Arl13a (ADP ribosylation factor like GTPase 13A) - Rat Genome Database

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Gene: Arl13a (ADP ribosylation factor like GTPase 13A) Rattus norvegicus
Analyze
Symbol: Arl13a
Name: 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 active in ciliary membrane and non-motile cilium. Orthologous to human ARL13A (ADP ribosylation factor 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 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
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X101,673,637 - 101,699,986 (+)NCBIGRCr8
mRatBN7.2X97,380,370 - 97,406,704 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX97,380,390 - 97,406,702 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX99,054,536 - 99,080,850 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X102,564,325 - 102,590,639 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X100,067,700 - 100,094,014 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X105,010,943 - 105,039,720 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX105,011,489 - 105,037,801 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X104,839,268 - 104,871,495 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X121,648,063 - 121,674,377 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
CeleraX98,422,452 - 98,425,344 (+)NCBICelera
Celera7113,749,933 - 113,766,179 (+)NCBICelera
Cytogenetic MapXq32NCBI
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

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 (+)NCBIGRCr8
mRatBN7.2X97,380,370 - 97,406,704 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX97,380,390 - 97,406,702 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_UtxX99,054,536 - 99,080,850 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X102,564,325 - 102,590,639 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X100,067,700 - 100,094,014 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X105,010,943 - 105,039,720 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX105,011,489 - 105,037,801 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0X104,839,268 - 104,871,495 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X121,648,063 - 121,674,377 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
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 (+)EnsemblGRCh38hg38GRCh38
GRCh37X100,224,697 - 100,245,820 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36X100,111,356 - 100,132,476 (+)NCBINCBI36Build 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 Ensembl
GRCm38X134,187,501 - 134,208,030 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX134,187,501 - 134,208,028 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X130,722,040 - 130,742,569 (+)NCBIGRCm37MGSCv37mm9NCBIm37
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 (+)Ensemblpanpan1.1panPan2
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_1.0
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_1.0
Arl13a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X63,392,005 - 63,410,081 (-)NCBIHiC_Itri_2
SpeTri2.0NW_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 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
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 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366606514,236,085 - 14,251,165 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Arl13a
72 total Variants
miRNA Target Status

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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X14843113120568734Rat
61431Cia19Collagen induced arthritis QTL 194.4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X65612192120568734Rat
724551Glom1Glomerulus QTL 12.80.0004kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli not directly contacting the kidney surface (CMO:0001002)X75294106120294106Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX41304447112935181Rat
1598837Memor13Memory QTL 133.2exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X41052407146860749Rat
1598872Memor14Memory QTL 144.5exploratory behavior trait (VT:0010471)difference between time of physical contact/close proximity of test subject and social stimulus during sample phase and test phase (CMO:0002678)X93956491138956491Rat


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 7
Low 3 4 27 11 19 11 2 2 11 6 11 2
Below cutoff 7 6 7 7 1 6

Sequence


RefSeq Acc Id: ENSRNOT00000085068   ⟹   ENSRNOP00000069009
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 EnsemblX97,380,390 - 97,406,702 (+)Ensembl
Rnor_6.0 EnsemblX105,011,489 - 105,037,801 (+)Ensembl
RefSeq 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
  ENSRNOP00000069009.2
  ENSRNOP00000091406
  ENSRNOP00000091406.1
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:
RefSeq Acc Id: ENSRNOP00000069009   ⟸   ENSRNOT00000085068
RefSeq Acc Id: XP_038955907   ⟸   XM_039099979
- Peptide Label: isoform X1
- UniProtKB: Q6AXT3 (UniProtKB/Swiss-Prot),   A0A8I6ADN1 (UniProtKB/TrEMBL)
RefSeq 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, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000085068.2 UniProtKB/TrEMBL
  ENSRNOT00000117619 ENTREZGENE
  ENSRNOT00000117619.1 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7135460 IMAGE-MGC_LOAD
InterPro P-loop_NTPase UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Small_GTPase_ARF/SAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
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, UniProtKB/TrEMBL
  ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 13B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Arf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Arl13a PhenoGen
PRINTS SAR1GTPBP UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE ARF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
RatGTEx ENSRNOG00000055454 RatGTEx
SMART ARF UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SAR UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6ADN1 ENTREZGENE, UniProtKB/TrEMBL
  A0A8L2R0C8 ENTREZGENE, UniProtKB/TrEMBL
  AR13A_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
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