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Aliases for LCA5L Gene

Aliases for LCA5L Gene

  • Lebercilin LCA5 Like 2 3
  • Leber Congenital Amaurosis 5-Like Protein 3 4
  • Lebercilin-Like Protein 3 4
  • LCA5L, Lebercilin Like 3 5
  • C21orf13 3 4
  • Chromosome 21 Open Reading Frame 13 2
  • Leber Congenital Amaurosis 5-Like 2

External Ids for LCA5L Gene

Previous HGNC Symbols for LCA5L Gene

  • C21orf13

Previous GeneCards Identifiers for LCA5L Gene

  • GC21M039702
  • GC21M040777
  • GC21M026246

Summaries for LCA5L Gene

GeneCards Summary for LCA5L Gene

LCA5L (Lebercilin LCA5 Like) is a Protein Coding gene. Diseases associated with LCA5L include Leber Congenital Amaurosis 5 and Leber Congenital Amaurosis. An important paralog of this gene is LCA5.

Additional gene information for LCA5L Gene

No data available for Entrez Gene Summary , CIViC summary , UniProtKB/Swiss-Prot , Tocris Summary , Gene Wiki entry , PharmGKB "VIP" Summary , fRNAdb sequence ontologies and piRNA Summary for LCA5L Gene

Genomics for LCA5L Gene

GeneHancer (GH) Regulatory Elements for LCA5L Gene

Promoters and enhancers for LCA5L 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
GH21J039444 Promoter/Enhancer 2 EPDnew Ensembl ENCODE 650.4 +0.2 227 2.4 ZNF652 ELF3 ZFX ZKSCAN8 ZNF148 NKRF POLR2A GTF2F1 CSDE1 ZNF687 LCA5L SH3BGR MIR6508 HMGN1 GET1 GC21P039407 WRB-SH3BGR
GH21J039450 Promoter/Enhancer 2.2 EPDnew FANTOM5 Ensembl ENCODE 50.8 -6.5 -6525 3.9 CC2D1A SP1 ZFX ZKSCAN8 ZNF148 MLLT1 CSDE1 BACH1 TRIM24 ZNF174 SH3BGR LCA5L HMGN1 GET1 BRWD1 PCP4 MIR6508 GC21P039465 WRB-SH3BGR
GH21J039441 Enhancer 1.2 FANTOM5 Ensembl ENCODE 28.9 +3.7 3683 1.9 CC2D1A CTCF RAD21 ARID2 IKZF1 REST TRIM22 ZNF561 SOX6 ARNT LCA5L SH3BGR GC21P039407 WRB-SH3BGR
GH21J038906 Promoter/Enhancer 2.1 FANTOM5 Ensembl ENCODE dbSUPER 15.4 +534.4 534364 9.6 ZNF473 MTA3 ZNF652 ELF3 MLLT1 GTF2F1 NFIB ZSCAN21 NCOA3 CDC5L HMGN1 LCA5L PSMG1 LINC00114 RPSAP64 LOC400867 ENSG00000205622
GH21J039311 Promoter/Enhancer 2.2 EPDnew Ensembl ENCODE 13 +132.3 132317 3.4 MTA3 SP1 CC2D1A ZFX ELF3 ZKSCAN8 MNT ZNF148 NKRF POLR2A BRWD1 GC21M039313 PIR35926 BRWD1-AS2 HMGN1 PSMG1 GET1 LCA5L BRWD1-AS1 SH3BGR
- Elite GeneHancer and/or Elite GeneHancer-gene association Download GeneHancer data from 2017 publication | Request up-to-date GeneHancer data (full dataset)

GeneHancers around LCA5L on UCSC Golden Path with GeneCards custom track

Top Transcription factor binding sites by QIAGEN in the LCA5L gene promoter:
  • c-Rel
  • CREB
  • deltaCREB
  • NF-kappaB
  • NF-kappaB1
  • NF-kappaB2
  • POU3F2
  • POU3F2 (N-Oct-5a)
  • POU3F2 (N-Oct-5b)
  • RFX1

Genomic Locations for LCA5L Gene

Genomic Locations for LCA5L Gene
chr21:39,405,844-39,445,805
(GRCh38/hg38)
Size:
39,962 bases
Orientation:
Minus strand
chr21:40,777,770-40,817,731
(GRCh37/hg19)
Size:
39,962 bases
Orientation:
Minus strand

