SECISBP2 SECIS binding protein 2 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SECISBP2provided by HGNC
Official Full Name: SECIS binding protein 2provided by HGNC
Primary source: HGNC:HGNC:30972
See related: Ensembl:ENSG00000187742 MIM:607693; AllianceGenome:HGNC:30972
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: SBP2; THMA1
Summary: The protein encoded by this gene is one of the essential components of the machinery involved in co-translational insertion of selenocysteine (Sec) into selenoproteins. Sec is encoded by the UGA codon, which normally signals translation termination. The recoding of UGA as Sec codon requires a Sec insertion sequence (SECIS) element; present in the 3' untranslated regions of eukaryotic selenoprotein mRNAs. This protein specifically binds to the SECIS element, which is stimulated by a Sec-specific translation elongation factor. Mutations in this gene have been associated with reduction in enzymatic activity of type II iodothyronine deiodinase (a selenoprotein) and abnormal thyroid hormone metabolism. Alternatively spliced transcript variants have been found for this gene. [provided by RefSeq, Aug 2017]
Expression: Ubiquitous expression in testis (RPKM 20.1), thyroid (RPKM 9.1) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 9q22.2

Exon count:: 22

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	9	NC_000009.12 (89318500..89367117)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	9	NC_060933.1 (101482274..101530894)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	9	NC_000009.11 (91933415..91974578)

Chromosome 9 - NC_000009.12 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
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?

Human Genetic Disorders Resulting in Systemic Selenoprotein Deficiency.
Title: Human Genetic Disorders Resulting in Systemic Selenoprotein Deficiency.
SECISBP2 is a novel prognostic predictor that regulates selenoproteins in diffuse large B-cell lymphoma.
Title: SECISBP2 is a novel prognostic predictor that regulates selenoproteins in diffuse large B-cell lymphoma.
Selenium-sensitive miR-181a-5p to participate and regulate SBP2 at post-transcriptional level.
Title: Selenium-sensitive miRNA-181a-5p targeting SBP2 regulates selenoproteins expression in cartilage.
SECISBP2 expression in healthy human palatal mucosa is strongly negatively correlated with serum cotinine levels.
Title: Whole transcriptome analysis of smoker palatal mucosa identifies multiple downregulated innate immunity genes.
In osteoarthritis pro-inflammatory factors mediate miR-181a-5p expression, and then miR-181a-5p regulates the pivotal selenoproteins GPX1 and GPX4 through its target SBP2, resulting in alterations to the overall activity of GPXs, which are the most important oxidation resistance proteins in cartilage.
Title: The hsa-miR-181a-5p reduces oxidation resistance by controlling SECISBP2 in osteoarthritis.
functions as a vital factor in selenoprotein translation and regulates the pro-oxidant/antioxidant balance in trophoblasts
Title: Loss of selenocysteine insertion sequence binding protein 2 suppresses the proliferation, migration/invasion and hormone secretion of human trophoblast cells via the PI3K/Akt and ERK signaling pathway.
SBP2 interacts directly with four proteins of the SMN complex and the methylosome core proteins.
Title: SECIS-binding protein 2 interacts with the SMN complex and the methylosome for selenoprotein mRNP assembly and translation.
SBP2 makes direct contacts with a discrete region of the human 28S rRNA.
Title: The SBP2 protein central to selenoprotein synthesis contacts the human ribosome at expansion segment 7L of the 28S rRNA.
The patient showed typical symptoms of SBP2 deficiency, and novel compound heterozygous mutations were identified in SBP2 (p.M515fsX563/p.Q79X).
Title: Novel compound heterozygous mutations in the SBP2 gene: characteristic clinical manifestations and the implications of GH and triiodothyronine in longitudinal bone growth and maturation.
Selenocysteine insertion sequence (SECIS)-binding protein 2 alters conformational dynamics of residues involved in tRNA accommodation in 80 S ribosomes.
Title: Selenocysteine insertion sequence (SECIS)-binding protein 2 alters conformational dynamics of residues involved in tRNA accommodation in 80 S ribosomes.

Submit: New GeneRIF Correction See all GeneRIFs (22)

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

Associated conditions

Description	Tests
Thyroid hormone metabolism, abnormal 1 MedGen: C5676891 OMIM: 609698 GeneReviews: Not available	Compare labs

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

D8S2279 (e-PCR)
- UniSTS:473907

RH69402 (e-PCR)
- UniSTS:33863

RH68462 (e-PCR)
- UniSTS:55394

D10S16 (e-PCR)
- UniSTS:155756

D1S1423 (e-PCR)
- UniSTS:149619

WI-18160 (e-PCR)
- UniSTS:76732

SGC31294 (e-PCR)
- UniSTS:75993

RH91496 (e-PCR)
- UniSTS:85246

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables DNA binding	EXP Inferred from Experiment more info	PubMed
enables RNA binding	HDA more info	PubMed
enables mRNA 3'-UTR binding	IBA Inferred from Biological aspect of Ancestor more info
enables mRNA 3'-UTR binding	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables ribonucleoprotein complex binding	IBA Inferred from Biological aspect of Ancestor more info
enables selenocysteine insertion sequence binding	IBA Inferred from Biological aspect of Ancestor more info
enables selenocysteine insertion sequence binding	IDA Inferred from Direct Assay more info	PubMed

