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Aliases for RTL9 Gene
Aliases for RTL9 Gene
External Ids for RTL9 Gene
- HGNC: 29245
- Entrez Gene: 57529
- Ensembl: ENSG00000243978
- OMIM: 300965
- UniProtKB: Q8NET4
Previous HGNC Symbols for RTL9 Gene
- RGAG1
Summaries for RTL9 Gene
GeneCards Summary for RTL9 Gene
RTL9 (Retrotransposon Gag Like 9) is a Protein Coding gene. Diseases associated with RTL9 include Febrile Seizures, Familial, 10 and Embryonal Testis Carcinoma. An important paralog of this gene is MUC4.
Additional gene information for RTL9 Gene
- HGNC(29245)
- Entrez Gene(57529)
- Ensembl(ENSG00000243978)
- OMIM(300965)
- UniProtKB(Q8NET4)
- Open Targets Platform(ENSG00000243978)
- Search for RTL9 at DataMed
- Search for RTL9 at HumanCyc
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 RTL9 Gene
Genomics for RTL9 Gene
GeneHancer (GH) Regulatory Elements Pubs
Promoters and enhancers for RTL9 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 |
|---|---|---|---|---|---|---|---|---|---|---|
| GH0XJ110346 | Promoter | 0.6 | EPDnew | 600.4 | -11.2 | -11240 | 0.1 | REST CTCF ZBTB33 RAD21 | GNG5P2 RTL9 RF00017-8619 AMMECR1 LOC101928589 | |
| GH0XJ110358 | Promoter | 0.3 | EPDnew | 600.7 | +0.7 | 729 | 0.1 | RTL9 AMMECR1 | ||
| GH0XJ110315 | Promoter/Enhancer | 1.9 | EPDnew Ensembl ENCODE CraniofacialAtlas | 11.9 | -40.9 | -40890 | 4.8 | RNF2 PRDM10 ZNF512 IKZF1 POLR2A PRDM1 RBFOX2 PATZ1 IKZF2 BRD9 | LOC105373312 lnc-CHRDL1-2 lnc-RTL9-6 AMMECR1 RTL9 AMMECR1-IT1 LOC101928589 | |
| GH0XJ110401 | Enhancer | 1.2 | FANTOM5 Ensembl ENCODE | 12.2 | +45.0 | 45031 | 3.9 | CEBPG PRDM10 IKZF1 REST RAD21 SOX6 ZNF341 CEBPA ATF7 EP300 | RTL9 AMMECR1 | |
| GH0XJ110176 | Enhancer | 1.1 | Ensembl ENCODE | 11.8 | -177.9 | -177870 | 6.9 | LEF1 JUND DDX20 MTA2 PKNOX1 DPF2 HDAC1 ZNF600 SOX6 GATAD2B | RTL9 LOC101928589 lnc-RTL9-2 lnc-TMEM164-2 TMEM164 |
- Elite GeneHancer and/or Elite GeneHancer-gene association
Download GeneHancer data from 2017 publication |
Request up-to-date GeneHancer data (full dataset)
GeneHancers around RTL9 on the GeneHancer Hub at the UCSC Golden Path
Cistromic (ChIP-Seq) regulation report from SPP (The Signaling Pathways Project) for RTL9
Genomic Locations for RTL9 Gene
Genomic Locations for RTL9 Gene
- chrX:110,358,101-110,456,334
- (GRCh38/hg38)
- Size:
- 98,234 bases
- Orientation:
- Plus strand
- chrX:109,602,044-109,699,562
- (GRCh37/hg19)
- Size:
- 97,519 bases
- Orientation:
- Plus strand
Genomic View for RTL9 Gene
Genes around RTL9 on UCSC Golden Path with GeneCards custom track
- Cytogenetic band:
-
- Xq23 by HGNC
- Xq23 by Entrez Gene
- Xq23 by Ensembl
RTL9 Gene in genomic location: bands according to
Ensembl, locations according to GeneLoc
(and/or Entrez Gene and/or Ensembl if different)
Genomic Neighborhood
• Exon Structure
• Gene Density
RefSeq DNA sequence for RTL9 Gene
Proteins for RTL9 Gene
-
Protein details for RTL9 Gene (UniProtKB/Swiss-Prot)
- Protein Symbol:
- Q8NET4-RTL9_HUMAN
- Recommended name:
- Retrotransposon Gag-like protein 9
- Protein Accession:
- Q8NET4
- Q9P2M8
Protein attributes for RTL9 Gene
- Size:
- 1388 amino acids
- Molecular mass:
- 144280 Da
- Quaternary structure:
- No Data Available
- SequenceCaution:
-
- Sequence=BAA92556.1; Type=Erroneous initiation; Note=Extended N-terminus.; Evidence={ECO:0000305};
- Miscellaneous:
-
- RTL9 is one of at least 11 genes called Mar or Mart related to long terminal repeat retrotransposons. They do not correspond to functional retrotransposons, but rather to neofunctionalized retrotransposons genes.
