Cd34 (CD34 molecule) - Rat Genome Database

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Gene: Cd34 (CD34 molecule) Rattus norvegicus
Analyze
Symbol: Cd34
Name: CD34 molecule
RGD ID: 1306863
Description: Predicted to enable RNA polymerase II-specific DNA-binding transcription factor binding activity; carbohydrate binding activity; and sulfate binding activity. Involved in glomerular filtration and mesangial cell-matrix adhesion. Located in apical plasma membrane; basal plasma membrane; and lysosome. Part of glomerular endothelium fenestra. Biomarker of diabetic retinopathy. Orthologous to human CD34 (CD34 molecule); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 3-chloropropane-1,2-diol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: CD34 antigen; hematopoietic progenitor cell antigen CD34; LOC305081
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
mRatBN7.213106,480,074 - 106,499,462 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13106,480,043 - 106,499,832 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx13108,997,703 - 109,016,794 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.013110,381,536 - 110,400,621 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.013107,606,042 - 107,625,155 (+)NCBIRnor_WKY
Rnor_6.013113,691,842 - 113,711,259 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13113,691,932 - 113,711,647 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013118,531,837 - 118,551,216 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413110,877,594 - 110,896,722 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera13105,904,553 - 105,923,681 (+)NCBICelera
Cytogenetic Map13q27NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
(S)-amphetamine  (ISO)
1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane  (ISO)
1,2-dichloroethane  (ISO)
1,2-dimethylhydrazine  (ISO)
17beta-estradiol  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (EXP,ISO)
3-chloropropane-1,2-diol  (EXP)
3-Nitrobenzanthrone  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-(ethoxymethylene)-2-phenyloxazol-5-one  (ISO)
4-hydroxyphenyl retinamide  (ISO)
5-fluorouracil  (ISO)
6-propyl-2-thiouracil  (EXP)
acetic acid  (ISO)
acrylamide  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (ISO)
aminoguanidine  (ISO)
antimycin A  (ISO)
antirheumatic drug  (ISO)
Aroclor 1254  (ISO)
arsenite(3-)  (ISO)
arsenous acid  (ISO)
asbestos  (ISO)
benzo[a]pyrene  (ISO)
benzo[b]fluoranthene  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
bleomycin A2  (ISO)
bromochloroacetic acid  (ISO)
cannabidiol  (ISO)
carbon nanotube  (ISO)
CGP 52608  (ISO)
chloroquine  (ISO)
choline  (ISO)
chrysene  (ISO)
clothianidin  (ISO)
copper atom  (EXP)
copper(0)  (EXP)
crocidolite asbestos  (ISO)
Curcumol  (ISO)
daunorubicin  (EXP)
DDT  (EXP)
dextran sulfate  (ISO)
diarsenic trioxide  (ISO)
dibenz[a,h]anthracene  (ISO)
dioxygen  (ISO)
diuron  (EXP)
doxorubicin  (ISO)
endosulfan  (EXP)
erythromycin A  (ISO)
ethanol  (EXP,ISO)
folic acid  (ISO)
formaldehyde  (EXP)
fulvestrant  (ISO)
isotretinoin  (ISO)
L-ascorbic acid  (ISO)
L-methionine  (ISO)
lidocaine  (EXP)
maneb  (EXP)
melphalan  (ISO)
nickel atom  (ISO)
omacetaxine mepesuccinate  (ISO)
orlistat  (ISO)
ozone  (ISO)
paracetamol  (ISO)
paraquat  (EXP)
phorbol 13-acetate 12-myristate  (ISO)
pirinixic acid  (ISO)
prednisolone  (ISO)
Quinupristin-dalfopristin  (ISO)
rotenone  (EXP,ISO)
silicon dioxide  (EXP)
sodium arsenate  (ISO)
sodium arsenite  (ISO)
sunitinib  (ISO)
tebuconazole  (EXP)
tetrachloromethane  (ISO)
tetraphene  (ISO)
triclosan  (ISO)
valproic acid  (ISO)
valsartan  (ISO)
zoledronic acid  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process
cell motility  (ISO)
cell-cell adhesion  (ISO,ISS)
cell-matrix adhesion  (IBA)
endothelial cell proliferation  (ISO,ISS)
endothelium development  (ISO)
extracellular exosome assembly  (ISO,ISS)
glomerular endothelium development  (ISO)
glomerular filtration  (IEP,ISO)
hematopoietic stem cell proliferation  (ISO,ISS)
hemopoiesis  (ISO,ISS)
leukocyte migration  (ISO)
mesangial cell-matrix adhesion  (IEP)
metanephric glomerular mesangial cell differentiation  (ISO)
negative regulation of blood coagulation  (ISO,ISS)
negative regulation of cellular response to heat  (ISO,ISS)
negative regulation of cellular response to hypoxia  (ISO,ISS)
negative regulation of gene expression  (ISO,ISS)
negative regulation of interleukin-2 production  (ISO,ISS)
negative regulation of neuron death  (ISO,ISS)
negative regulation of nitric oxide biosynthetic process  (ISO,ISS)
negative regulation of tumor necrosis factor production  (ISO,ISS)
paracrine signaling  (ISO,ISS)
positive regulation of angiogenesis  (ISO,ISS)
positive regulation of gene expression  (ISO)
positive regulation of glial cell-derived neurotrophic factor production  (ISO)
positive regulation of granulocyte colony-stimulating factor production  (ISO,ISS)
positive regulation of interleukin-10 production  (ISO,ISS)
positive regulation of odontogenesis  (ISO,ISS)
positive regulation of transforming growth factor beta production  (ISO,ISS)
positive regulation of vasculogenesis  (ISO,ISS)
regulation of blood pressure  (ISO,ISS)
signal transduction  (ISO)
stem cell proliferation  (ISO)
tissue homeostasis  (ISO,ISS)
transdifferentiation  (ISO)
vascular wound healing  (ISO)

