CHRFAM7A CHRNA7 (exons 5-10) and FAM7A (exons A-E) fusion [Homo sapiens (human)] - Gene

Summary

Official Symbol: CHRFAM7Aprovided by HGNC
Official Full Name: CHRNA7 (exons 5-10) and FAM7A (exons A-E) fusionprovided by HGNC
Primary source: HGNC:HGNC:15781
See related: Ensembl:ENSG00000166664 MIM:609756; AllianceGenome:HGNC:15781
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: D-10; CHRNA7; NACHRA7; CHRNA7-DR1
Summary: The nicotinic acetylcholine receptors (nAChRs) are members of a superfamily of ligand-gated ion channels that mediate fast signal transmission at synapses. The family member CHRNA7, which is located on chromosome 15 in a region associated with several neuropsychiatric disorders, is partially duplicated and forms a hybrid with a novel gene from the family with sequence similarity 7 (FAM7A). Alternative splicing has been observed, and two variants exist, for this hybrid gene. The N-terminally truncated products predicted by the largest open reading frames for each variant would lack the majority of the neurotransmitter-gated ion-channel ligand binding domain but retain the transmembrane region that forms the ion channel. Although current evidence supports transcription of this hybrid gene, translation of the nicotinic acetylcholine receptor-like protein-encoding open reading frames has not been confirmed. [provided by RefSeq, Jul 2008]
Expression: Broad expression in adrenal (RPKM 4.3), small intestine (RPKM 4.0) and 19 other tissues See more
Orthologs: all
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Genomic context

Location:: 15q13.2

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	15	NC_000015.10 (30360566..30393900, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	15	NC_060939.1 (28153934..28187176, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	15	NC_000015.9 (30652769..30685864, complement)

Chromosome 15 - NC_000015.10 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Go to reference sequence details

Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

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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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

The human-specific nicotinic receptor subunit CHRFAM7A reduces alpha7 receptor function in human induced pluripotent stem cells-derived and transgenic mouse neurons.
Title: The human-specific nicotinic receptor subunit CHRFAM7A reduces α7 receptor function in human induced pluripotent stem cells-derived and transgenic mouse neurons.
CHRFAM7A diversifies human immune adaption through Ca[2+] signalling and actin cytoskeleton reorganization.
Title: CHRFAM7A diversifies human immune adaption through Ca(2+) signalling and actin cytoskeleton reorganization.
Unraveling the molecular interactions between alpha7 nicotinic receptor and a RIC3 variant associated with backward speech.
Title: Unraveling the molecular interactions between α7 nicotinic receptor and a RIC3 variant associated with backward speech.
Structural mechanisms of alpha7 nicotinic receptor allosteric modulation and activation.
Title: Structural mechanisms of α7 nicotinic receptor allosteric modulation and activation.
Human-specific CHRFAM7A primes macrophages for a heightened pro-inflammatory response at the earlier stage of inflammation.
Title: Human-specific CHRFAM7A primes macrophages for a heightened pro-inflammatory response at the earlier stage of inflammation.
An original potentiating mechanism revealed by the cryo-EM structures of the human alpha7 nicotinic receptor in complex with nanobodies.
Title: An original potentiating mechanism revealed by the cryo-EM structures of the human α7 nicotinic receptor in complex with nanobodies.
Human-specific duplicate CHRFAM7A gene is associated with more severe osteoarthritis and amplifies pain behaviours.
Title: Human-specific duplicate CHRFAM7A gene is associated with more severe osteoarthritis and amplifies pain behaviours.
Up-regulation of the human-specific CHRFAM7A gene protects against renal fibrosis in mice with obstructive nephropathy.
Title: Up-regulation of the human-specific CHRFAM7A gene protects against renal fibrosis in mice with obstructive nephropathy.
The Human-Restricted Isoform of the alpha7 nAChR, CHRFAM7A: A Double-Edged Sword in Neurological and Inflammatory Disorders.
Title: The Human-Restricted Isoform of the α7 nAChR, CHRFAM7A: A Double-Edged Sword in Neurological and Inflammatory Disorders.
CHRFAM7A Overexpression Attenuates Cerebral Ischemia-Reperfusion Injury via Inhibiting Microglia Pyroptosis Mediated by the NLRP3/Caspase-1 pathway.
Title: CHRFAM7A Overexpression Attenuates Cerebral Ischemia-Reperfusion Injury via Inhibiting Microglia Pyroptosis Mediated by the NLRP3/Caspase-1 pathway.