Post-translational modifications for RTL9 Gene
Other Protein References for RTL9 Gene
- ENSEMBL proteins:
- REFSEQ proteins:
Antibody Products
- G Biosciences Immunotag™ RGAG1 Antibody
- Creative Diagnostics Anti-RGAG1 (aa 588-733) polyclonal antibody
-
Custom Antibody ServicesOriGene Antibodies for RTL9
- Novus Biologicals Antibodies for RTL9
- Invitrogen Antibodies for RTL9 (AFLGC-RTL9)
- antibodies-online: Show 4 available RGAG1 Antibodies ranked by validation data
Protein Products
- Search Origene for Purified Proteins, MassSpec and Protein Over-expression Lysates for RTL9
- Origene Custom Protein Services for RTL9
- Novus Biologicals proteins for RTL9
Assay Products
-
Boster Bio ELISA Kits for RTL9
No data available for DME Specific Peptides for RTL9 Gene
Domains & Families for RTL9 Gene
Gene Families for RTL9 Gene
- HGNC:
- Human Protein Atlas (HPA):
-
- Predicted intracellular proteins
Suggested Antigen Peptide Sequences for RTL9 Gene
- GenScript: Design optimal peptide antigens:
-
- cDNA FLJ60962, highly similar to Homo sapiens retrotransposon gag domain containing 1 (RGAG1), mRNA (B4DYG8_HUMAN)
- Tumor antigen BJ-HCC-23 (RGAG1_HUMAN)
No data available for Graphical View of Domain Structure and UniProtKB/Swiss-Prot for RTL9 Gene
Function for RTL9 Gene
Phenotypes From GWAS Catalog for RTL9 Gene
Phenotypes for RTL9 Gene
- GenomeRNAi human phenotypes for RTL9:
Animal Model Products
- Taconic Biosciences: Generate A Custom CRISPR Mouse Model For Your Study
CRISPR Products
- Applied Biological Materials (abm): CRISPR Clones for RTL9 - Select products 50% OFF >
- * RTL9 CRISPR as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
-
OriGene CRISPR knockouts for RTL9
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for RTL9
- Browse OriGene Inhibitory RNA Products For RTL9
Clone Products
- Applied Biological Materials (abm): Clones for RTL9 - Select products 50% OFF >
- * RTL9 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
- Sino Biological Human cDNA Clone for RTL9
Cell Line Products
-
Horizon Cell Lines for RTL9
No data available for Molecular function , Enzyme Numbers (IUBMB) , Gene Ontology (GO) - Molecular Function , Human Phenotype Ontology , Animal Models , miRNA , Transcription Factor Targets and HOMER Transcription for RTL9 Gene
Localization for RTL9 Gene
| Compartment | Confidence |
|---|---|
| nucleus | 2 |
| cytoskeleton | 1 |
| cytosol | 1 |
| mitochondrion | 0 |
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 RTL9 Gene
Pathways & Interactions for RTL9 Gene
Interacting Proteins for RTL9 Gene
GPS-Prot Interaction Network for RTL9
No data available for Pathways by source and SIGNOR curated interactions for RTL9 Gene
Transcripts for RTL9 Gene
mRNA/cDNA for RTL9 Gene
- 1 REFSEQ mRNAs :
- 5 NCBI additional mRNA sequence :
- 3 Ensembl transcripts including schematic representations, and UCSC links to gene/alias where relevant :
-
- ENST00000465301 5426 nts (view in UCSC)
