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NLGN4Y neuroligin 4 Y-linked [ Homo sapiens (human) ]

Gene ID: 22829, updated on 11-Apr-2024

Summary

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Official Symbol
NLGN4Yprovided by HGNC
Official Full Name
neuroligin 4 Y-linkedprovided by HGNC
Primary source
HGNC:HGNC:15529
See related
Ensembl:ENSG00000165246 MIM:400028; AllianceGenome:HGNC:15529
Gene type
protein coding
RefSeq status
REVIEWED
Organism
Homo sapiens
Lineage
Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as
HNL4Y
Summary
This gene encodes a type I membrane protein that belongs to the family of neuroligins, which are cell adhesion molecules present at the postsynaptic side of the synapse, and may be essential for the formation of functional synapses. Alternatively spliced transcript variants have been found for this gene.[provided by RefSeq, Mar 2011]
Expression
Biased expression in brain (RPKM 2.6), prostate (RPKM 1.8) and 13 other tissues See more
Orthologs
all
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Genomic context

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Location:
Yq11.221
Exon count:
16
Annotation release Status Assembly Chr Location
RS_2023_10 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (14522616..14845654)
RS_2023_10 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (15429244..15752217)
105.20220307 previous assembly GRCh37.p13 (GCF_000001405.25) Y NC_000024.9 (16634496..16957534)

Chromosome Y - NC_000024.10Genomic Context describing neighboring genes Neighboring gene patatin-like phospholipase domain containing 4 pseudogene 1 Neighboring gene patatin like phospholipase domain containing 4 pseudogene 1 Neighboring gene MED14-independent group 3 enhancer GRCh37_chrY:16452370-16453569 Neighboring gene AGK pseudogene 1 Neighboring gene NLGN4Y antisense RNA 1 Neighboring gene mediator complex subunit 13 pseudogene 1 Neighboring gene CYCS pseudogene 46

Genomic regions, transcripts, and products

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Go to nucleotide: Graphics FASTA GenBank

Expression

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  • Project title: HPA RNA-seq normal tissues
  • Description: RNA-seq was performed of tissue samples from 95 human individuals representing 27 different tissues in order to determine tissue-specificity of all protein-coding genes
  • BioProject: PRJEB4337
  • Publication: PMID 24309898
  • Analysis date: Wed Apr 4 07:08:55 2018

Bibliography

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Related articles in PubMed

  1. Male homosexuality and maternal immune responsivity to the Y-linked protein NLGN4Y. Bogaert AF, et al. Proc Natl Acad Sci U S A, 2018 Jan 9. PMID 29229842, Free PMC Article
  2. Constructing Bayesian networks by integrating gene expression and copy number data identifies NLGN4Y as a novel regulator of prostate cancer progression. Gong Y, et al. Oncotarget, 2016 Oct 18. PMID 27626693, Free PMC Article
  3. Behavioral phenotypes in males with XYY and possible role of increased NLGN4Y expression in autism features. Ross JL, et al. Genes Brain Behav, 2015 Feb. PMID 25558953, Free PMC Article
  4. A Cluster of Autism-Associated Variants on X-Linked NLGN4X Functionally Resemble NLGN4Y. Nguyen TA, et al. Neuron, 2020 Jun 3. PMID 32243781, Free PMC Article
  5. Association of Y chromosome haplotypes with autism. Serajee FJ, et al. J Child Neurol, 2009 Oct. PMID 19605777

