CC2D1B coiled-coil and C2 domain containing 1B [Homo sapiens (human)] - Gene

Summary

Official Symbol: CC2D1Bprovided by HGNC
Official Full Name: coiled-coil and C2 domain containing 1Bprovided by HGNC
Primary source: HGNC:HGNC:29386
See related: Ensembl:ENSG00000154222 AllianceGenome:HGNC:29386
Gene type: protein coding
RefSeq status: VALIDATED
Organism: Homo sapiens
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Primates; Haplorrhini; Catarrhini; Hominidae; Homo
Also known as: Lgd1
Summary: Predicted to enable DNA-binding transcription factor activity, RNA polymerase II-specific and RNA polymerase II cis-regulatory region sequence-specific DNA binding activity. Predicted to be involved in regulation of transcription by RNA polymerase II. Predicted to act upstream of or within negative regulation of transcription by RNA polymerase II. Located in nucleoplasm. [provided by Alliance of Genome Resources, Nov 2024]
Expression: Ubiquitous expression in testis (RPKM 5.5), lung (RPKM 5.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1p32.3

Exon count:: 24

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (52350597..52366205, complement)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (52232062..52247670, complement)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (52816269..52831877, complement)

Chromosome 1 - NC_000001.11 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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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?

Unravelling of Hidden Secrets: The Tumour Suppressor Lethal (2) Giant Discs (Lgd)/CC2D1, Notch Signalling and Cancer.
Title: Unravelling of Hidden Secrets: The Tumour Suppressor Lethal (2) Giant Discs (Lgd)/CC2D1, Notch Signalling and Cancer.
CC2D1B is essential for ESCRT-III activity during mitotic reformation of the nuclear envelope.
Title: CC2D1B Coordinates ESCRT-III Activity during the Mitotic Reformation of the Nuclear Envelope.
CC2D1B regulates degradation and signaling of EGFR and TLR4.
Title: CC2D1A and CC2D1B regulate degradation and signaling of EGFR and TLR4.
Human Freud-2/CC2D1B binds to the 5-HT1A dual repressor element and represses the human 5-HT1A receptor gene to regulate its expression in non-serotonergic cells and neurons.
Title: Human Freud-2/CC2D1B: a novel repressor of postsynaptic serotonin-1A receptor expression.
Paper describes a function of Cc2d1b/Cc2d1a and their Drosophila homologue l(2)gd in D.melanogaster in Notch trafficking.
Title: The Drosophila Notch inhibitor and tumor suppressor gene lethal (2) giant discs encodes a conserved regulator of endosomal trafficking.

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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)

Interactions

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Products	Interactant	Other Gene	Complex	Source	Pubs	Description

General gene information

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Markers

D1S2512 (e-PCR)
- UniSTS:154116

D1S3534 (e-PCR)
- UniSTS:39776

D1S1423 (e-PCR)
- UniSTS:149619

SHGC-74828 (e-PCR)
- UniSTS:20877

A005E48 (e-PCR)
- UniSTS:50854

D1S2354 (e-PCR)
- UniSTS:78276

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA-binding transcription factor activity, RNA polymerase II-specific	IBA Inferred from Biological aspect of Ancestor more info
enables DNA-binding transcription repressor activity, RNA polymerase II-specific	IEA Inferred from Electronic Annotation more info
enables RNA polymerase II cis-regulatory region sequence-specific DNA binding	IBA Inferred from Biological aspect of Ancestor more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in negative regulation of transcription by RNA polymerase II	IEA Inferred from Electronic Annotation more info
involved_in regulation of transcription by RNA polymerase II	IBA Inferred from Biological aspect of Ancestor more info

Component	Evidence Code	Pubs
located_in cytosol	IEA Inferred from Electronic Annotation more info
located_in endosome membrane	IEA Inferred from Electronic Annotation more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in nuclear envelope	TAS Traceable Author Statement more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: coiled-coil and C2 domain-containing protein 1B

Names: FRE under dual repression-binding protein 2; five prime repressor element under dual repression-binding protein 2; freud-2; lethal (2) giant discs homolog 1

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_001330585.2 → NP_001317514.1 coiled-coil and C2 domain-containing protein 1B isoform 2

Status: VALIDATED

Description

Transcript Variant: This variant (2) uses an alternate in-frame splice junction and differs in the 3' UTR compared to variant 1. The resulting isoform (2) has the same N- and C-termini but is shorter compared to isoform 1.

Source sequence(s)

AL513218

Consensus CDS

CCDS81323.1

UniProtKB/Swiss-Prot

Q5T0F9

Related

ENSP00000284376.3, ENST00000284376.8
NM_032449.3 → NP_115825.1 coiled-coil and C2 domain-containing protein 1B isoform 1

See identical proteins and their annotated locations for NP_115825.1

Status: VALIDATED

Description

Transcript Variant: This variant (1) represents the longer transcript and encodes the longer isoform (1).

Source sequence(s)

AB058739, AL513218, BM975102, BQ073406, DB458797

Consensus CDS

CCDS30714.1

UniProtKB/Swiss-Prot

Q49AE8, Q5T0F8, Q5T0F9, Q5T0G0, Q6ZNQ1, Q96AP3, Q96I04, Q96JJ1

Related

ENSP00000360642.2, ENST00000371586.6

Conserved Domains (2) summary

smart00685
Location:537 → 594

DM14; Repeats in fly CG4713, worm Y37H9A.3 and human FLJ20241

cd08690
Location:696 → 853

C2_Freud-1; C2 domain found in 5' repressor element under dual repression binding protein-1 (Freud-1)