Genomic View for LCA5L Gene

Genes around LCA5L on UCSC Golden Path with GeneCards custom track

Cytogenetic band:
LCA5L Gene in genomic location: bands according to Ensembl, locations according to GeneLoc (and/or Entrez Gene and/or Ensembl if different)
Genomic Location for LCA5L Gene
GeneLoc Logo Genomic Neighborhood Exon StructureGene Density

RefSeq DNA sequence for LCA5L Gene

Proteins for LCA5L Gene

  • Protein details for LCA5L Gene (UniProtKB/Swiss-Prot)

    Protein Symbol:
    O95447-LCA5L_HUMAN
    Recommended name:
    Lebercilin-like protein
    Protein Accession:
    O95447
    Secondary Accessions:
    • D3DSI0
    • Q3ZCT0

    Protein attributes for LCA5L Gene

    Size:
    670 amino acids
    Molecular mass:
    76505 Da
    Quaternary structure:
    No Data Available
    SequenceCaution:
    • Sequence=CAB90455.1; Type=Erroneous initiation; Evidence={ECO:0000305};

neXtProt entry for LCA5L Gene

Post-translational modifications for LCA5L Gene

  • Modification sites at PhosphoSitePlus
  • Modification sites at neXtProt

No data available for DME Specific Peptides for LCA5L Gene

Domains & Families for LCA5L Gene

Gene Families for LCA5L Gene

Human Protein Atlas (HPA):
  • Predicted intracellular proteins

Protein Domains for LCA5L Gene

InterPro:
ProtoNet:

Suggested Antigen Peptide Sequences for LCA5L Gene

GenScript: Design optimal peptide antigens:
  • Leber congenital amaurosis 5-like protein (LCA5L_HUMAN)

Graphical View of Domain Structure for InterPro Entry

O95447

UniProtKB/Swiss-Prot:

LCA5L_HUMAN :
  • Belongs to the LCA5 family.
Family:
  • Belongs to the LCA5 family.
genes like me logo Genes that share domains with LCA5L: view

Function for LCA5L Gene

Phenotypes From GWAS Catalog for LCA5L Gene

Gene Ontology (GO) - Molecular Function for LCA5L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005515 protein binding IPI 25416956
genes like me logo Genes that share ontologies with LCA5L: view
genes like me logo Genes that share phenotypes with LCA5L: view

Animal Model Products

CRISPR Products

miRNA for LCA5L Gene

miRTarBase miRNAs that target LCA5L

Clone Products

  • Applied Biological Materials (abm): Clones for LCA5L - Now 50% OFF >
  • * LCA5L as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * LCA5L tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

No data available for Molecular function , Enzyme Numbers (IUBMB) , Human Phenotype Ontology , Animal Models , Transcription Factor Targets and HOMER Transcription for LCA5L Gene

Localization for LCA5L 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 LCA5L gene
Compartment Confidence
cytoskeleton 3
nucleus 3
cytosol 2

Subcellular locations from the

Human Protein Atlas (HPA)
  • Cytosol (1)
  • Nucleoplasm (1)
See all subcellular structures

Gene Ontology (GO) - Cellular Components for LCA5L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0005930 axoneme IBA 21873635
genes like me logo Genes that share ontologies with LCA5L: view

No data available for Subcellular locations from UniProtKB/Swiss-Prot for LCA5L Gene

Pathways & Interactions for LCA5L Gene

PathCards logo

SuperPathways for LCA5L Gene

No Data Available

Gene Ontology (GO) - Biological Process for LCA5L Gene

GO ID Qualified GO term Evidence PubMed IDs
GO:0042073 intraciliary transport IBA 21873635
genes like me logo Genes that share ontologies with LCA5L: view

No data available for Pathways by source and SIGNOR curated interactions for LCA5L Gene

Drugs & Compounds for LCA5L Gene

No Compound Related Data Available

Transcripts for LCA5L Gene

mRNA/cDNA for LCA5L Gene

Unigene Clusters for LCA5L Gene

Leber congenital amaurosis 5-like:
Representative Sequences:

CRISPR Products

Clone Products

  • Applied Biological Materials (abm): Clones for LCA5L - Now 50% OFF >
  • * LCA5L as ready-to-use vector or virus: ORF | Lenti- | Retro- | Adeno- | AAV- | Protein Vector - Browse All
  • * LCA5L tags and reporters available: His, HA, Myc, Flag, GFP, RFP, Luciferase - Browse All

Alternative Splicing Database (ASD) splice patterns (SP) for LCA5L Gene

ExUns: 1a · 1b · 1c ^ 2a · 2b ^ 3 ^ 4 ^ 5 ^ 6 ^ 7a · 7b · 7c ^ 8 ^ 9a · 9b · 9c · 9d ^ 10 ^ 11a · 11b · 11c ^ 12 ^ 13 ^ 14 ^ 15 ^ 16 ^
SP1: - -
SP2: - - - - - - - -
SP3: - - - - -
SP4: - - - - - - - -
SP5: - - -
SP6: - - - -
SP7:
SP8: - - -
SP9:
SP10: - - - - - - - - - -
SP11: - - -

ExUns: 17
SP1:
SP2:
SP3:
SP4:
SP5:
SP6:
SP7:
SP8:
SP9:
SP10:
SP11:

Relevant External Links for LCA5L Gene

GeneLoc Exon Structure for
LCA5L
ECgene alternative splicing isoforms for
LCA5L

Expression for LCA5L Gene

mRNA expression in normal human tissues from GTEx, Illumina, BioGPS, and CGAP SAGE for LCA5L Gene

mRNA differential expression in normal tissues according to GTEx for LCA5L Gene

This gene is overexpressed in Testis (x18.7).

Protein differential expression in normal tissues from HIPED for LCA5L Gene

This gene is overexpressed in Tlymphocyte (22.0), Platelet (10.9), Plasma (8.5), Frontal cortex (7.9), Monocytes (7.2), and Pancreatic juice (7.0).

Integrated Proteomics: protein expression in normal tissues and cell lines from ProteomicsDB and MOPED for LCA5L Gene



Protein tissue co-expression partners for LCA5L Gene

NURSA nuclear receptor signaling pathways regulating expression of LCA5L Gene:

LCA5L

SOURCE GeneReport for Unigene cluster for LCA5L Gene:

Hs.517284
genes like me logo Genes that share expression patterns with LCA5L: view

No data available for mRNA expression in embryonic tissues and stem cells from LifeMap Discovery , mRNA Expression by UniProt/SwissProt , Evidence on tissue expression from TISSUES and Phenotype-based relationships between genes and organs from Gene ORGANizer for LCA5L Gene

Orthologs for LCA5L Gene

This gene was present in the common ancestor of animals.

Orthologs for LCA5L Gene

Organism Taxonomy Gene Similarity Type Details
chimpanzee
(Pan troglodytes)
Mammalia LCA5L 35 34
  • 99.2 (n)
OneToOne
cow
(Bos Taurus)
Mammalia LCA5L 35 34
  • 77.91 (n)
OneToOne
rat
(Rattus norvegicus)
Mammalia Lca5l 34
  • 77.28 (n)
mouse
(Mus musculus)
Mammalia Lca5l 17 35 34
  • 70.76 (n)
oppossum
(Monodelphis domestica)
Mammalia LCA5L 35
  • 50 (a)
OneToOne
platypus
(Ornithorhynchus anatinus)
Mammalia LCA5L 35
  • 44 (a)
OneToOne
chicken
(Gallus gallus)
Aves LCA5L 35 34
  • 59.85 (n)
OneToOne
lizard
(Anolis carolinensis)
Reptilia LCA5L 35
  • 28 (a)
OneToOne
fruit fly
(Drosophila melanogaster)
Insecta CG6652 35
  • 16 (a)
OneToMany
Species where no ortholog for LCA5L was found in the sources mined by GeneCards:
  • A. gosspyii yeast (Ashbya 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)
  • Chromalveolata (Phytophthora infestans)
  • common water flea (Daphnia pulex)
  • corn (Zea mays)
  • dog (Canis familiaris)
  • E. coli (Escherichia coli)
  • filamentous fungi (Aspergillus nidulans)
  • Firmicute bacteria (Streptococcus pneumoniae)
  • fission yeast (Schizosaccharomyces pombe)
  • 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)
  • orangutan (Pongo pygmaeus)
  • pig (Sus scrofa)
  • rainbow trout (Oncorhynchus mykiss)
  • rice (Oryza sativa)
  • rice blast fungus (Magnaporthe grisea)
  • schistosome parasite (Schistosoma mansoni)
  • sea anemone (Nematostella vectensis)
  • sea squirt (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 LCA5L Gene

ENSEMBL:
Gene Tree for LCA5L (if available)
TreeFam:
Gene Tree for LCA5L (if available)
Aminode:
Evolutionary constrained regions (ECRs) for LCA5L: view image

Paralogs for LCA5L Gene

Paralogs for LCA5L Gene

(1) SIMAP similar genes for LCA5L Gene using alignment to 10 proteins:

  • LCA5L_HUMAN
  • C9J198_HUMAN
  • C9J293_HUMAN
  • C9J5D2_HUMAN
  • C9J9Z3_HUMAN
  • C9JFB6_HUMAN
  • C9JIJ8_HUMAN
  • C9JRD7_HUMAN
  • C9JYR0_HUMAN
  • U3KPS7_HUMAN
genes like me logo Genes that share paralogs with LCA5L: view

Variants for LCA5L Gene

Sequence variations from dbSNP and Humsavar for LCA5L Gene

SNP ID Clin Chr 21 pos Variation AA Info Type
rs1000007702 -- 39,431,803(-) A/G intron_variant
rs1000123303 -- 39,431,504(-) AT/ intron_variant
rs1000134360 -- 39,445,607(-) T/G 5_prime_UTR_variant, genic_upstream_transcript_variant, intron_variant, upstream_transcript_variant
rs1000186755 -- 39,406,547(-) C/G/T coding_sequence_variant, missense_variant
rs1000377015 -- 39,409,685(-) T/G intron_variant

Structural Variations from Database of Genomic Variants (DGV) for LCA5L Gene

Variant ID Type Subtype PubMed ID
dgv4433n100 CNV gain 25217958
esv25616 CNV loss 19812545
esv2672503 CNV deletion 23128226
esv2723433 CNV deletion 23290073
esv3647018 CNV loss 21293372
esv3647019 CNV loss 21293372
nsv1061454 CNV gain 25217958

Variation tolerance for LCA5L Gene

Residual Variation Intolerance Score: 76.9% of all genes are more intolerant (likely to be disease-causing)
Gene Damage Index Score: 5.74; 73.31% of all genes are more intolerant (likely to be disease-causing)

Additional Variant Information for LCA5L Gene

SNPedia medical, phenotypic, and genealogical associations of SNPs for
LCA5L

SNP Genotyping and Copy Number Assay Products

No data available for Polymorphic Variants from UniProtKB/Swiss-Prot for LCA5L Gene

Disorders for LCA5L Gene

MalaCards: The human disease database

(2) MalaCards diseases for LCA5L Gene - From: GeneCards

Disorder Aliases PubMed IDs
leber congenital amaurosis 5
  • lca5
leber congenital amaurosis
  • lca
- elite association - COSMIC cancer census association via MalaCards
Search LCA5L in MalaCards View complete list of genes associated with diseases

Additional Disease Information for LCA5L

genes like me logo Genes that share disorders with LCA5L: view

No data available for UniProtKB/Swiss-Prot and Genatlas for LCA5L Gene

Publications for LCA5L Gene

  1. 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 58
  2. The DNA sequence of human chromosome 21. (PMID: 10830953) Hattori M … Chromosome 21 mapping and sequencing consortium (Nature 2000) 3 4 58
  3. E3 ubiquitin ligase RNF123 targets lamin B1 and lamin-binding proteins. (PMID: 29676528) Khanna R … Parnaik VK (The FEBS journal 2018) 3 58
  4. Architecture of the human interactome defines protein communities and disease networks. (PMID: 28514442) Huttlin EL … Harper JW (Nature 2017) 3 58
  5. A Global Analysis of the Receptor Tyrosine Kinase-Protein Phosphatase Interactome. (PMID: 28065597) Yao Z … Stagljar I (Molecular cell 2017) 3 58

Products for LCA5L Gene

Sources for LCA5L Gene

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