Arl13a (ARF like GTPase 13A) - Rat Genome Database

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Gene: Arl13a (ARF like GTPase 13A) Rattus norvegicus
Analyze
Symbol: Arl13a
Name: ARF like GTPase 13A (Ensembl:ADP ribosylation factor like GTPase 13A)
RGD ID: 1562947
Description: Predicted to enable GTP binding activity and GTPase activity. Predicted to be involved in non-motile cilium assembly and receptor localization to non-motile cilium. Predicted to be located in cilium. Predicted to be active in ciliary membrane; motile cilium; and non-motile cilium. Orthologous to human ARL13A (ARF like GTPase 13A); INTERACTS WITH bisphenol A; indole-3-methanol; N-acetyl-L-cysteine.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: ADP ribosylation factor like GTPase 13A; ADP-ribosylation factor-like 13A; ADP-ribosylation factor-like protein 13A; LOC501617; similar to ADP-ribosylation factor-like 2-like 1 isoform 1
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X101,673,637 - 101,699,986 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX101,673,652 - 101,699,984 (+)EnsemblGRCr8
mRatBN7.2X97,380,370 - 97,406,704 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX97,380,390 - 97,406,702 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX99,054,536 - 99,080,850 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X102,564,325 - 102,590,639 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X100,067,700 - 100,094,014 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X105,010,943 - 105,039,720 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX105,011,489 - 105,037,801 (+)Ensemblrn6Rnor6.0
Rnor_5.0X104,839,268 - 104,871,495 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X121,648,063 - 121,674,377 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX98,422,452 - 98,425,344 (+)NCBICelera
Celera7113,749,933 - 113,766,179 (+)NCBICelera
Cytogenetic MapXq32NCBI
JBrowse:




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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
4. 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.

Genomics

Comparative Map Data
Arl13a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X101,673,637 - 101,699,986 (+)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX101,673,652 - 101,699,984 (+)EnsemblGRCr8
mRatBN7.2X97,380,370 - 97,406,704 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX97,380,390 - 97,406,702 (+)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX99,054,536 - 99,080,850 (+)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X102,564,325 - 102,590,639 (+)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X100,067,700 - 100,094,014 (+)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X105,010,943 - 105,039,720 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX105,011,489 - 105,037,801 (+)Ensemblrn6Rnor6.0
Rnor_5.0X104,839,268 - 104,871,495 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X121,648,063 - 121,674,377 (+)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX98,422,452 - 98,425,344 (+)NCBICelera
Celera7113,749,933 - 113,766,179 (+)NCBICelera
Cytogenetic MapXq32NCBI
ARL13A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X100,969,708 - 100,990,831 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX100,969,708 - 100,990,831 (+)Ensemblhg38GRCh38
GRCh37X100,224,697 - 100,245,820 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X100,111,356 - 100,132,476 (+)NCBIBuild 36Build 36hg18NCBI36
CeleraX100,743,491 - 100,764,612 (+)NCBICelera
Cytogenetic MapXq22.1NCBI
HuRefX90,022,196 - 90,038,409 (+)NCBIHuRef
HuRefX90,047,410 - 90,050,053 (+)NCBIHuRef
CHM1_1X100,117,563 - 100,138,958 (+)NCBICHM1_1
T2T-CHM13v2.0X99,412,390 - 99,434,268 (+)NCBIT2T-CHM13v2.0
Arl13a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X133,088,250 - 133,108,779 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX133,088,250 - 133,108,777 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm38X134,187,501 - 134,208,030 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX134,187,501 - 134,208,028 (+)Ensemblmm10GRCm38
MGSCv37X130,722,040 - 130,742,569 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X129,533,851 - 129,554,380 (+)NCBIMGSCv36mm8
CeleraX117,064,321 - 117,084,890 (+)NCBICelera
Cytogenetic MapXE3NCBI
cM MapX55.9NCBI
ARL13A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X100,568,623 - 100,618,337 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X100,572,227 - 100,621,941 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X90,173,938 - 90,188,922 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X100,310,188 - 100,329,374 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX100,310,188 - 100,329,374 (+)EnsemblpanPan2panpan1.1
ARL13A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X74,912,223 - 74,919,327 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
ROS_Cfam_1.0X76,325,477 - 76,338,018 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.1X73,894,228 - 73,906,801 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X75,554,363 - 75,566,893 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X75,317,074 - 75,329,628 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Arl13a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X63,392,005 - 63,410,081 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493681366,944 - 76,886 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_00493681366,944 - 80,346 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
ARL13A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX82,671,561 - 82,684,002 (+)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X82,670,773 - 82,681,890 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X90,588,750 - 90,610,134 (+)NCBISscrofa10.2Sscrofa10.2susScr3
ARL13A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X89,310,424 - 89,332,926 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX89,312,723 - 89,330,634 (+)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366606514,236,085 - 14,251,165 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Arl13a
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1X86,521,353 - 86,541,487 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Arl13a
130 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:124
Count of miRNA genes:97
Interacting mature miRNAs:98
Transcripts:ENSRNOT00000036291
Prediction methods:Microtar, Miranda, Pita, 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
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between duration of physical contact or close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X97528096142528096Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X80434318125434318Rat
738029Stresp2Stress response QTL 23.40.0004stress-related behavior trait (VT:0010451)defensive burying - approachX92979612117740458Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat
2302047Pia34Pristane induced arthritis QTL 345.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1996916163141916163Rat