- ENST00000520821 532 nts (view in UCSC)
- ENST00000540313 5225 nts (view in UCSC)
CRISPR Products
- Applied Biological Materials (abm): CRISPR Clones for RTL9 - Select products 50% OFF >
- * RTL9 CRISPR as ready-to-use vector or virus: ORF | Lenti- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
-
OriGene CRISPR knockouts for RTL9
miRNA Products
Inhibitory RNA Products
- Origene shrna, sirna, and RNAi products in human, mouse, rat for RTL9
- Browse OriGene Inhibitory RNA Products For RTL9
Clone Products
- Applied Biological Materials (abm): Clones for RTL9 - Select products 50% OFF >
- * RTL9 as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
- * Gene synthesis, site-directed mutagenesis, subcloning, and more services - Browse All
- Sino Biological Human cDNA Clone for RTL9
Relevant External Links for RTL9 Gene
- GeneLoc Exon Structure for
- RTL9
Expression for RTL9 Gene
Transcriptomic regulation report from SPP (The Signaling Pathways Project) for RTL9
No Expression Related Data Available
Primer Products
-
OriGene qPCR primer pairs for RTL9
No data available for mRNA expression in normal human tissues , mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA differential expression in normal tissues , 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 RTL9 Gene
Orthologs for RTL9 Gene
This gene was present in the common ancestor of chordates.
| Organism | Taxonomy | Gene | Similarity | Type | Details |
|---|---|---|---|---|---|
| Chimpanzee (Pan troglodytes) |
Mammalia | RGAG1 30 31 |
|
OneToOne | |
| Dog (Canis familiaris) |
Mammalia | RGAG1 30 31 |
|
OneToOne | |
| Cow (Bos Taurus) |
Mammalia | RGAG1 30 31 |
|
OneToOne | |
| Mouse (Mus musculus) |
Mammalia | Rgag1 30 31 |
|
OneToOne | |
| Rtl9 17 |
|
||||
| Rat (Rattus norvegicus) |
Mammalia | LOC100912526 30 |
|
||
| Lizard (Anolis carolinensis) |
Reptilia | RGAG1 31 |
|
OneToOne |
- Species where no ortholog for RTL9 was found in the sources mined by GeneCards:
-
- A. gosspyii yeast (Eremothecium gossypii)
- Actinobacteria (Mycobacterium tuberculosis)
- African clawed frog (Xenopus laevis)
- African malaria mosquito (Anopheles gambiae)
- Alicante grape (Vitis vinifera)
- Alpha proteobacteria (Wolbachia pipientis)
- Amoeba (Dictyostelium discoideum)
- Archea (Pyrococcus horikoshii)
- Baker's yeast (Saccharomyces cerevisiae)
- Barley (Hordeum vulgare)
- Beta proteobacteria (Neisseria meningitidis)
- Bread mold (Neurospora crassa)
- Chicken (Gallus gallus)
- Chromalveolata (Phytophthora infestans)
- Common water flea (Daphnia pulex)
- Corn (Zea mays)
- E. coli (Escherichia coli)
- Filamentous fungi (Aspergillus nidulans)
- Firmicute Bacteria (Streptococcus pneumoniae)
- Fission Yeast (Schizosaccharomyces pombe)
- Fruit Fly (Drosophila melanogaster)
- Green Algae (Chlamydomonas reinhardtii)
- Honey Bee (Apis mellifera)
- K. Lactis Yeast (Kluyveromyces lactis)
- Loblloly Pine (Pinus taeda)
- Malaria Parasite (Plasmodium falciparum)
