q8TDK5 ENTREZGENE
  Q8TDK6 ENTREZGENE
UniProt Secondary B3KX89 UniProtKB/Swiss-Prot
  Q8TDK5 UniProtKB/Swiss-Prot
  Q8TDK6 UniProtKB/Swiss-Prot