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
11 10 17 53 50 49 18 70 18 4 171 104 1 37 30 32 31 9 9

Sequence


Ensembl Acc Id: ENSRNOT00000085068   ⟹   ENSRNOP00000069009
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX101,673,652 - 101,699,984 (+)Ensembl
mRatBN7.2 EnsemblX97,380,390 - 97,406,702 (+)Ensembl
Rnor_6.0 EnsemblX105,011,489 - 105,037,801 (+)Ensembl
Ensembl Acc Id: ENSRNOT00000117619   ⟹   ENSRNOP00000091406
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX97,380,390 - 97,406,702 (+)Ensembl
RefSeq Acc Id: NM_001024366   ⟹   NP_001019537
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,673,672 - 101,699,986 (+)NCBI
mRatBN7.2X97,380,390 - 97,406,704 (+)NCBI
Rnor_6.0X105,011,489 - 105,037,803 (+)NCBI
Rnor_5.0X104,839,268 - 104,871,495 (+)NCBI
RGSC_v3.4X121,648,063 - 121,674,377 (+)RGD
Celera7113,749,933 - 113,766,179 (+)NCBI
CeleraX98,422,452 - 98,425,344 (+)NCBI
Sequence:
RefSeq Acc Id: XM_008773430   ⟹   XP_008771652
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,673,637 - 101,699,986 (+)NCBI
mRatBN7.2X97,380,370 - 97,406,408 (+)NCBI
Rnor_6.0X105,010,943 - 105,039,720 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039099979   ⟹   XP_038955907
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X101,673,640 - 101,699,986 (+)NCBI
mRatBN7.2X97,380,399 - 97,406,475 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001019537 (Get FASTA)   NCBI Sequence Viewer  
  XP_008771652 (Get FASTA)   NCBI Sequence Viewer  
  XP_038955907 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH79325 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000069009
GenBank Protein Q6AXT3 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001019537   ⟸   NM_001024366
- UniProtKB: Q6AXT3 (UniProtKB/Swiss-Prot),   A0A8I6ADN1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008771652   ⟸   XM_008773430
- Peptide Label: isoform X2
- UniProtKB: A0A8L2R0C8 (UniProtKB/TrEMBL),   A0A8I6ADN1 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000069009   ⟸   ENSRNOT00000085068
RefSeq Acc Id: XP_038955907   ⟸   XM_039099979
- Peptide Label: isoform X1
- UniProtKB: Q6AXT3 (UniProtKB/Swiss-Prot),   A0A8I6ADN1 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000091406   ⟸   ENSRNOT00000117619

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q6AXT3-F1-model_v2 AlphaFold Q6AXT3 1-395 view protein structure

Transcriptome

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

Promoters
RGD ID:13701931
Promoter ID:EPDNEW_R12455
Type:single initiation site
Name:Arl13a_1
Description:ADP ribosylation factor like GTPase 13A
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_6.0X105,011,472 - 105,011,532EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1562947 AgrOrtholog
BioCyc Gene G2FUF-1692 BioCyc
Ensembl Genes ENSRNOG00000055454 Ensembl, ENTREZGENE
Ensembl Transcript ENSRNOT00000085068 ENTREZGENE
Gene3D-CATH 3.40.50.300 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7135460 IMAGE-MGC_LOAD
InterPro Ciliary_GTPase UniProtKB/Swiss-Prot
  P-loop_NTPase UniProtKB/Swiss-Prot
  Small_GTPase_ARF/SAR UniProtKB/Swiss-Prot
KEGG Report rno:501617 UniProtKB/Swiss-Prot
MGC_CLONE MGC:94504 IMAGE-MGC_LOAD
NCBI Gene 501617 ENTREZGENE
PANTHER ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 13A UniProtKB/Swiss-Prot
  ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 13B UniProtKB/Swiss-Prot
Pfam Arf UniProtKB/Swiss-Prot
PhenoGen Arl13a PhenoGen
PRINTS SAR1GTPBP UniProtKB/Swiss-Prot
PROSITE ARF UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000055454 RatGTEx
SMART ARF UniProtKB/Swiss-Prot
  SAR UniProtKB/Swiss-Prot
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot
UniProt A0A8I6ADN1 ENTREZGENE
  A0A8L2R0C8 ENTREZGENE, UniProtKB/TrEMBL
  AR13A_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2024-11-07 Arl13a  ARF like GTPase 13A  Arl13a  ADP ribosylation factor like GTPase 13A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2015-12-23 Arl13a  ADP ribosylation factor like GTPase 13A  Arl13a  ADP-ribosylation factor-like 13A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-05 Arl13a  ADP-ribosylation factor-like 13A  LOC501617  similar to ADP-ribosylation factor-like 2-like 1 isoform 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-02-09 LOC501617  similar to ADP-ribosylation factor-like 2-like 1 isoform 1      Symbol and Name status set to provisional 70820 PROVISIONAL