- Medicago Trunc (Medicago Truncatula)
- Moss (Physcomitrella patens)
- Oppossum (Monodelphis domestica)
- Orangutan (Pongo pygmaeus)
- Pig (Sus scrofa)
- Platypus (Ornithorhynchus anatinus)
- Rainbow Trout (Oncorhynchus mykiss)
- Rice (Oryza sativa)
- Rice Blast Fungus (Magnaporthe grisea)
- Schistosome Parasite (Schistosoma mansoni)
- Sea Anemone (Nematostella vectensis)
- Sea Vase (Ciona intestinalis)
- Sea Squirt (Ciona savignyi)
- Sea Urchin (Strongylocentrotus purpuratus)
- Sorghum (Sorghum bicolor)
- Soybean (Glycine max)
- Stem Rust Fungus (Puccinia graminis)
- Sugarcane (Saccharum officinarum)
- Thale Cress (Arabidopsis thaliana)
- Tomato (Lycopersicon esculentum)
- Toxoplasmosis (Toxoplasma gondii)
- Trichoplax (Trichoplax adhaerens)
- Tropical Clawed Frog (Silurana tropicalis)
- Wheat (Triticum aestivum)
- Worm (Caenorhabditis elegans)
- Zebrafish (Danio rerio)
Evolution for RTL9 Gene
- ENSEMBL:
- Gene Tree for RTL9 (if available)
- TreeFam:
- Gene Tree for RTL9 (if available)
- Aminode:
- Evolutionary constrained regions (ECRs) for RTL9: view image
Paralogs for RTL9 Gene
Variants for RTL9 Gene
Sequence variations, with clinical significance, from ClinVar and Humsavar, with links to dbSNP for RTL9 Gene
| SNP ID | Clinical significance and condition | Chr 0X pos | Variation | AA Info | Type |
|---|---|---|---|---|---|
| rs760284501 | Uncertain Significance: not provided | 110,452,751(+) | G/A | MISSENSE_VARIANT | |
| rs771130284 | Uncertain Significance: Spinocerebellar ataxia, X-linked | 110,453,979(+) | C/T | MISSENSE_VARIANT | |
| rs35495390 | - | p.Pro777Ser |
| Variant ID | Type | Subtype | PubMed ID |
|---|---|---|---|
| esv2758884 | CNV | loss | 17122850 |
Residual Variation Intolerance Score:
90.7% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score:
3.59;
56.22% of all genes are more intolerant (likely to be disease-causing)
Additional Variant Information for RTL9 Gene
- SNPedia medical, phenotypic, and genealogical associations of SNPs for
- RTL9
No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for RTL9 Gene
Disorders for RTL9 Gene
| Disorder | Aliases | PubMed IDs |
|---|---|---|
| febrile seizures, familial, 10 |
|
|
| embryonal testis carcinoma |
|
|
| familial febrile seizures |
|
|
| non-syndromic x-linked intellectual disability |
|
|
Search RTL9 in MalaCards
View complete list of genes associated with diseases
Additional Disease Information for RTL9
No data available for UniProtKB/Swiss-Prot and Genatlas for RTL9 Gene
Publications for RTL9 Gene
- A family of neofunctionalized Ty3/gypsy retrotransposon genes in mammalian genomes. (PMID: 16093683) Brandt J … Volff JN (Cytogenetic and genome research 2005) 2 3 4
- Prediction of the coding sequences of unidentified human genes. XVI. The complete sequences of 150 new cDNA clones from brain which code for large proteins in vitro. (PMID: 10718198) Nagase T … Ohara O (DNA research : an international journal for rapid publication of reports on genes and genomes 2000) 2 3 4
