ARL2-SNX15 (ARL2-SNX15 readthrough (NMD candidate)) - Rat Genome Database

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Gene: ARL2-SNX15 (ARL2-SNX15 readthrough (NMD candidate)) Homo sapiens
Analyze
Symbol: ARL2-SNX15
Name: ARL2-SNX15 readthrough (NMD candidate)
RGD ID: 7370113
HGNC Page HGNC:49197
Description: Predicted to enable GTP binding activity and GTPase activity. Predicted to be involved in protein folding. Predicted to be located in centrosome and cytoplasm.
Type: ncrna (Ensembl: protein-coding)
RefSeq Status: VALIDATED
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381165,014,160 - 65,040,572 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1165,014,182 - 65,040,570 (+)EnsemblGRCh38hg38GRCh38
GRCh371164,781,632 - 64,808,044 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map11q13.1NCBI
HuRef1161,108,599 - 61,134,872 (+)NCBIHuRef
CHM1_11164,665,310 - 64,691,755 (+)NCBICHM1_1
T2T-CHM13v2.01165,007,423 - 65,033,855 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
clothianidin  (EXP)

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
centrosome  (IEA)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:14702039   PMID:20967262   PMID:36215168  


Genomics

Variants

.
Variants in ARL2-SNX15
26 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
NM_013306.4(SNX15):c.682C>T (p.Pro228Ser) single nucleotide variant Malignant melanoma [RCV000069602] Chr11:65038589 [GRCh38]
Chr11:64806061 [GRCh37]
Chr11:64562637 [NCBI36]
Chr11:11q13.1		 not provided
NM_013306.4(SNX15):c.664+1249T>A single nucleotide variant Lung cancer [RCV000110222] Chr11:65036912 [GRCh38]
Chr11:64804384 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_013306.5(SNX15):c.286C>T (p.Arg96Trp) single nucleotide variant Inborn genetic diseases [RCV003295547] Chr11:65034876 [GRCh38]
Chr11:64802348 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_001667.4(ARL2):c.44G>T (p.Arg15Leu) single nucleotide variant Microcornea, rod-cone dystrophy, cataract, and posterior staphyloma 1 [RCV001263461] Chr11:65014251 [GRCh38]
Chr11:64781723 [GRCh37]
Chr11:11q13.1		 pathogenic
NM_013306.5(SNX15):c.689A>C (p.His230Pro) single nucleotide variant Inborn genetic diseases [RCV002991023] Chr11:65038596 [GRCh38]
Chr11:64806068 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_001667.4(ARL2):c.500C>T (p.Pro167Leu) single nucleotide variant Inborn genetic diseases [RCV002883896] Chr11:65021800 [GRCh38]
Chr11:64789272 [GRCh37]
Chr11:11q13.1		 likely benign
NM_001667.4(ARL2):c.287G>A (p.Arg96His) single nucleotide variant Inborn genetic diseases [RCV002754687] Chr11:65018681 [GRCh38]
Chr11:64786153 [GRCh37]
Chr11:11q13.1		 likely benign
NM_001667.4(ARL2):c.443G>A (p.Arg148His) single nucleotide variant Inborn genetic diseases [RCV002754714] Chr11:65021743 [GRCh38]
Chr11:64789215 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_013306.5(SNX15):c.1021C>G (p.Pro341Ala) single nucleotide variant Inborn genetic diseases [RCV002946481] Chr11:65039784 [GRCh38]
Chr11:64807256 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_013306.5(SNX15):c.983G>T (p.Arg328Leu) single nucleotide variant Inborn genetic diseases [RCV002818731] Chr11:65039746 [GRCh38]
Chr11:64807218 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_013306.5(SNX15):c.88G>C (p.Val30Leu) single nucleotide variant Inborn genetic diseases [RCV002925729] Chr11:65027625 [GRCh38]
Chr11:64795097 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_013306.5(SNX15):c.680G>C (p.Ser227Thr) single nucleotide variant Inborn genetic diseases [RCV003000495] Chr11:65038587 [GRCh38]
Chr11:64806059 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_001667.4(ARL2):c.416G>A (p.Arg139His) single nucleotide variant Inborn genetic diseases [RCV002694566] Chr11:65020495 [GRCh38]
Chr11:64787967 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_013306.5(SNX15):c.530C>T (p.Pro177Leu) single nucleotide variant Inborn genetic diseases [RCV002987698] Chr11:65035529 [GRCh38]
Chr11:64803001 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_013306.5(SNX15):c.646G>T (p.Asp216Tyr) single nucleotide variant Inborn genetic diseases [RCV002742237] Chr11:65035645 [GRCh38]
Chr11:64803117 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_013306.5(SNX15):c.314G>A (p.Arg105His) single nucleotide variant Inborn genetic diseases [RCV002875291] Chr11:65034904 [GRCh38]
Chr11:64802376 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_013306.5(SNX15):c.430C>T (p.Pro144Ser) single nucleotide variant Inborn genetic diseases [RCV002854702] Chr11:65035116 [GRCh38]
Chr11:64802588 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_013306.5(SNX15):c.706A>G (p.Thr236Ala) single nucleotide variant Inborn genetic diseases [RCV002989559] Chr11:65038613 [GRCh38]
Chr11:64806085 [GRCh37]
Chr11:11q13.1		 likely benign
NM_001667.4(ARL2):c.419A>T (p.Glu140Val) single nucleotide variant Inborn genetic diseases [RCV002723238] Chr11:65020498 [GRCh38]
Chr11:64787970 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_001667.4(ARL2):c.221G>A (p.Arg74Gln) single nucleotide variant Inborn genetic diseases [RCV002944428] Chr11:65018615 [GRCh38]
Chr11:64786087 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_013306.5(SNX15):c.866C>T (p.Ala289Val) single nucleotide variant Inborn genetic diseases [RCV003218751] Chr11:65038773 [GRCh38]
Chr11:64806245 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_001667.4(ARL2):c.124G>A (p.Asp42Asn) single nucleotide variant Inborn genetic diseases [RCV003194581] Chr11:65018422 [GRCh38]
Chr11:64785894 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_001667.4(ARL2):c.442C>T (p.Arg148Cys) single nucleotide variant Inborn genetic diseases [RCV003190039] Chr11:65021742 [GRCh38]
Chr11:64789214 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_013306.5(SNX15):c.157A>G (p.Ser53Gly) single nucleotide variant Inborn genetic diseases [RCV003357624] Chr11:65032452 [GRCh38]
Chr11:64799924 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_013306.5(SNX15):c.464G>A (p.Arg155Gln) single nucleotide variant Inborn genetic diseases [RCV003344202] Chr11:65035150 [GRCh38]
Chr11:64802622 [GRCh37]
Chr11:11q13.1		 uncertain significance
NM_013306.5(SNX15):c.868G>A (p.Ala290Thr) single nucleotide variant Inborn genetic diseases [RCV003342817] Chr11:65038775 [GRCh38]
Chr11:64806247 [GRCh37]
Chr11:11q13.1		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1001
Count of miRNA genes:584
Interacting mature miRNAs:642
Transcripts:ENST00000301886
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
RH11499  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371164,807,747 - 64,807,916UniSTSGRCh37
Build 361164,564,323 - 64,564,492RGDNCBI36
Celera1162,133,678 - 62,133,847RGD
Cytogenetic Map11qUniSTS
Cytogenetic Map11q12UniSTS
Cytogenetic Map11q13.1UniSTS
HuRef1161,134,575 - 61,134,744UniSTS
GeneMap99-GB4 RH Map11245.99UniSTS
NCBI RH Map11573.2UniSTS


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 entire extraembryonic component pharyngeal arch
High
Medium 7 7 3 2 3 1 2 4 25 1 12 4 4 1 2 2
Low 2 2 1 2 2 6
Below cutoff 36 19 12 90 12 46 21 53 32 86 98 4

Sequence


Reference Sequences
RefSeq Acc Id: ENST00000301886   ⟹   ENSP00000476630
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1165,014,182 - 65,040,570 (+)Ensembl
RefSeq Acc Id: NR_037650
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381165,014,160 - 65,040,572 (+)NCBI
GRCh371164,781,585 - 64,808,044 (+)NCBI
HuRef1161,108,599 - 61,134,872 (+)NCBI
CHM1_11164,665,310 - 64,691,755 (+)NCBI
T2T-CHM13v2.01165,007,423 - 65,033,855 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein BAG53293 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSP00000476630.1
Reference Protein Sequences
RefSeq Acc Id: ENSP00000476630   ⟸   ENST00000301886


Additional Information

Database Acc Id Source(s)
COSMIC ARL2-SNX15 COSMIC
Ensembl Genes ENSG00000273003 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENST00000301886 ENTREZGENE
  ENST00000301886.3 UniProtKB/TrEMBL
Gene3D-CATH 3.40.50.300 UniProtKB/TrEMBL
GTEx ENSG00000273003 GTEx
HGNC ID HGNC:49197 ENTREZGENE
Human Proteome Map ARL2-SNX15 Human Proteome Map
InterPro ARL2/3 UniProtKB/TrEMBL
  P-loop_NTPase UniProtKB/TrEMBL
  Small_GTP-bd_dom UniProtKB/TrEMBL
  Small_GTPase_ARF/SAR UniProtKB/TrEMBL
NCBI Gene ARL2-SNX15 ENTREZGENE
PANTHER ADP-RIBOSYLATION FACTOR-LIKE PROTEIN 2 UniProtKB/TrEMBL
  PTHR45697 UniProtKB/TrEMBL
Pfam Arf UniProtKB/TrEMBL
PRINTS SAR1GTPBP UniProtKB/TrEMBL
PROSITE ARF UniProtKB/TrEMBL
RNAcentral URS00025E3521 RNACentral
SMART ARF UniProtKB/TrEMBL
Superfamily-SCOP SSF52540 UniProtKB/TrEMBL
UniProt V9GYD0_HUMAN UniProtKB/TrEMBL