See all (23) citations in PubMed

GeneRIFs: Gene References Into Functions

What's a GeneRIF?
  1. A Cluster of Autism-Associated Variants on X-Linked NLGN4X Functionally Resemble NLGN4Y.
    Title: A Cluster of Autism-Associated Variants on X-Linked NLGN4X Functionally Resemble NLGN4Y.
  2. Results suggest an association between a maternal immune response to neuroligin 4 Y-linked (NLGN4Y) and subsequent sexual orientation in male offspring.
    Title: Male homosexuality and maternal immune responsivity to the Y-linked protein NLGN4Y.
  3. Results suggest that NLGN4Y is an important negative regulator in prostate cancer progression.
    Title: Constructing Bayesian networks by integrating gene expression and copy number data identifies NLGN4Y as a novel regulator of prostate cancer progression.
  4. Expression of NLGN4Y, a gene that may be involved in synaptic function, is increased in boys with XYY
    Title: Behavioral phenotypes in males with XYY and possible role of increased NLGN4Y expression in autism features.
  5. investigated 12 single-nucleotide polymorphisms in Y-linked neuroligin 4, transducin b-like 1, and eukaryotic translation initiation factor 1a genes, results suggest a Y chromosome effect in autism
    Title: Association of Y chromosome haplotypes with autism.
  6. Observational study of gene-disease association. (HuGE Navigator)
    Title: Association of Y chromosome haplotypes with autism.
  7. The coding sequences and splice junctions of the NLGN4Y gene were analyzed in 335 male samples (290 with autism and 45 with mental retardation) to analyze sequence variants in NLGN4Y that are associated with autism or mental retardation.
    Title: Analysis of the neuroligin 4Y gene in patients with autism.
  8. Neuroligin mutations most probably represent rare causes of autism; it is unlikely that the allelic variants in any of these genes would be major risk factors for autism.
    Title: Analysis of four neuroligin genes as candidates for autism.
Submit: New GeneRIF Correction

Phenotypes

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Find tests for this gene in the NIH Genetic Testing Registry (GTR)

Review eQTL and phenotype association data in this region using PheGenI

Variation

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See variants in ClinVar

See studies and variants in dbVar

See Variation Viewer (GRCh37.p13)

See Variation Viewer (GRCh38)

Genotypes

Pathways from PubChem

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Interactions

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Products Interactant Other Gene Complex Source Pubs Description

General gene information

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Markers

Homology

Clone Names

  • KIAA0951

Gene Ontology Provided by GOA

Function Evidence Code Pubs
enables cell adhesion molecule binding TAS
Traceable Author Statement
more info
 PubMed 
enables neurexin family protein binding IBA
Inferred from Biological aspect of Ancestor
more info
  
enables protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables scaffold protein binding IPI
Inferred from Physical Interaction
more info
 PubMed 
enables signaling receptor activity IBA
Inferred from Biological aspect of Ancestor
more info
  
Process Evidence Code Pubs
involved_in chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in learning IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in modulation of chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in neuron cell-cell adhesion TAS
Traceable Author Statement
more info
 PubMed 
involved_in postsynaptic membrane assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in presynapse assembly TAS
Traceable Author Statement
more info
 PubMed 
involved_in presynaptic membrane assembly IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in social behavior IMP
Inferred from Mutant Phenotype
more info
 PubMed 
involved_in synaptic vesicle endocytosis IBA
Inferred from Biological aspect of Ancestor
more info
  
involved_in vocalization behavior IMP
Inferred from Mutant Phenotype
more info
 PubMed 
Component Evidence Code Pubs
located_in asymmetric, glutamatergic, excitatory synapse TAS
Traceable Author Statement
more info
 PubMed 
is_active_in cell surface IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in membrane TAS
Traceable Author Statement
more info
 PubMed 
is_active_in plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in plasma membrane TAS
Traceable Author Statement
more info
  
located_in postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
  
is_active_in postsynaptic specialization membrane IBA
Inferred from Biological aspect of Ancestor
more info
  
located_in presynapse IEA
Inferred from Electronic Annotation
more info
  
located_in symmetric, GABA-ergic, inhibitory synapse TAS
Traceable Author Statement
more info
 PubMed 
is_active_in synapse IBA
Inferred from Biological aspect of Ancestor
more info
  

General protein information

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Preferred Names
neuroligin-4, Y-linked
Names
alternative HNL4Y

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

Genomic

  1. NG_028212.1 RefSeqGene

    Range
    6922..328047
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001164238.1 → NP_001157710.1  neuroligin-4, Y-linked isoform 2 precursor

    See identical proteins and their annotated locations for NP_001157710.1

    Status: REVIEWED

    Description
    Transcript Variant: This variant (2) lacks several exons from the 3' end, and contains 2 alternate exons, including the 3' terminal exon, compared to variant 1. This results in a frame-shift, and a shorter isoform (2) with a distinct C-terminus compared to isoform 1.
    Source sequence(s)
    AF376804, BC032567, BF222878
    UniProtKB/TrEMBL
    H0Y7G6
    Related
    ENSP00000412638.1, ENST00000413217.1
    Conserved Domains (1) summary
    cl21494
    Location:42 → 229
    Abhydrolase; alpha/beta hydrolases

  2. NM_001206850.2 → NP_001193779.1  neuroligin-4, Y-linked isoform 3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (3) contains several differences compared to variant 1, which results in translation initiation from an in-frame downstream AUG, and an isoform (3) with a shorter N-terminus compared to isoform 1.
    Source sequence(s)
    AB023168, AC011903, AF376804, DC360504
    Consensus CDS
    CCDS56619.1
    UniProtKB/Swiss-Prot
    Q8NFZ3
    Related
    ENSP00000372325.1, ENST00000382872.5
    Conserved Domains (2) summary
    COG0657
    Location:1 → 98
    Aes; Acetyl esterase/lipase [Lipid transport and metabolism]
    pfam00135
    Location:1 → 422
    COesterase; Carboxylesterase family

  3. NM_001365584.1 → NP_001352513.1  neuroligin-4, Y-linked isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Consensus CDS
    CCDS94714.1
    UniProtKB/TrEMBL
    A6NMU8, B4DHI3
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 610
    COesterase; Carboxylesterase family

  4. NM_001365586.1 → NP_001352515.1  neuroligin-4, Y-linked isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Consensus CDS
    CCDS94714.1
    UniProtKB/TrEMBL
    A6NMU8, B4DHI3
    Related
    ENSP00000496594.1, ENST00000643089.1
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 610
    COesterase; Carboxylesterase family

  5. NM_001365588.1 → NP_001352517.1  neuroligin-4, Y-linked isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Consensus CDS
    CCDS94714.1
    UniProtKB/TrEMBL
    A6NMU8, B4DHI3
    Related
    ENSP00000510011.1, ENST00000684976.1
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 610
    COesterase; Carboxylesterase family

  6. NM_001365590.1 → NP_001352519.1  neuroligin-4, Y-linked isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Consensus CDS
    CCDS14788.1
    UniProtKB/Swiss-Prot
    F5H6W0, Q14D08, Q7Z3T5, Q8N5B6, Q8NFZ3, Q9Y2F8
    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 590
    COesterase; Carboxylesterase family

  7. NM_001365591.1 → NP_001352520.1  neuroligin-4, Y-linked isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Consensus CDS
    CCDS14788.1
    UniProtKB/Swiss-Prot
    F5H6W0, Q14D08, Q7Z3T5, Q8N5B6, Q8NFZ3, Q9Y2F8
    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 590
    COesterase; Carboxylesterase family

  8. NM_001365592.1 → NP_001352521.1  neuroligin-4, Y-linked isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Consensus CDS
    CCDS14788.1
    UniProtKB/Swiss-Prot
    F5H6W0, Q14D08, Q7Z3T5, Q8N5B6, Q8NFZ3, Q9Y2F8
    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 590
    COesterase; Carboxylesterase family

  9. NM_001365593.1 → NP_001352522.1  neuroligin-4, Y-linked isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Consensus CDS
    CCDS14788.1
    UniProtKB/Swiss-Prot
    F5H6W0, Q14D08, Q7Z3T5, Q8N5B6, Q8NFZ3, Q9Y2F8
    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 590
    COesterase; Carboxylesterase family

  10. NM_001394830.1 → NP_001381759.1  neuroligin-4, Y-linked isoform 4 precursor

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Consensus CDS
    CCDS94714.1
    UniProtKB/TrEMBL
    A6NMU8, B4DHI3
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 610
    COesterase; Carboxylesterase family

  11. NM_001394831.1 → NP_001381760.1  neuroligin-4, Y-linked isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Consensus CDS
    CCDS14788.1
    UniProtKB/Swiss-Prot
    F5H6W0, Q14D08, Q7Z3T5, Q8N5B6, Q8NFZ3, Q9Y2F8
    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Related
    ENSP00000342535.5, ENST00000339174.9
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 590
    COesterase; Carboxylesterase family

  12. NM_014893.5 → NP_055708.3  neuroligin-4, Y-linked isoform 1 precursor

    See identical proteins and their annotated locations for NP_055708.3

    Status: REVIEWED

    Description
    Transcript Variant: This variant (1) encodes the longer isoform (1).
    Source sequence(s)
    AC011903, AF376804, BM722570
    Consensus CDS
    CCDS14788.1
    UniProtKB/Swiss-Prot
    F5H6W0, Q14D08, Q7Z3T5, Q8N5B6, Q8NFZ3, Q9Y2F8
    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Related
    ENSP00000348169.2, ENST00000355905.6
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 590
    COesterase; Carboxylesterase family

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p14 Primary Assembly

    Range
    14522616..14845654
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_047442722.1 → XP_047298678.1  neuroligin-4, Y-linked isoform X5

  2. XM_006724874.3 → XP_006724937.1  neuroligin-4, Y-linked isoform X1

    See identical proteins and their annotated locations for XP_006724937.1

    UniProtKB/TrEMBL
    A6NMU8, B4DHI3
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 610
    COesterase; Carboxylesterase family

  3. XM_047442720.1 → XP_047298676.1  neuroligin-4, Y-linked isoform X2

    UniProtKB/Swiss-Prot
    F5H6W0, Q14D08, Q7Z3T5, Q8N5B6, Q8NFZ3, Q9Y2F8

  4. XM_011531428.2 → XP_011529730.1  neuroligin-4, Y-linked isoform X1

    See identical proteins and their annotated locations for XP_011529730.1

    UniProtKB/TrEMBL
    A6NMU8, B4DHI3
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 610
    COesterase; Carboxylesterase family

  5. XM_047442719.1 → XP_047298675.1  neuroligin-4, Y-linked isoform X2

    UniProtKB/Swiss-Prot
    F5H6W0, Q14D08, Q7Z3T5, Q8N5B6, Q8NFZ3, Q9Y2F8

  6. XM_011531430.3 → XP_011529732.1  neuroligin-4, Y-linked isoform X1

    See identical proteins and their annotated locations for XP_011529732.1

    UniProtKB/TrEMBL
    A6NMU8, B4DHI3
    Related
    ENSP00000372320.1, ENST00000382868.5
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 610
    COesterase; Carboxylesterase family

  7. XM_047442721.1 → XP_047298677.1  neuroligin-4, Y-linked isoform X5

  8. XM_017030041.2 → XP_016885530.1  neuroligin-4, Y-linked isoform X5

    UniProtKB/TrEMBL
    H0Y7G6
    Conserved Domains (1) summary
    cl21494
    Location:42 → 229
    Abhydrolase; alpha/beta hydrolases

  9. XM_024452490.2 → XP_024308258.1  neuroligin-4, Y-linked isoform X1

    UniProtKB/TrEMBL
    A6NMU8, B4DHI3
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 610
    COesterase; Carboxylesterase family

  10. XM_011531427.3 → XP_011529729.1  neuroligin-4, Y-linked isoform X1

    See identical proteins and their annotated locations for XP_011529729.1

    UniProtKB/TrEMBL
    A6NMU8, B4DHI3
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 610
    COesterase; Carboxylesterase family

  11. XM_017030036.2 → XP_016885525.1  neuroligin-4, Y-linked isoform X2

    UniProtKB/Swiss-Prot
    F5H6W0, Q14D08, Q7Z3T5, Q8N5B6, Q8NFZ3, Q9Y2F8
    UniProtKB/TrEMBL
    A8K4S1, B3KP11
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 590
    COesterase; Carboxylesterase family

  12. XM_011531429.3 → XP_011529731.1  neuroligin-4, Y-linked isoform X1

    See identical proteins and their annotated locations for XP_011529731.1

    UniProtKB/TrEMBL
    A6NMU8, B4DHI3
    Conserved Domains (1) summary
    pfam00135
    Location:44 → 610
    COesterase; Carboxylesterase family

  13. XM_017030039.2 → XP_016885528.1  neuroligin-4, Y-linked isoform X3

    UniProtKB/TrEMBL
    A8K4S1, B3KP11

  14. XM_017030040.2 → XP_016885529.1  neuroligin-4, Y-linked isoform X4

    UniProtKB/Swiss-Prot
    Q8NFZ3
    Conserved Domains (2) summary
    COG0657
    Location:1 → 98
    Aes; Acetyl esterase/lipase [Lipid transport and metabolism]
    pfam00135
    Location:1 → 422
    COesterase; Carboxylesterase family

Alternate T2T-CHM13v2.0

Genomic

  1. NC_060948.1 Alternate T2T-CHM13v2.0

    Range
    15429244..15752217
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. XM_054328269.1 → XP_054184244.1  neuroligin-4, Y-linked isoform X5

  2. XM_054328260.1 → XP_054184235.1  neuroligin-4, Y-linked isoform X1

    UniProtKB/TrEMBL
    B4DHI3

  3. XM_054328264.1 → XP_054184239.1  neuroligin-4, Y-linked isoform X2

    UniProtKB/Swiss-Prot
    F5H6W0, Q14D08, Q7Z3T5, Q8N5B6, Q8NFZ3, Q9Y2F8

  4. XM_054328261.1 → XP_054184236.1  neuroligin-4, Y-linked isoform X1

    UniProtKB/TrEMBL
    B4DHI3

  5. XM_054328263.1 → XP_054184238.1  neuroligin-4, Y-linked isoform X2

    UniProtKB/Swiss-Prot
    F5H6W0, Q14D08, Q7Z3T5, Q8N5B6, Q8NFZ3, Q9Y2F8

  6. XM_054328257.1 → XP_054184232.1  neuroligin-4, Y-linked isoform X1

    UniProtKB/TrEMBL
    B4DHI3

  7. XM_054328268.1 → XP_054184243.1  neuroligin-4, Y-linked isoform X5

  8. XM_054328267.1 → XP_054184242.1  neuroligin-4, Y-linked isoform X5

  9. XM_054328259.1 → XP_054184234.1  neuroligin-4, Y-linked isoform X1

    UniProtKB/TrEMBL
    B4DHI3

  10. XM_054328256.1 → XP_054184231.1  neuroligin-4, Y-linked isoform X1

    UniProtKB/TrEMBL
    B4DHI3

  11. XM_054328262.1 → XP_054184237.1  neuroligin-4, Y-linked isoform X2

    UniProtKB/Swiss-Prot
    F5H6W0, Q14D08, Q7Z3T5, Q8N5B6, Q8NFZ3, Q9Y2F8

  12. XM_054328258.1 → XP_054184233.1  neuroligin-4, Y-linked isoform X1

    UniProtKB/TrEMBL
    B4DHI3

  13. XM_054328265.1 → XP_054184240.1  neuroligin-4, Y-linked isoform X3

  14. XM_054328266.1 → XP_054184241.1  neuroligin-4, Y-linked isoform X4

Suppressed Reference Sequence(s)

The following Reference Sequences have been suppressed. Explain

  1. NR_028319.1: Suppressed sequence

    Description
    NR_028319.1: This RefSeq was removed because it is now thought that this transcript does encode a protein.

  2. NR_046355.2: Suppressed sequence

    Description
    NR_046355.2: This RefSeq was removed because it is now thought that this transcript does encode a protein.
Nucleotide Protein
Heading Accession and Version
Protein Accession Links
GenPept Link UniProtKB Link
Q8NFZ3.1 GenPept UniProtKB/Swiss-Prot:Q8NFZ3

Gene LinkOut

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