- Transposable elements as a source of genetic innovation: expression and evolution of a family of retrotransposon-derived neogenes in mammals. (PMID: 15716091) Brandt J … Volff JN (Gene 2005) 2 3
- The status, quality, and expansion of the NIH full-length cDNA project: the Mammalian Gene Collection (MGC). (PMID: 15489334) Gerhard DS … MGC Project Team (Genome research 2004) 3 4
- Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3
ExternalLinks
Products for RTL9 Gene
- Custom Antibody ServicesOriGene Antibodies for RTL9
- Browse OriGene ELISA Kits
- Custom Assay Services
- Search Origene for Purified Proteins, MassSpec and Protein Over-expression Lysates for RTL9
- Origene Custom Protein Services for RTL9
- Origene shrna, sirna, and RNAi products in human, mouse, rat for RTL9
- Browse OriGene Inhibitory RNA Products For RTL9
- OriGene qPCR primer pairs for RTL9
- OriGene CRISPR knockouts for RTL9
- Custom cloning services - gene synthesis, subcloning, mutagenesis, variant library, vector shuttling
- Browse OriGene miRNA Products For RTL9
- Sino Biological Human cDNA Clone for RTL9
- Browse Sino Biological Recombinant Proteins
- Browse Sino Biological Cell Lysates
- Browse Sino Biological Antibodies
- Browse Sino Biological Assays
- Browse cDNA Clones
- Browse ELISA Kits
- Browse CRO Services
- High-throughput Antibody Production Service
- Protein Production Service
- Epitope Tag Antibodies & Reporter Protein Antibodies
- Lentiviral ORF Clones
- Novus Biologicals Antibodies for RTL9
- Novus Biologicals proteins for RTL9
- Browse Antibodies
- Browse Peptides and Proteins
- Browse Lysates
- Browse ELISA Kits
- Invitrogen Antibodies for RTL9 (AFLGC-RTL9)
- VectorBuilder Custom and pre-made DNA vectors for RTL9 (ie. gene expression, shRNA knockdown, CRISPR)
- VectorBuilder Viral vectors for RTL9 (ie. lentivirus, AAV, adenovirus)
- VectorBuilder CRISPR vectors for RTL9 (ie. knockout, knockin, CRISPRa, CRISPRi)
- VectorBuilder Virus packaging for RTL9 CRISPR vectors (ie. lentivirus, AAV, adenovirus)
- VectorBuilder Stable cell line generation for RTL9
- antibodies-online: Show 4 available RGAG1 Antibodies ranked by validation data
- antibodies-online: Search results for available RGAG1 related products ranked by validation data
- antibodies-online: Search results for available RGAG1 related products ranked by validation data
- Horizon Cell Lines for RTL9
- Browse GeneCopoeia Cell Lines
- Search GeneCopoeia for knockout CRISPR/Cas9 clones, lentivirus, and/or AAV products for RTL9
- Search GeneCopoeia for ORF cDNA, lentivirus, AAV viral particles, and/or promoter clone products for RTL9
- Search GeneCopoeia for miRNA 3'UTR Target clone products for RTL9
- Search GeneCopoeia for shRNA, lentivirus, and/or AAV clone products for RTL9
Sources for RTL9 Gene
- (1) GeneCards
- (2) HGNC
- (3) NCBI Entrez Gene