Submit: New GeneRIF Correction See all GeneRIFs (43)

Phenotypes

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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)

HIV-1 interactions

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Protein interactions

Protein	Gene	Interaction	Pubs
Envelope surface glycoprotein gp120	env	HIV-1 IIIB Env (gp120) engages CXCR4 and downregulates CHRFAM7A expression in neuronal cells; this effect can be inhibited AMD3100 treatment	PubMed

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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

D15S610E (e-PCR)
- UniSTS:12292

RH26807 (e-PCR)
- UniSTS:89112

SHGC-12902 (e-PCR)
- UniSTS:1097

RH78395 (e-PCR)
- UniSTS:82771

CHRFAM7A_s9 (e-PCR)
- UniSTS:510361

RH11309 (e-PCR)
- UniSTS:60335

STS-X70297 (e-PCR)
- UniSTS:54453

WI-19149 (e-PCR)
- UniSTS:29623

CHRNA7 (e-PCR)
- UniSTS:479949

NoName (e-PCR)
- UniSTS:479961

NoName (e-PCR)
- UniSTS:487145

D15S937 (e-PCR)
- UniSTS:153848

SHGC-36068 (e-PCR)
- UniSTS:65528

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables acetylcholine-gated monoatomic cation-selective channel activity	IBA Inferred from Biological aspect of Ancestor more info
enables transmembrane signaling receptor activity	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in B cell activation	IEA Inferred from Electronic Annotation more info
involved_in T cell activation	IEA Inferred from Electronic Annotation more info
involved_in associative learning	IEA Inferred from Electronic Annotation more info
involved_in behavioral response to ethanol	IEA Inferred from Electronic Annotation more info
involved_in behavioral response to nicotine	IEA Inferred from Electronic Annotation more info
involved_in chemical synaptic transmission	IBA Inferred from Biological aspect of Ancestor more info
involved_in dendrite arborization	IEA Inferred from Electronic Annotation more info
involved_in dendritic spine organization	IEA Inferred from Electronic Annotation more info
involved_in endocytosis	IEA Inferred from Electronic Annotation more info
involved_in establishment of localization in cell	IEA Inferred from Electronic Annotation more info
involved_in excitatory postsynaptic potential	IEA Inferred from Electronic Annotation more info
involved_in flagellated sperm motility	IEA Inferred from Electronic Annotation more info
involved_in generation of ovulation cycle rhythm	IEA Inferred from Electronic Annotation more info
involved_in memory	IEA Inferred from Electronic Annotation more info
involved_in monoatomic ion transmembrane transport	IBA Inferred from Biological aspect of Ancestor more info
involved_in monoatomic ion transmembrane transport	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of interleukin-1 beta production	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of interleukin-6 production	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of tumor necrosis factor production	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of ERK1 and ERK2 cascade	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of amyloid-beta formation	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of excitatory postsynaptic potential	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of heart rate involved in baroreceptor response to decreased systemic arterial blood pressure	IEA Inferred from Electronic Annotation more info
involved_in positive regulation of long-term synaptic potentiation	IEA Inferred from Electronic Annotation more info
involved_in regulation of amyloid fibril formation	IEA Inferred from Electronic Annotation more info
involved_in regulation of membrane potential	IBA Inferred from Biological aspect of Ancestor more info
involved_in regulation of norepinephrine secretion	IEA Inferred from Electronic Annotation more info
involved_in regulation of synapse structural plasticity	IEA Inferred from Electronic Annotation more info
involved_in regulation of synaptic transmission, dopaminergic	IEA Inferred from Electronic Annotation more info
involved_in response to amyloid-beta	IEA Inferred from Electronic Annotation more info
involved_in response to cold	IEA Inferred from Electronic Annotation more info
involved_in response to food	IEA Inferred from Electronic Annotation more info
involved_in sensory processing	IEA Inferred from Electronic Annotation more info
involved_in synaptic transmission, cholinergic	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
part_of acetylcholine-gated channel complex	IBA Inferred from Biological aspect of Ancestor more info
located_in apical plasma membrane	IEA Inferred from Electronic Annotation more info
located_in axolemma	IEA Inferred from Electronic Annotation more info
located_in cholinergic synapse	IEA Inferred from Electronic Annotation more info
located_in external side of plasma membrane	IEA Inferred from Electronic Annotation more info
is_active_in neuron projection	IBA Inferred from Biological aspect of Ancestor more info
is_active_in plasma membrane	IBA Inferred from Biological aspect of Ancestor more info
located_in postsynaptic specialization membrane	IEA Inferred from Electronic Annotation more info
located_in presynaptic membrane	IEA Inferred from Electronic Annotation more info
is_active_in synapse	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: CHRNA7-FAM7A fusion protein