Process	Evidence Code	Pubs
involved_in RNA catabolic process	IEA Inferred from Electronic Annotation more info
involved_in forebrain neuron development	IEA Inferred from Electronic Annotation more info
involved_in mRNA stabilization	IEA Inferred from Electronic Annotation more info
involved_in negative regulation of nuclear-transcribed mRNA catabolic process, nonsense-mediated decay	IEA Inferred from Electronic Annotation more info
involved_in selenocysteine incorporation	IBA Inferred from Biological aspect of Ancestor more info
involved_in selenocysteine incorporation	IDA Inferred from Direct Assay more info	PubMed
involved_in striatum development	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
is_active_in mitochondrion	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleoplasm	IDA Inferred from Direct Assay more info
part_of ribonucleoprotein complex	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: selenocysteine insertion sequence-binding protein 2

Names: Sec insertion sequence-binding protein 2

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

NG_012177.2 RefSeqGene

Range

5002..46165

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GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

NM_001282688.2 → NP_001269617.1 selenocysteine insertion sequence-binding protein 2 isoform 2

Status: REVIEWED

Description

Transcript Variant: This variant (2) uses an alternate in-frame acceptor splice site in the 5' coding region compared to variant 1. The encoded isoform (2) is 1 aa shorter than isoform 1.

Source sequence(s)

AF380995, AK302852, AL160054, BG572344, BX000356

UniProtKB/TrEMBL

B4DZC7

Conserved Domains (1) summary

pfam01248
Location:656 → 756

Ribosomal_L7Ae; Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
NM_001282689.2 → NP_001269618.1 selenocysteine insertion sequence-binding protein 2 isoform 3

See identical proteins and their annotated locations for NP_001269618.1

Status: REVIEWED

Description

Transcript Variant: This variant (3) uses an alternate in-frame acceptor splice site in the 5' coding region, which results in translation initiation from an alternate start codon compared to variant 1. The encoded isoform (3) is shorter, with a distinct N-terminus compared to isoform 1.

Source sequence(s)

AK290182, AL929575, BG572344, BP219148

Consensus CDS

CCDS65076.1

UniProtKB/TrEMBL

B4DR97

Related

ENSP00000364959.3, ENST00000339901.8

Conserved Domains (1) summary

pfam01248
Location:584 → 684

Ribosomal_L7Ae; Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
NM_001282690.1 → NP_001269619.1 selenocysteine insertion sequence-binding protein 2 isoform 4

See identical proteins and their annotated locations for NP_001269619.1

Status: REVIEWED

Description

Transcript Variant: This variant (4) contains an alternate 5' terminal exon, which results in translation initiation from an in-frame downstream start codon compared to variant 1. The encoded isoform (4) has a shorter N-terminus compared to isoform 1

Source sequence(s)

AK299161, AL160054, AL929575, BG572344, BX000356

Consensus CDS

CCDS65077.1

UniProtKB/TrEMBL

B4DR97

Related

ENSP00000436650.2, ENST00000534113.6

Conserved Domains (1) summary

pfam01248
Location:589 → 689

Ribosomal_L7Ae; Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
NM_001354696.2 → NP_001341625.1 selenocysteine insertion sequence-binding protein 2 isoform 5

Status: REVIEWED

Description

Transcript Variant: This variant (5) uses an alternate in-frame acceptor splice site in the mid-coding region compared to variant 1. The encoded shorter isoform (5) lacks an internal protein segment compared to isoform 1.

Source sequence(s)

BC068466, BC099900, BG572344, BP219148

UniProtKB/TrEMBL

Q59H19

Conserved Domains (1) summary

pfam01248
Location:618 → 718

Ribosomal_L7Ae; Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
NM_001354697.2 → NP_001341626.1 selenocysteine insertion sequence-binding protein 2 isoform 6

Status: REVIEWED

Description

Transcript Variant: This variant (6) uses an alternate in-frame acceptor splice site in the mid-coding region compared to variant 1. The encoded shorter isoform (6) lacks an internal protein segment compared to isoform 1.

