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

Gene ID: 22829, updated on 25-Jan-2022

Summary

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
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Genomic context

See NLGN4Y in Genome Data Viewer
Location:
Yq11.221
Exon count:
16
Annotation release Status Assembly Chr Location
109.20211119 current GRCh38.p13 (GCF_000001405.39) Y NC_000024.10 (14522616..14845654)
105.20201022 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 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

Expression

  • 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

GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Pathways from PubChem

Interactions

Products Interactant Other Gene Complex Source Pubs Description

General gene information

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
PubMed 
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
PubMed 
Process Evidence Code Pubs
involved_in chemical synaptic transmission IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
involved_in neuron cell-cell adhesion IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
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
PubMed 
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
PubMed 
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
PubMed 
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
PubMed 
is_active_in integral component of plasma membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
is_active_in integral component of postsynaptic specialization membrane IBA
Inferred from Biological aspect of Ancestor
more info
PubMed 
located_in plasma membrane TAS
Traceable Author Statement
more info
 
located_in postsynaptic density membrane IEA
Inferred from Electronic Annotation
more info
 
located_in presynapse IEA
Inferred from Electronic Annotation
more info
 
located_in spanning component of membrane TAS
Traceable Author Statement
more info
PubMed 
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
PubMed 

General protein information

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
    6139..326361
    Download
    GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

  1. NM_001164238.1NP_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/Swiss-Prot
    Q8NFZ3
    Related
    ENSP00000412638.1, ENST00000413217.1
    Conserved Domains (1) summary
    cl21494
    Location:42229
    Abhydrolase; alpha/beta hydrolases
  2. NM_001206850.2NP_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:198
    Aes; Acetyl esterase/lipase [Lipid transport and metabolism]
    pfam00135
    Location:1422
    COesterase; Carboxylesterase family
  3. NM_001365584.1NP_001352513.1  neuroligin-4, Y-linked isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Conserved Domains (1) summary
    pfam00135
    Location:44610
    COesterase; Carboxylesterase family
  4. NM_001365586.1NP_001352515.1  neuroligin-4, Y-linked isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Related
    ENSP00000496594.1, ENST00000643089.1
    Conserved Domains (1) summary
    pfam00135
    Location:44610
    COesterase; Carboxylesterase family
  5. NM_001365588.1NP_001352517.1  neuroligin-4, Y-linked isoform 4

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Related
    ENSP00000510011.1, ENST00000684976.1
    Conserved Domains (1) summary
    pfam00135
    Location:44610
    COesterase; Carboxylesterase family
  6. NM_001365590.1NP_001352519.1  neuroligin-4, Y-linked isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Conserved Domains (1) summary
    pfam00135
    Location:44590
    COesterase; Carboxylesterase family
  7. NM_001365591.1NP_001352520.1  neuroligin-4, Y-linked isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Conserved Domains (1) summary
    pfam00135
    Location:44590
    COesterase; Carboxylesterase family
  8. NM_001365592.1NP_001352521.1  neuroligin-4, Y-linked isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Conserved Domains (1) summary
    pfam00135
    Location:44590
    COesterase; Carboxylesterase family
  9. NM_001365593.1NP_001352522.1  neuroligin-4, Y-linked isoform 1 precursor

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Conserved Domains (1) summary
    pfam00135
    Location:44590
    COesterase; Carboxylesterase family
  10. NM_001394830.1NP_001381759.1  neuroligin-4, Y-linked

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Conserved Domains (1) summary
    pfam00135
    Location:44610
    COesterase; Carboxylesterase family
  11. NM_001394831.1NP_001381760.1  neuroligin-4, Y-linked

    Status: REVIEWED

    Source sequence(s)
    AC010726, AC010879, AC010979, AC011903
    Related
    ENSP00000342535.5, ENST00000339174.9
    Conserved Domains (1) summary
    pfam00135
    Location:44590
    COesterase; Carboxylesterase family
  12. NM_014893.5NP_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
    Q8NFZ3
    UniProtKB/TrEMBL
    A0A024R9E7
    Related
    ENSP00000348169.2, ENST00000355905.6
    Conserved Domains (1) summary
    pfam00135
    Location:44590
    COesterase; Carboxylesterase family

RefSeqs of Annotated Genomes: Homo sapiens Updated Annotation Release 109.20211119

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

Reference GRCh38.p13 Primary Assembly

Genomic

  1. NC_000024.10 Reference GRCh38.p13 Primary Assembly

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

mRNA and Protein(s)

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

    See identical proteins and their annotated locations for XP_006724937.1

    UniProtKB/TrEMBL
    B4DHI3
    Conserved Domains (1) summary
    pfam00135
    Location:44610
    COesterase; Carboxylesterase family
  2. XM_011531430.2XP_011529732.1  neuroligin-4, Y-linked isoform X1

    See identical proteins and their annotated locations for XP_011529732.1

    UniProtKB/TrEMBL
    B4DHI3
    Related
    ENSP00000372320.1, ENST00000382868.5
    Conserved Domains (1) summary
    pfam00135
    Location:44610
    COesterase; Carboxylesterase family
  3. XM_017030041.1XP_016885530.1  neuroligin-4, Y-linked isoform X5

    UniProtKB/Swiss-Prot
    Q8NFZ3
    Conserved Domains (1) summary
    cl21494
    Location:42229
    Abhydrolase; alpha/beta hydrolases
  4. XM_011531428.1XP_011529730.1  neuroligin-4, Y-linked isoform X1

    See identical proteins and their annotated locations for XP_011529730.1

    UniProtKB/TrEMBL
    B4DHI3
    Conserved Domains (1) summary
    pfam00135
    Location:44610
    COesterase; Carboxylesterase family
  5. XM_024452490.1XP_024308258.1  neuroligin-4, Y-linked isoform X1

    Conserved Domains (1) summary
    pfam00135
    Location:44610
    COesterase; Carboxylesterase family
  6. XM_011531427.2XP_011529729.1  neuroligin-4, Y-linked isoform X1

    See identical proteins and their annotated locations for XP_011529729.1

    UniProtKB/TrEMBL
    B4DHI3
    Conserved Domains (1) summary
    pfam00135
    Location:44610
    COesterase; Carboxylesterase family
  7. XM_017030036.1XP_016885525.1  neuroligin-4, Y-linked isoform X2

    UniProtKB/Swiss-Prot
    Q8NFZ3
    UniProtKB/TrEMBL
    A0A024R9E7
    Conserved Domains (1) summary
    pfam00135
    Location:44590
    COesterase; Carboxylesterase family
  8. XM_011531429.2XP_011529731.1  neuroligin-4, Y-linked isoform X1

    See identical proteins and their annotated locations for XP_011529731.1

    UniProtKB/TrEMBL
    B4DHI3
    Conserved Domains (1) summary
    pfam00135
    Location:44610
    COesterase; Carboxylesterase family
  9. XM_017030039.1XP_016885528.1  neuroligin-4, Y-linked isoform X3

  10. XM_017030040.1XP_016885529.1  neuroligin-4, Y-linked isoform X4

    UniProtKB/Swiss-Prot
    Q8NFZ3
    Conserved Domains (2) summary
    COG0657
    Location:198
    Aes; Acetyl esterase/lipase [Lipid transport and metabolism]
    pfam00135
    Location:1422
    COesterase; Carboxylesterase family

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.
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