Names: CHRNA7 (cholinergic receptor, nicotinic, alpha 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion; CHRNA7 (cholinergic receptor, nicotinic, alpha polypeptide 7, exons 5-10) and FAM7A (family with sequence similarity 7A, exons A-E) fusion; Neuronal acetylcholine receptor subunit alpha-7; alpha 7 neuronal nicotinic acetylcholine receptor-FAM7A hybrid; alpha-7 nicotinic cholinergic receptor subunit

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.

mRNA and Protein(s)

NM_139320.2 → NP_647536.1 CHRNA7-FAM7A fusion protein isoform 1

See identical proteins and their annotated locations for NP_647536.1

Status: REVIEWED

Description

Transcript Variant: This variant (1) is the full-length variant and encodes the longer isoform (1).

Source sequence(s)

AC019322

Consensus CDS

CCDS32184.1

UniProtKB/Swiss-Prot

A8KAB9, Q494W8

UniProtKB/TrEMBL

A0A0G2JMC1

Related

ENSP00000299847.3, ENST00000299847.7

Conserved Domains (1) summary

TIGR00860
Location:28 → 400

LIC; Cation transporter family protein
NM_148911.1 → NP_683709.1 CHRNA7-FAM7A fusion protein isoform 2

See identical proteins and their annotated locations for NP_683709.1

Status: REVIEWED

Description

Transcript Variant: This variant (2) lacks an internal exon compared to variant 1, and is missing the translation initiation site used by the longer variant. Translation from variant 2 initiates at a downstream site relative to variant 1, resulting in isoform (2), which is truncated at the N-terminus compared to isoform 1.

Source sequence(s)

AC019322

Consensus CDS

CCDS42008.1

UniProtKB/TrEMBL

A0A0A6YYA8, A0A0G2JNX5

Related

ENSP00000380927.3, ENST00000397827.7

Conserved Domains (1) summary

TIGR00860
Location:3 → 309

LIC; Cation transporter family protein

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

NC_000015.10 Reference GRCh38.p14 Primary Assembly

Range

30360566..30393900 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_011522153.3 → XP_011520455.1 CHRNA7-FAM7A fusion protein isoform X1

See identical proteins and their annotated locations for XP_011520455.1

UniProtKB/Swiss-Prot

A8KAB9, Q494W8

UniProtKB/TrEMBL

A0A0G2JMC1

Conserved Domains (1) summary

TIGR00860
Location:28 → 400

LIC; Cation transporter family protein
XM_011522155.4 → XP_011520457.1 CHRNA7-FAM7A fusion protein isoform X3

UniProtKB/TrEMBL

A0A1B0GTT9

Conserved Domains (2) summary

pfam02931
Location:18 → 140

Neur_chan_LBD; Neurotransmitter-gated ion-channel ligand binding domain

pfam02932
Location:147 → 203

Neur_chan_memb; Neurotransmitter-gated ion-channel transmembrane region
XM_005254750.4 → XP_005254807.1 CHRNA7-FAM7A fusion protein isoform X2

See identical proteins and their annotated locations for XP_005254807.1

UniProtKB/TrEMBL

A0A0A6YYA8, A0A0G2JNX5

Related

ENSP00000385389.3, ENST00000401522.7

Conserved Domains (1) summary

TIGR00860
Location:3 → 309

LIC; Cation transporter family protein

Reference GRCh38.p14 PATCHES

Genomic

NW_011332701.1 Reference GRCh38.p14 PATCHES

Range

2533056..2566055 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Reference GRCh38.p14 ALT_REF_LOCI_2

Genomic

NT_187660.1 Reference GRCh38.p14 ALT_REF_LOCI_2

Range

2645540..2678539 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

Alternate T2T-CHM13v2.0

Genomic

NC_060939.1 Alternate T2T-CHM13v2.0

Range

28153934..28187176 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054379105.1 → XP_054235080.1 CHRNA7-FAM7A fusion protein isoform X1

UniProtKB/Swiss-Prot

A8KAB9, Q494W8
XM_054379107.1 → XP_054235082.1 CHRNA7-FAM7A fusion protein isoform X3
XM_054379106.1 → XP_054235081.1 CHRNA7-FAM7A fusion protein isoform X2

UniProtKB/TrEMBL

A0A0A6YYA8