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

    Gene ID: 22829, updated on 2-Nov-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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    See NLGN4Y in Genome Data Viewer
    Location:
    Yq11.221
    Exon count:
    16
    Annotation release Status Assembly Chr Location
    RS_2024_08 current GRCh38.p14 (GCF_000001405.40) Y NC_000024.10 (14522616..14845654)
    RS_2024_08 current T2T-CHM13v2.0 (GCF_009914755.1) Y NC_060948.1 (15429244..15752217)
    RS_2024_09 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 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. 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
    3. 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
    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. Analysis of the neuroligin 4Y gene in patients with autism. Yan J, et al. Psychiatr Genet, 2008 Aug. PMID 18628683

    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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    NEW Try the new Transcript table

    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_2024_08

    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

    The following LinkOut resources are supplied by external providers. These providers are responsible for maintaining the links.

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