Aliases for SPATA42 Gene

Data sources for SPATA42 Gene:

Subcategory (RNA class) for SPATA42 Gene

lncRNA

Aliases for SPATA42 Gene

External Ids for SPATA42 Gene

Previous GeneCards Identifiers for SPATA42 Gene

  • GC01P109402
  • GC01P108857

Summaries for SPATA42 Gene

GeneCards Summary for SPATA42 Gene

SPATA42 (Spermatogenesis Associated 42) is an RNA Gene, and is affiliated with the lncRNA class. Diseases associated with SPATA42 include Spermatogenic Failure, X-Linked, 1.

Additional gene information for SPATA42 Gene

No data available for Entrez Gene Summary , CIViC Summary , UniProtKB/Swiss-Prot Summary , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , Rfam classification and piRNA Summary for SPATA42 Gene

Genomics for SPATA42 Gene

GeneHancer (GH) Regulatory Elements Pubs

Promoters and enhancers for SPATA42 Gene
GeneHancer (GH) Identifier GH Type GH
Score
GH Sources Gene Association Score Total Score TSS distance (kb) Number of Genes Away Size (kb) Transcription Factor
Binding Sites
Gene Targets
GH01J108856 Promoter 0.3 EPDnew 250.3 +43.6 43609 0.1 SPATA42 lnc-AKNAD1-2 GPSM2 lnc-AKNAD1-1 AKNAD1 STXBP3
GH01J108896 Enhancer 0.8 Ensembl ENCODE 17.9 +83.5 83488 2.9 CTCF REST TRIM22 RAD21 RFX5 SMC3 ZBTB33 TFDP1 ZNF143 TBL1XR1 SPATA42 AKNAD1 ENSG00000251484 HSALNG0005839 piR-30791-003 HSALNG0005837 GPSM2
GH01J108875 Promoter/Enhancer 2 EPDnew Ensembl ENCODE CraniofacialAtlas 6.5 +64.3 64308 3.9 TBP ZBTB10 IKZF1 SMAD5 HES1 MBD2 ZNF217 BHLHE40 ELF1 NONO GPSM2 HSALNG0005837 PRPF38B PSRC1 SPATA42 CLCC1 piR-30791-003 AKNAD1
GH01J108913 Enhancer 1 Ensembl ENCODE 11.1 +99.7 99724 1.4 IKZF1 ARNT TAL1 TAF9B ZNF316 PRDM6 NFE2 NCOA2 ATF1 SMARCA4 AKNAD1 SPATA42 WDR47 RANP5 CLCC1 HSALNG0005839 MN296835 GPSM2
GH01J108862 Enhancer 0.7 Ensembl 12.7 +49.3 49324 1.8 IKZF1 ZNF316 PRDM6 ZNF362 MAFF CAVIN1 CEBPG SP7 NR2C1 MAFK lnc-AKNAD1-2 SPATA42 GPSM2 HSALNG0005836 LOC107985159 lnc-AKNAD1-1 AKNAD1 STXBP3
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around SPATA42 on the GeneHancer Hub at the UCSC Golden Path

Genomic Locations for SPATA42 Gene

Latest Assembly
chr1:108,813,577-108,860,397
(GRCh38/hg38)
Size:
46,821 bases
Orientation:
Plus strand

Previous Assembly
chr1:109,399,839-109,401,146
(GRCh37/hg19 by Entrez Gene)
Size:
1,308 bases
Orientation:
Plus strand

chr1:109,399,839-109,401,146
(GRCh37/hg19 by Ensembl)
Size:
1,308 bases
Orientation:
Plus strand

Genomic View for SPATA42 Gene

Genes around SPATA42 on UCSC Golden Path with GeneCards custom track
SPATA42 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Cytogenetic band:
SPATA42 Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for SPATA42 Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for SPATA42 Gene

Proteins for SPATA42 Gene

Post-translational modifications for SPATA42 Gene

No Post-translational modifications

No data available for DME Specific Peptides for SPATA42 Gene

Domains & Families for SPATA42 Gene

Gene Families for SPATA42 Gene

genes like me logo Genes that share domains with SPATA42: view

No data available for Protein Domains , Suggested Antigen Peptide Sequences , Graphical View of Domain Structure and UniProtKB/Swiss-Prot for SPATA42 Gene

Function for SPATA42 Gene

No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Phenotypes , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for SPATA42 Gene

Localization for SPATA42 Gene

Subcellular locations from

COMPARTMENTS
Extracellular space Cytosol Plasma membrane Cytoskeleton Lysosome Endosome Peroxisome ER Golgi Apparatus Nucleus Mitochondrion 0 1 2 3 4 5 Confidence
COMPARTMENTS Subcellular localization image for SPATA42 gene
Compartment Confidence
extracellular 1

No data available for Subcellular locations from UniProtKB/Swiss-Prot , Subcellular locations from the Human Protein Atlas (HPA) and Gene Ontology (GO) - Cellular Components for SPATA42 Gene

Pathways & Interactions for SPATA42 Gene

PathCards logo

SuperPathways for SPATA42 Gene

No Data Available

Gene Ontology (GO) - Biological Process for SPATA42 Gene

None

No data available for Pathways by source , Interacting Proteins and SIGNOR curated interactions for SPATA42 Gene

Drugs & Compounds for SPATA42 Gene

No Compound Related Data Available

Transcripts for SPATA42 Gene

Non-coding RNA (ncRNA) Transcripts from RNAcentral for SPATA42 Gene

RNAcentral Transcript ID Subcategory Length (nts) # of Sources Source Identifiers and Annotations
URS0000071D11_9606 lncRNA 535 3

Ensembl: ENST00000369989 (view in UCSC) ,

LNCipedia: SPATA42:1,

NONCODE: NONHSAT005003.2,

URS00001D559B_9606 lncRNA 443 3

Ensembl: ENST00000417241 (view in UCSC) ,

LncBook: HSALNT0012147,

LNCipedia: SPATA42:3,

URS000075BBB0_9606 lncRNA 535 1

RefSeq: NR_034168,

URS0000EF2A90_9606 lncRNA 472 1

Ensembl: ENST00000662170 (view in UCSC) ,

URS000075AB99_9606 lncRNA 468 1

RefSeq: NR_049777,

SPATA42 in the GeneCaRNA (GeneCards ncRNA compendium) hub on the UCSC Golden Path

Additional transcripts not in RNAcentral for SPATA42 Gene

3 NCBI additional mRNA sequence :

Alternative Splicing Database (ASD) splice patterns (SP) for SPATA42 Gene

No ASD Table

Relevant External Links for SPATA42 Gene

GeneLoc Exon Structure for
SPATA42

Expression for SPATA42 Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and SAGE for SPATA42 Gene

mRNA differential expression in normal tissues according to GTEx for SPATA42 Gene

This gene is overexpressed in Testis (x51.7).

Transcriptomic regulation report from SPP (The Signaling Pathways Project) for SPATA42

genes like me logo Genes that share expression patterns with SPATA42: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , Protein differential expression in normal tissues , Protein expression , Protein tissue co-expression partners , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for SPATA42 Gene

Orthologs for SPATA42 Gene

Evolution for SPATA42 Gene

ENSEMBL:
Gene Tree for SPATA42 (if available)
TreeFam:
Gene Tree for SPATA42 (if available)

No data available for Orthologs for SPATA42 Gene

Paralogs for SPATA42 Gene

No data available for Paralogs for SPATA42 Gene

Variants for SPATA42 Gene

dbSNP identifiers (rs#s) for variants without ClinVar clinical significance for SPATA42 Gene

All consequence types are included: molecular consequences (e.g. missense, synonymous), and location-based (e.g. intron, upstream).

Structural Variations from Database of Genomic Variants (DGV) for SPATA42 Gene

Variant ID Type Subtype PubMed ID
esv3587139 CNV gain 21293372
esv3587140 CNV gain 21293372
nsv1013192 CNV gain 25217958

Additional Variant Information for SPATA42 Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
SPATA42

SNP Genotyping and Copy Number Assays for research

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot , Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP and Variation tolerance for SPATA42 Gene

Disorders for SPATA42 Gene

MalaCards: The human disease database

(1) MalaCards diseases for SPATA42 Gene - From: COP

Disorder Aliases PubMed IDs
spermatogenic failure, x-linked, 1
  • spgfx1
- elite association - COSMIC cancer census association via MalaCards

Additional Disease Information for SPATA42

genes like me logo Genes that share disorders with SPATA42: view

No data available for UniProtKB/Swiss-Prot and Genatlas for SPATA42 Gene

Publications for SPATA42 Gene

No publications were found for SPATA42 Gene.

Products for SPATA42 Gene

Sources for SPATA42 Gene