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Glomerular CD34 expression in short- and long-term diabetes. Acevedo LM, etal., J Histochem Cytochem. 2008 Jun;56(6):605-14. doi: 10.1369/jhc.7A7354.2008. Epub 2008 Mar 3.
2. 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.
3. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
4. Repression of microRNA-21 inhibits retinal vascular endothelial cell growth and angiogenesis via PTEN dependent-PI3K/Akt/VEGF signaling pathway in diabetic retinopathy. Lu JM, etal., Exp Eye Res. 2020 Jan;190:107886. doi: 10.1016/j.exer.2019.107886. Epub 2019 Nov 21.
5. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Nine Genes Mediate the Therapeutic Effects of Iodine-131 Radiotherapy in Thyroid Carcinoma Patients. Shuwen H, etal., Dis Markers. 2020 Jun 16;2020:9369341. doi: 10.1155/2020/9369341. eCollection 2020.
Additional References at PubMed
PMID:1868864   PMID:7525669   PMID:9042286   PMID:9324354   PMID:9815891   PMID:10337918   PMID:10943842   PMID:12714519   PMID:12900455   PMID:12939361   PMID:14597732   PMID:15249540  
PMID:15701716   PMID:15969628   PMID:16571751   PMID:17261663   PMID:17464107   PMID:17505307   PMID:17717145   PMID:17882221   PMID:19220583   PMID:19360001   PMID:19465515   PMID:19833765  
PMID:20354148   PMID:20684325   PMID:21162801   PMID:21464233   PMID:21708977   PMID:21835908   PMID:21873977   PMID:22978573   PMID:23395097   PMID:25898000   PMID:26271978   PMID:31395804  
PMID:34052675  


Genomics

Comparative Map Data
Cd34
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.213106,480,074 - 106,499,462 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl13106,480,043 - 106,499,832 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx13108,997,703 - 109,016,794 (+)NCBIRnor_SHR
UTH_Rnor_SHRSP_BbbUtx_1.013110,381,536 - 110,400,621 (+)NCBIRnor_SHRSP
UTH_Rnor_WKY_Bbb_1.013107,606,042 - 107,625,155 (+)NCBIRnor_WKY
Rnor_6.013113,691,842 - 113,711,259 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl13113,691,932 - 113,711,647 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.013118,531,837 - 118,551,216 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.413110,877,594 - 110,896,722 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera13105,904,553 - 105,923,681 (+)NCBICelera
Cytogenetic Map13q27NCBI
CD34
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381207,880,972 - 207,911,125 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p13 Ensembl1207,880,972 - 207,911,402 (-)EnsemblGRCh38hg38GRCh38
GRCh371208,054,317 - 208,084,470 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361206,126,506 - 206,151,306 (-)NCBINCBI36Build 36hg18NCBI36
Build 341204,448,278 - 204,472,910NCBI
Celera1181,290,338 - 181,315,139 (-)NCBICelera
Cytogenetic Map1q32.2NCBI
HuRef1178,734,078 - 178,758,883 (-)NCBIHuRef
CHM1_11209,332,232 - 209,357,037 (-)NCBICHM1_1
T2T-CHM13v2.01207,127,718 - 207,157,876 (-)NCBIT2T-CHM13v2.0
Cd34
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391194,621,129 - 194,643,600 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1194,621,127 - 194,643,587 (+)EnsemblGRCm39 Ensembl
GRCm381194,938,821 - 194,961,292 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1194,938,819 - 194,961,279 (+)EnsemblGRCm38mm10GRCm38
MGSCv371196,765,015 - 196,787,486 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361196,639,632 - 196,662,003 (+)NCBIMGSCv36mm8
Celera1201,838,605 - 201,861,076 (+)NCBICelera
Cytogenetic Map1H6NCBI
cM Map198.38NCBI
Cd34
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495540643,117,816 - 43,130,463 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495540643,116,688 - 43,130,405 (-)NCBIChiLan1.0ChiLan1.0
CD34
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11188,272,551 - 188,297,384 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1188,272,551 - 188,297,384 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01183,459,028 - 183,489,583 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
CD34
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.176,734,363 - 6,747,991 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl76,734,363 - 6,748,581 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha76,297,083 - 6,321,394 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.076,422,992 - 6,447,293 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl76,422,992 - 6,447,293 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.176,355,774 - 6,380,048 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.076,458,250 - 6,482,488 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.076,499,295 - 6,523,438 (-)NCBIUU_Cfam_GSD_1.0
Cd34
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934467,790,294 - 67,811,581 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049365575,030,788 - 5,051,864 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CD34
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl9134,913,121 - 134,937,762 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.19134,912,793 - 134,937,763 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.29148,445,995 - 148,470,638 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CD34
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12521,534,969 - 21,559,951 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2521,534,983 - 21,561,215 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605522,145,967 - 22,170,846 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cd34
(Heterocephalus glaber - naked mole-rat)
Naked Mole-rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248073,936,028 - 3,957,249 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248073,936,043 - 3,958,274 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cd34
61 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:172
Count of miRNA genes:99
Interacting mature miRNAs:106
Transcripts:ENSRNOT00000010148, ENSRNOT00000057160
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
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1361825626106807694Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1365103704106807694Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1365103704106807694Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1380753256106807694Rat


