Dnaaf1 (dynein, axonemal, assembly factor 1) - Rat Genome Database

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Gene: Dnaaf1 (dynein, axonemal, assembly factor 1) Rattus norvegicus
Analyze
Symbol: Dnaaf1
Name: dynein, axonemal, assembly factor 1
RGD ID: 1310542
Description: Predicted to enable dynein complex binding activity. Predicted to be involved in several processes, including cilium assembly; determination of left/right symmetry; and regulation of cilium beat frequency. Predicted to be located in cilium. Predicted to be active in axoneme. Human ortholog(s) of this gene implicated in primary ciliary dyskinesia 13. Orthologous to human DNAAF1 (dynein axonemal assembly factor 1); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil; aflatoxin B1.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: dynein assembly factor 1, axonemal; dynein axonemal assembly factor 1; leucine rich repeat containing 50; leucine-rich repeat-containing protein 50; LOC361419; Lrrc50; RGD1310542; similar to RIKEN cDNA 4930457P18
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81964,532,859 - 64,560,942 (+)NCBIGRCr8
mRatBN7.21947,624,534 - 47,652,314 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1947,624,181 - 47,652,313 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1954,426,330 - 54,446,664 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01955,107,213 - 55,127,282 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01957,320,678 - 57,340,793 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01952,217,427 - 52,245,930 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1952,217,984 - 52,245,929 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01962,966,204 - 62,994,144 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41949,821,884 - 49,842,234 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11949,826,764 - 49,847,114 (+)NCBI
Celera1946,891,007 - 46,911,375 (+)NCBICelera
Cytogenetic Map19q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
axoneme  (IBA,IEA,ISO,ISS)
cell projection  (IEA)
cilium  (IEA)

Molecular Function
dynein complex binding  (IBA,IEA,ISO,ISS)

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. 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
5. 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:15489334   PMID:18385425   PMID:19944400   PMID:19944405  


Genomics

Comparative Map Data
Dnaaf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81964,532,859 - 64,560,942 (+)NCBIGRCr8
mRatBN7.21947,624,534 - 47,652,314 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1947,624,181 - 47,652,313 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1954,426,330 - 54,446,664 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01955,107,213 - 55,127,282 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01957,320,678 - 57,340,793 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01952,217,427 - 52,245,930 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1952,217,984 - 52,245,929 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01962,966,204 - 62,994,144 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41949,821,884 - 49,842,234 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11949,826,764 - 49,847,114 (+)NCBI
Celera1946,891,007 - 46,911,375 (+)NCBICelera
Cytogenetic Map19q12NCBI
DNAAF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381684,145,308 - 84,177,920 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1684,145,287 - 84,178,767 (+)EnsemblGRCh38hg38GRCh38
GRCh371684,178,913 - 84,211,526 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361682,736,366 - 82,769,025 (+)NCBINCBI36Build 36hg18NCBI36
Celera1668,480,658 - 68,513,333 (+)NCBICelera
Cytogenetic Map16q24.1NCBI
HuRef1669,932,647 - 69,965,301 (+)NCBIHuRef
CHM1_11685,590,244 - 85,622,911 (+)NCBICHM1_1
T2T-CHM13v2.01690,211,391 - 90,243,993 (+)NCBIT2T-CHM13v2.0
Dnaaf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398120,301,974 - 120,325,193 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl8120,301,974 - 120,325,193 (+)EnsemblGRCm39 Ensembl
GRCm388119,575,235 - 119,598,454 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8119,575,235 - 119,598,454 (+)EnsemblGRCm38mm10GRCm38
MGSCv378122,099,135 - 122,122,354 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv368122,461,212 - 122,484,431 (+)NCBIMGSCv36mm8
Celera8123,792,687 - 123,815,934 (+)NCBICelera
Cytogenetic Map8E1NCBI
cM Map867.98NCBI
Dnaaf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955564132,760 - 149,399 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955564132,497 - 149,399 (-)NCBIChiLan1.0ChiLan1.0
DNAAF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21893,891,995 - 93,926,562 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11699,809,144 - 99,842,902 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01664,810,498 - 64,843,705 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11684,153,949 - 84,184,991 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1684,154,130 - 84,184,914 (+)Ensemblpanpan1.1panPan2
DNAAF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1568,184,532 - 68,205,651 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl568,184,532 - 68,205,656 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha568,198,602 - 68,219,645 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0568,482,202 - 68,503,551 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl568,482,202 - 68,503,557 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1568,430,068 - 68,451,328 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0568,266,559 - 68,287,805 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0568,682,282 - 68,703,584 (-)NCBIUU_Cfam_GSD_1.0
Dnaaf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934927,903,299 - 27,920,183 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366413,657,058 - 3,673,729 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366413,656,331 - 3,674,907 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DNAAF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl64,457,291 - 4,479,828 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.164,457,283 - 4,483,641 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.265,038,956 - 5,061,559 (-)NCBISscrofa10.2Sscrofa10.2susScr3
DNAAF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1569,554,454 - 69,586,476 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl569,554,578 - 69,586,365 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660476,167,981 - 6,201,533 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Dnaaf1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247463,412,888 - 3,441,710 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Dnaaf1
118 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:141
Count of miRNA genes:120
Interacting mature miRNAs:124
Transcripts:ENSRNOT00000020917
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
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191563020157337602Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192048357557337602Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194434021455283277Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)192932249057337602Rat
2317848Alcrsp21Alcohol response QTL 211.8999999761581420.05response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)19320477748204777Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191545586057337602Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193383821455283146Rat
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19218792756457239Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19409615555283277Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)191715443357337602Rat