- (4) UniProtKB/Swiss-Prot
- (5) Ensembl
- (6) OMIM
- (7) GeneLoc
- (8) Gene Wiki
- (9) UCSC
- (10) PhosphoSitePlus
- (11) Cell Signaling Technology
- (12) GO
- (13) UniProtKB/TrEMBL
- (14) InterPro
- (15) ProtoNet
- (16) Blocks
- (17) MGI
- (18) IUBMB
- (19) KEGG
- (20) MINT
- (21) STRING
- (22) IntAct
- (23) Novoseek
- (24) PharmGKB
- (25) DrugBank
- (26) HMDB
- (27) ASD
- (28) SAGE
- (29) SOURCE
- (30) HomoloGene
- (31) PanEnsembl
- (32) euGenes
- (33) SGD
- (34) FlyBase
- (35) WormBase
- (36) Pseudogene
- (37) DGV
- (38) dbSNP
- (39) GenAtlas
- (40) HGMD
- (41) GAD
- (42) BGMUT
- (43) HuGE
- (44) Atlas
- (45) GenBank
- (46) HORDE
- (47) HUGE
- (48) IMGT
- (49) Leiden
- (50) miRBase
- (51) DME
- (52) OriGene
- (53) PubMed
- (54) R&D Systems
- (55) TGDB
- (56) Tocris
- (57) Abcam
- (58) Novus Biologicals
- (59) ProSpec
- (60) Sino Biological
- (61) GenScript
- (62) Qiagen
- (63) OCA
- (64) Proteopedia
- (65) MOPED
- (66) neXtProt
- (67) Reactome
- (68) GeneGo (Thomson Reuters)
- (69) DISEASES
- (70) SIMAP
- (71) GenomeRNAi
- (72) LifeMap
- (73) miRTarBase
- (74) MalaCards
- (75) Invitrogen
- (76) BitterDB
- (77) ESI-BIO
- (78) RefSeq
- (79) BioSystems
- (80) MaxQB
- (81) IUPHAR
- (82) BioGPS
- (83) Illumina
- (84) COMPARTMENTS
- (85) HOMER
- (86) PaxDb
- (87) ApexBio
- (88) Addgene
- (89) antibodies-online
- (90) CYP
- (91) NONCODE
- (92) TreeFam
- (93) PathCards
- (94) GeneReviews
- (95) GeneTex
- (96) Taconic Biosciences
- (97) GTEx
- (98) ProteomicsDB
- (99) SCBT
- (100) DGIdb
- (101) ClinicalTrials
- (102) RVIS
- (103) SIGNOR
- (104) diseasecard
- (105) NIH Rare Diseases
- (106) Orphanet
- (107) UMLS
- (108) GTR
- (109) Disease Ontology
- (110) Genetics Home Reference
- (111) MeSH
- (112) MedlinePlus
- (113) CDC
- (114) NINDS
- (115) NCBI Bookshelf
- (116) ClinVar
- (117) Gene Damage Index
- (118) HPO
- (119) UDN
- (120) VISTA
- (121) FANTOM5
- (122) ENCODE
- (123) ProSci
- (124) Horizon
- (125) The Signaling Pathways Project (SPP)
- (126) IID
- (127) VectorBuilder
- (128) SNPedia
- (129) BRCA Exchange
- (130) CIViC
- (131) ProteoGenix
- (132) dbSUPER
- (133) TISSUES
- (134) Gene ORGANizer
- (135) abm
- (136) Human Protein Atlas
- (137) GWAS Catalog
- (138) Monarch Initiative
- (139) DataMed
- (140) HumanCyc
- (141) UCNEbase
- (142) EPDnew
- (143) Applied Biosystems
- (144) GlyConnect
- (145) Aminode
- (146) GeneCopoeia
- (147) GPS-Prot
- (148) RNACentral
- (149) LncRNADisease
- (150) LOVD
- (151) miR2Disease
- (152) DiseaseEnhancer
- (153) Boster Bio
- (154) Biorbyt
- (155) Biocompare
- (156) Mastermind
- (157) CTD^2 Dashboard
- (158) CraniofacialAtlas
- (159) GeneImprint
- (160) Synthego
- (161) ENA
- (162) GtRNAdb
- (163) LncBase
- (164) LncBook
- (165) LNCipedia
- (166) Modomics
- (167) PDBe
- (168) Rfam
- (169) SILVA
- (170) snOPY
- (171) SRPDB
- (172) GENCODE
- (173) TarBase
- (174) Signalway Antibody
- (175) Open Targets Platform
- (176) 5SRRNADB
- (177) snoDB
- (178) MirGeneDB