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 2 43 20 4 8 4 8 11 72 35 35 11 8
Low 1 37 37 11 37 2 6
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000057160   ⟹   ENSRNOP00000053987
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl13113,692,131 - 113,710,937 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000084709   ⟹   ENSRNOP00000074896
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl13106,480,043 - 106,499,832 (+)Ensembl
Rnor_6.0 Ensembl13113,691,932 - 113,711,647 (+)Ensembl
RefSeq Acc Id: NM_001107202   ⟹   NP_001100672
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.213106,480,335 - 106,499,462 (+)NCBI
Rnor_6.013113,692,131 - 113,711,259 (+)NCBI
Rnor_5.013118,531,837 - 118,551,216 (+)NCBI
RGSC_v3.413110,877,594 - 110,896,722 (+)RGD
Celera13105,904,553 - 105,923,681 (+)RGD
Sequence:
RefSeq Acc Id: XM_008769857   ⟹   XP_008768079
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.213106,480,074 - 106,499,462 (+)NCBI
Rnor_6.013113,691,842 - 113,711,121 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001100672 (Get FASTA)   NCBI Sequence Viewer  
  XP_008768079 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein ACA42446 (Get FASTA)   NCBI Sequence Viewer  
  ACA42447 (Get FASTA)   NCBI Sequence Viewer  
  EDL95047 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001100672   ⟸   NM_001107202
- Peptide Label: precursor
- UniProtKB: B1PLB1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008768079   ⟸   XM_008769857
- Peptide Label: isoform X1
- UniProtKB: B1PLB2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000053987   ⟸   ENSRNOT00000057160
RefSeq Acc Id: ENSRNOP00000074896   ⟸   ENSRNOT00000084709

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-B1PLB1-F1-model_v2 AlphaFold B1PLB1 1-386 view protein structure

Transcriptome

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

Promoters
RGD ID:13699136
Promoter ID:EPDNEW_R9656
Type:initiation region
Name:Cd34_1
Description:CD34 molecule
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_6.013113,692,109 - 113,692,169EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306863 AgrOrtholog
BioCyc Gene G2FUF-16747 BioCyc
Ensembl Genes ENSRNOG00000045558 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000074896 ENTREZGENE
  ENSRNOP00000074896.1 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000084709 ENTREZGENE
  ENSRNOT00000084709.2 UniProtKB/TrEMBL
InterPro CD34 UniProtKB/TrEMBL
  CD34/Podocalyxin UniProtKB/TrEMBL
KEGG Report rno:305081 UniProtKB/TrEMBL
NCBI Gene 305081 ENTREZGENE
PANTHER CD34 UniProtKB/TrEMBL
Pfam CD34_antigen UniProtKB/TrEMBL
PhenoGen Cd34 PhenoGen
PRINTS CD34ANTIGEN UniProtKB/TrEMBL
UniProt B1PLB1 ENTREZGENE, UniProtKB/TrEMBL
  B1PLB2 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-06-27 Cd34  CD34 molecule  Cd34  CD34 antigen   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Cd34  CD34 antigen   Cd34_predicted  CD34 antigen (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Cd34_predicted  CD34 antigen (predicted)      Symbol and Name status set to approved 70820 APPROVED