Markers in Region
RH134909  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21947,652,582 - 47,652,773 (+)MAPPERmRatBN7.2
Rnor_6.01952,246,199 - 52,246,389NCBIRnor6.0
Rnor_5.01962,994,413 - 62,994,603UniSTSRnor5.0
RGSC_v3.41949,842,503 - 49,842,693UniSTSRGSC3.4
Celera1946,911,644 - 46,911,834UniSTS
RH 3.4 Map19649.0UniSTS
Cytogenetic Map19q12UniSTS
AI145291  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21947,652,061 - 47,652,279 (+)MAPPERmRatBN7.2
Rnor_6.01952,245,678 - 52,245,895NCBIRnor6.0
Rnor_5.01962,993,892 - 62,994,109UniSTSRnor5.0
RGSC_v3.41949,841,982 - 49,842,199UniSTSRGSC3.4
Celera1946,911,123 - 46,911,340UniSTS
RH 3.4 Map19653.0UniSTS
Cytogenetic Map19q12UniSTS


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
nervous system
renal system
reproductive system
respiratory system
9 9 49 113 82 81 50 25 50 6 205 94 93 45 60 31

Sequence


Ensembl Acc Id: ENSRNOT00000020917   ⟹   ENSRNOP00000020917
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1947,631,959 - 47,652,313 (+)Ensembl
Rnor_6.0 Ensembl1952,225,582 - 52,245,929 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000079580   ⟹   ENSRNOP00000073360
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1947,624,181 - 47,652,313 (+)Ensembl
Rnor_6.0 Ensembl1952,217,984 - 52,245,914 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000105457   ⟹   ENSRNOP00000085726
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1947,634,543 - 47,652,313 (+)Ensembl
RefSeq Acc Id: NM_001014154   ⟹   NP_001014176
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81964,540,594 - 64,560,942 (+)NCBI
mRatBN7.21947,631,959 - 47,652,314 (+)NCBI
Rnor_6.01952,225,582 - 52,245,930 (+)NCBI
Rnor_5.01962,966,204 - 62,994,144 (+)NCBI
RGSC_v3.41949,821,884 - 49,842,234 (+)RGD
Celera1946,891,007 - 46,911,375 (+)RGD
Sequence:
RefSeq Acc Id: XM_017601323   ⟹   XP_017456812
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81964,532,859 - 64,560,942 (+)NCBI
mRatBN7.21947,624,534 - 47,652,311 (+)NCBI
Rnor_6.01952,217,427 - 52,245,930 (+)NCBI
Sequence:
RefSeq Acc Id: XM_063278144   ⟹   XP_063134214
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81964,532,862 - 64,560,942 (+)NCBI
RefSeq Acc Id: XM_063278145   ⟹   XP_063134215
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81964,540,525 - 64,560,942 (+)NCBI
RefSeq Acc Id: NP_001014176   ⟸   NM_001014154
- UniProtKB: Q6AYH9 (UniProtKB/Swiss-Prot),   A6IZJ4 (UniProtKB/TrEMBL),   A0A8I6A474 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_017456812   ⟸   XM_017601323
- Peptide Label: isoform X3
- UniProtKB: A0A0G2K5B1 (UniProtKB/TrEMBL),   A0A8I6A474 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000073360   ⟸   ENSRNOT00000079580
Ensembl Acc Id: ENSRNOP00000020917   ⟸   ENSRNOT00000020917
Ensembl Acc Id: ENSRNOP00000085726   ⟸   ENSRNOT00000105457
RefSeq Acc Id: XP_063134214   ⟸   XM_063278144
- Peptide Label: isoform X1
RefSeq Acc Id: XP_063134215   ⟸   XM_063278145
- Peptide Label: isoform X2
Protein Domains
LRRCT

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6AYH9-F1-model_v2 AlphaFold Q6AYH9 1-633 view protein structure

Transcriptome

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

Promoters
RGD ID:13701182
Promoter ID:EPDNEW_R11704
Type:initiation region
Name:Dnaaf1_1
Description:dynein, axonemal, assembly factor 1
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_6.01952,225,587 - 52,225,647EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310542 AgrOrtholog
BioCyc Gene G2FUF-5513 BioCyc
Ensembl Genes ENSRNOG00000015590 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000020917 ENTREZGENE
  ENSRNOT00000020917.5 UniProtKB/Swiss-Prot
  ENSRNOT00000079580 ENTREZGENE
  ENSRNOT00000079580.2 UniProtKB/TrEMBL
  ENSRNOT00000105457.1 UniProtKB/TrEMBL
Gene3D-CATH 3.80.10.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7114363 IMAGE-MGC_LOAD
InterPro Cilia_flagella_integrity UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Leu-rich_rpt UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LRR_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:361419 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:93967 IMAGE-MGC_LOAD
NCBI Gene 361419 ENTREZGENE
PANTHER PROTEIN PHOSPHATASE 1 REGULATORY SUBUNIT SDS22-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR45973:SF19 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam LRR_9 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Dnaaf1 PhenoGen
PROSITE LRR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000015590 RatGTEx
SMART LRR_SD22 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP Outer arm dynein light chain 1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K5B1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I6A474 ENTREZGENE, UniProtKB/TrEMBL
  A6IZJ4 ENTREZGENE, UniProtKB/TrEMBL
  DAAF1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2011-08-02 Dnaaf1  dynein, axonemal, assembly factor 1  Lrrc50  leucine rich repeat containing 50  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Lrrc50  leucine rich repeat containing 50  RGD1310542  similar to RIKEN cDNA 4930457P18  Symbol and Name updated 1299863 APPROVED
2005-12-06 RGD1310542  similar to RIKEN cDNA 4930457P18  RGD1310542_predicted  similar to RIKEN cDNA 4930457P18 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1310542_predicted  similar to RIKEN cDNA 4930457P18 (predicted)  LOC361419_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC361419_predicted  similar to RIKEN cDNA 4930457P18 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL