SETDB2-PHF11 SETDB2-PHF11 readthrough [Homo sapiens (human)] - Gene

Summary

Gene symbol: SETDB2-PHF11
Gene description: SETDB2-PHF11 readthrough
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
Summary: This gene represents naturally-occurring readthrough transcription between the upstream SETDB2 (SET domain bifurcated 2) gene to the downstream PHF11 (PHD finger protein 11) gene. Readthrough transcripts may encode fusion proteins with similarity to proteins encoded by each of the individual genes or may encode candidates for nonsense-mediated decay (NMD). [provided by RefSeq, Mar 2016]
Expression: Ubiquitous expression in lymph node (RPKM 11.8), spleen (RPKM 10.7) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 13q14.2

Exon count:: 23

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	13	NC_000013.11 (49444274..49528976)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	13	NC_060937.1 (48662906..48747507)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	13	NC_000013.10 (50018410..50103112)

Chromosome 13 - NC_000013.11 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
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?

detects readthrough transcripts by PCR
Title: Positional cloning of a quantitative trait locus on chromosome 13q14 that influences immunoglobulin E levels and asthma.

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)

General gene information

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General protein information

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Preferred Names: SETDB2-PHF11 protein

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_001320727.2 → NP_001307656.1 SETDB2-PHF11 protein

Status: VALIDATED

Description

Transcript Variant: This variant (1) encodes a putative protein.

Source sequence(s)

AL136218, AL139321

Conserved Domains (4) summary

smart00317
Location:355 → 416

SET; SET (Su(var)3-9, Enhancer-of-zeste, Trithorax) domain

cd01395
Location:152 → 212

HMT_MBD; Methyl-CpG binding domains (MBD) present in putative histone methyltransferases (HMT) such as CLLD8 and SETDB1 proteins; CLLD8 contains a MBD, a PreSET and a bifurcated SET domain, suggesting that CLLD8 might be associated with methylation-mediated ...

cd15712
Location:539 → 653

ePHD_PHF11; Extended PHD finger found in PHD finger protein 11 (PHF11)

pfam05033
Location:234 → 347

Pre-SET; Pre-SET motif

RNA

NR_135324.2 RNA Sequence

Status: VALIDATED

Description

Transcript Variant: This variant (2) lacks two exons and contains three alternate exons compared to variant 1. This variant is represented as non-coding because the use of the 5'-most expected translational start codon, as used in variant 1, renders the transcript a candidate for nonsense-mediated mRNA decay (NMD).

Source sequence(s)

AL136218, AL139321