Source sequence(s)

BC068466, BG572344, BP219148, KX533480

UniProtKB/TrEMBL

Q59H19

Conserved Domains (1) summary

pfam01248
Location:619 → 719

Ribosomal_L7Ae; Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
NM_001354698.2 → NP_001341627.1 selenocysteine insertion sequence-binding protein 2 isoform 7

Status: REVIEWED

Description

Transcript Variant: This variant (7) uses an alternate in-frame acceptor splice site and lacks an in-frame exon in the mid-coding region compared to variant 1. The encoded shorter isoform (7) lacks two internal protein segments compared to isoform 1.

Source sequence(s)

BC099900, BG572344, BP219148, KX533480

UniProtKB/TrEMBL

Q59H19

Conserved Domains (1) summary

pfam01248
Location:588 → 688

Ribosomal_L7Ae; Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
NM_001354702.2 → NP_001341631.1 selenocysteine insertion sequence-binding protein 2 isoform 8

Status: REVIEWED

Description

Transcript Variant: This variant (8) uses an alternate acceptor splice site in the mid-coding region and initiates translation from an alternate start codon compared to variant 1. The encoded isoform (8) is shorter, with a distinct N-terminus compared to isoform 1.

Source sequence(s)

AI127999, BC068466, BG572344, BP219148

Conserved Domains (1) summary

pfam01248
Location:362 → 462

Ribosomal_L7Ae; Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
NM_024077.5 → NP_076982.3 selenocysteine insertion sequence-binding protein 2 isoform 1

See identical proteins and their annotated locations for NP_076982.3

Status: REVIEWED

Description

Transcript Variant: This variant (1) represents the predominant transcript, and encodes the longest isoform (1).

Source sequence(s)

BC068466, BG572344, BP219148

Consensus CDS

CCDS6683.1

UniProtKB/Swiss-Prot

F8W892, Q5HYY1, Q7L1Z0, Q8IYC0, Q96T21, Q9H0A1

UniProtKB/TrEMBL

B4DZC7

Related

ENSP00000364965.3, ENST00000375807.8

Conserved Domains (1) summary

pfam01248
Location:657 → 757

Ribosomal_L7Ae; Ribosomal protein L7Ae/L30e/S12e/Gadd45 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

NC_000009.12 Reference GRCh38.p14 Primary Assembly

Range

89318500..89367117

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047423856.1 → XP_047279812.1 selenocysteine insertion sequence-binding protein 2 isoform X5

UniProtKB/Swiss-Prot

F8W892, Q5HYY1, Q7L1Z0, Q8IYC0, Q96T21, Q9H0A1

UniProtKB/TrEMBL

B4DZC7
XM_047423857.1 → XP_047279813.1 selenocysteine insertion sequence-binding protein 2 isoform X5

UniProtKB/Swiss-Prot

F8W892, Q5HYY1, Q7L1Z0, Q8IYC0, Q96T21, Q9H0A1

UniProtKB/TrEMBL

B4DZC7
XM_047423859.1 → XP_047279815.1 selenocysteine insertion sequence-binding protein 2 isoform X8

UniProtKB/TrEMBL

Q59H19
XM_017015122.3 → XP_016870611.1 selenocysteine insertion sequence-binding protein 2 isoform X7

UniProtKB/TrEMBL

B4DZC7
XM_024447666.2 → XP_024303434.1 selenocysteine insertion sequence-binding protein 2 isoform X9

UniProtKB/TrEMBL

A0A1S5UZH3, Q59H19

Conserved Domains (1) summary

pfam01248
Location:589 → 689

Ribosomal_L7Ae; Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
XM_047423854.1 → XP_047279810.1 selenocysteine insertion sequence-binding protein 2 isoform X1

UniProtKB/TrEMBL

B4DR97
XM_011519000.3 → XP_011517302.1 selenocysteine insertion sequence-binding protein 2 isoform X1

See identical proteins and their annotated locations for XP_011517302.1

UniProtKB/TrEMBL

B4DR97

Conserved Domains (1) summary

pfam01248
Location:589 → 689

Ribosomal_L7Ae; Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
XM_047423855.1 → XP_047279811.1 selenocysteine insertion sequence-binding protein 2 isoform X3

UniProtKB/TrEMBL

B4DR97
XM_011519001.2 → XP_011517303.1 selenocysteine insertion sequence-binding protein 2 isoform X2

UniProtKB/TrEMBL

B4DR97

Conserved Domains (1) summary

pfam01248
Location:559 → 659

Ribosomal_L7Ae; Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
XM_011519002.2 → XP_011517304.1 selenocysteine insertion sequence-binding protein 2 isoform X3

UniProtKB/TrEMBL

B4DR97

Conserved Domains (1) summary

pfam01248
Location:551 → 651

Ribosomal_L7Ae; Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
XM_047423858.1 → XP_047279814.1 selenocysteine insertion sequence-binding protein 2 isoform X6

UniProtKB/TrEMBL

B4DR97
XM_011519003.2 → XP_011517305.1 selenocysteine insertion sequence-binding protein 2 isoform X4

UniProtKB/TrEMBL

B4DR97

Conserved Domains (1) summary

pfam01248
Location:550 → 650

Ribosomal_L7Ae; Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
XM_047423860.1 → XP_047279816.1 selenocysteine insertion sequence-binding protein 2 isoform X10

UniProtKB/TrEMBL

B4DR97
XM_024447667.2 → XP_024303435.1 selenocysteine insertion sequence-binding protein 2 isoform X11

UniProtKB/TrEMBL

B4DR97

Conserved Domains (1) summary

pfam01248
Location:545 → 645

Ribosomal_L7Ae; Ribosomal protein L7Ae/L30e/S12e/Gadd45 family
XM_047423861.1 → XP_047279817.1 selenocysteine insertion sequence-binding protein 2 isoform X12

UniProtKB/TrEMBL

B4DR97
XM_047423862.1 → XP_047279818.1 selenocysteine insertion sequence-binding protein 2 isoform X13
XM_047423863.1 → XP_047279819.1 selenocysteine insertion sequence-binding protein 2 isoform X14

UniProtKB/TrEMBL

Q9H948

RNA

XR_007061351.1 RNA Sequence
XR_007061350.1 RNA Sequence
XR_007061352.1 RNA Sequence
XR_007061353.1 RNA Sequence
XR_007061354.1 RNA Sequence
XR_007061347.1 RNA Sequence
XR_929840.2 RNA Sequence
XR_007061346.1 RNA Sequence
XR_007061345.1 RNA Sequence
XR_007061348.1 RNA Sequence
XR_007061349.1 RNA Sequence
XR_007061355.1 RNA Sequence
XR_007061356.1 RNA Sequence

Alternate T2T-CHM13v2.0

Genomic

NC_060933.1 Alternate T2T-CHM13v2.0

Range

101482274..101530894

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054363775.1 → XP_054219750.1 selenocysteine insertion sequence-binding protein 2 isoform X5

UniProtKB/Swiss-Prot

F8W892, Q5HYY1, Q7L1Z0, Q8IYC0, Q96T21, Q9H0A1

UniProtKB/TrEMBL

B4DZC7
XM_054363776.1 → XP_054219751.1 selenocysteine insertion sequence-binding protein 2 isoform X5

UniProtKB/Swiss-Prot

F8W892, Q5HYY1, Q7L1Z0, Q8IYC0, Q96T21, Q9H0A1

UniProtKB/TrEMBL

B4DZC7
XM_054363779.1 → XP_054219754.1 selenocysteine insertion sequence-binding protein 2 isoform X8

UniProtKB/TrEMBL

Q59H19
XM_054363778.1 → XP_054219753.1 selenocysteine insertion sequence-binding protein 2 isoform X7

UniProtKB/TrEMBL

B4DZC7
XM_054363780.1 → XP_054219755.1 selenocysteine insertion sequence-binding protein 2 isoform X9

UniProtKB/TrEMBL

A0A1S5UZH3, Q59H19
XM_054363770.1 → XP_054219745.1 selenocysteine insertion sequence-binding protein 2 isoform X1

UniProtKB/TrEMBL

B4DR97
XM_054363769.1 → XP_054219744.1 selenocysteine insertion sequence-binding protein 2 isoform X1

UniProtKB/TrEMBL

B4DR97
XM_054363773.1 → XP_054219748.1 selenocysteine insertion sequence-binding protein 2 isoform X3

UniProtKB/TrEMBL

B4DR97
XM_054363771.1 → XP_054219746.1 selenocysteine insertion sequence-binding protein 2 isoform X2

UniProtKB/TrEMBL

B4DR97
XM_054363772.1 → XP_054219747.1 selenocysteine insertion sequence-binding protein 2 isoform X3

UniProtKB/TrEMBL

B4DR97
XM_054363777.1 → XP_054219752.1 selenocysteine insertion sequence-binding protein 2 isoform X6

UniProtKB/TrEMBL

B4DR97
XM_054363774.1 → XP_054219749.1 selenocysteine insertion sequence-binding protein 2 isoform X4

UniProtKB/TrEMBL

B4DR97
XM_054363781.1 → XP_054219756.1 selenocysteine insertion sequence-binding protein 2 isoform X10

UniProtKB/TrEMBL

B4DR97
XM_054363782.1 → XP_054219757.1 selenocysteine insertion sequence-binding protein 2 isoform X11

UniProtKB/TrEMBL

B4DR97
XM_054363783.1 → XP_054219758.1 selenocysteine insertion sequence-binding protein 2 isoform X12

UniProtKB/TrEMBL

B4DR97
XM_054363784.1 → XP_054219759.1 selenocysteine insertion sequence-binding protein 2 isoform X13
XM_054363785.1 → XP_054219760.1 selenocysteine insertion sequence-binding protein 2 isoform X14

UniProtKB/TrEMBL

Q9H948