SYNDIG1 synapse differentiation inducing 1 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SYNDIG1provided by HGNC
Official Full Name: synapse differentiation inducing 1provided by HGNC
Primary source: HGNC:HGNC:15885
See related: Ensembl:ENSG00000101463 MIM:614311; AllianceGenome:HGNC:15885
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: DSPC2; IFITMD5; TMEM90B; C20orf39
Summary: This gene encodes a protein that belongs to the interferon-induced transmembrane family of proteins. A similar protein in rat is thought to regulate the development of excitatory synapses. [provided by RefSeq, Jul 2013]
Expression: Biased expression in brain (RPKM 1.9), heart (RPKM 1.6) and 11 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 20p11.21

Exon count:: 12

Annotation release	Status	Assembly	Chr	Location
RS_2024_08	current	GRCh38.p14 (GCF_000001405.40)	20	NC_000020.11 (24469629..24666616)
RS_2024_08	current	T2T-CHM13v2.0 (GCF_009914755.1)	20	NC_060944.1 (24531610..24729659)
RS_2024_09	previous assembly	GRCh37.p13 (GCF_000001405.25)	20	NC_000020.10 (24450265..24647252)

Chromosome 20 - NC_000020.11 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: Tissue-specific circular RNA induction during human fetal development
Description: 35 human fetal samples from 6 tissues (3 - 7 replicates per tissue) collected between 10 and 20 weeks gestational time were sequenced using Illumina TruSeq Stranded Total RNA
BioProject: PRJNA270632
Publication: PMID 26076956
Analysis date: Mon Apr 2 22:54:59 2018

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

Clinical trial of gene-disease association and gene-environment interaction. (HuGE Navigator)
Title: Personalized smoking cessation: interactions between nicotine dose, dependence and quit-success genotype score.

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)

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

D20S1035 (e-PCR)
- UniSTS:15879

D20S558E (e-PCR)
- UniSTS:13103

D20S754 (e-PCR)
- UniSTS:58939

RH121314 (e-PCR)
- UniSTS:138579

STS-AA019613 (e-PCR)
- UniSTS:66656

D20S486 (e-PCR)
- UniSTS:42337

RH48635 (e-PCR)
- UniSTS:36482

G69455 (e-PCR)
- UniSTS:229524

SHGC-142801 (e-PCR)
- UniSTS:171668

D20S954 (e-PCR)
- UniSTS:69306

RH98971 (e-PCR)
- UniSTS:90554

D20S844 (e-PCR)
- UniSTS:76490

D20S462 (e-PCR)
- UniSTS:81657

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables glutamate receptor binding	ISS Inferred from Sequence or Structural Similarity more info
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed
enables protein homodimerization activity	ISS Inferred from Sequence or Structural Similarity more info

Process	Evidence Code	Pubs
involved_in intracellular protein transport	ISS Inferred from Sequence or Structural Similarity more info
involved_in positive regulation of synapse assembly	IBA Inferred from Biological aspect of Ancestor more info
involved_in positive regulation of synapse assembly	IDA Inferred from Direct Assay more info	PubMed
involved_in regulation of postsynapse assembly	IEA Inferred from Electronic Annotation more info
involved_in synaptic vesicle clustering	IBA Inferred from Biological aspect of Ancestor more info
involved_in synaptic vesicle clustering	ISS Inferred from Sequence or Structural Similarity more info

Component	Evidence Code	Pubs
located_in cell body	ISS Inferred from Sequence or Structural Similarity more info
located_in dendritic shaft	ISS Inferred from Sequence or Structural Similarity more info
located_in dendritic spine	ISS Inferred from Sequence or Structural Similarity more info
located_in early endosome membrane	ISS Inferred from Sequence or Structural Similarity more info
is_active_in excitatory synapse	IBA Inferred from Biological aspect of Ancestor more info
located_in excitatory synapse	ISS Inferred from Sequence or Structural Similarity more info
located_in glutamatergic synapse	IEA Inferred from Electronic Annotation more info
is_active_in intracellular membrane-bounded organelle	IBA Inferred from Biological aspect of Ancestor more info
located_in intracellular membrane-bounded organelle	IDA Inferred from Direct Assay more info
located_in plasma membrane	ISS Inferred from Sequence or Structural Similarity more info
located_in postsynaptic density	ISS Inferred from Sequence or Structural Similarity more info
is_active_in postsynaptic density membrane	IBA Inferred from Biological aspect of Ancestor more info
is_active_in synaptic vesicle membrane	IBA Inferred from Biological aspect of Ancestor more info

General protein information

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Preferred Names: synapse differentiation-inducing gene protein 1

Names: dispanin subfamily C member 2; interferon induced transmembrane protein domain containing 5; synapse differentiation induced gene 1; transmembrane protein 90B

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_001323606.2 → NP_001310535.1 synapse differentiation-inducing gene protein 1

Status: REVIEWED

Source sequence(s)

AL034426, AL049594, AL157413, DB306704

Consensus CDS

CCDS13164.1

UniProtKB/Swiss-Prot

Q6IA30, Q9H514, Q9H7V2

Conserved Domains (1) summary

pfam04505
Location:177 → 242

CD225; Interferon-induced transmembrane protein
NM_001323607.2 → NP_001310536.1 synapse differentiation-inducing gene protein 1

Status: REVIEWED

Source sequence(s)

AL034426, AL049594, AL157413, DB306704

Consensus CDS

CCDS13164.1

UniProtKB/Swiss-Prot

Q6IA30, Q9H514, Q9H7V2

Conserved Domains (1) summary

pfam04505
Location:177 → 242

CD225; Interferon-induced transmembrane protein
NM_024893.3 → NP_079169.1 synapse differentiation-inducing gene protein 1

See identical proteins and their annotated locations for NP_079169.1

Status: REVIEWED

Source sequence(s)

AK024282, DB306704

Consensus CDS

CCDS13164.1

UniProtKB/Swiss-Prot

Q6IA30, Q9H514, Q9H7V2

Related

ENSP00000366058.3, ENST00000376862.4

Conserved Domains (1) summary

pfam04505
Location:177 → 242

CD225; Interferon-induced transmembrane protein

RNA

NR_147606.2 RNA Sequence

Status: REVIEWED

Source sequence(s)

AL034426, AL049594, AL157413

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_000020.11 Reference GRCh38.p14 Primary Assembly

Range

24469629..24666616

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_047440499.1 → XP_047296455.1 synapse differentiation-inducing gene protein 1 isoform X3
XM_011529356.4 → XP_011527658.1 synapse differentiation-inducing gene protein 1 isoform X4

Conserved Domains (1) summary

pfam04505
Location:177 → 206

CD225; Interferon-induced transmembrane protein
XM_011529358.3 → XP_011527660.1 synapse differentiation-inducing gene protein 1 isoform X5

Conserved Domains (1) summary

pfam04505
Location:177 → 206

CD225; Interferon-induced transmembrane protein
XM_011529350.2 → XP_011527652.1 synapse differentiation-inducing gene protein 1 isoform X1

See identical proteins and their annotated locations for XP_011527652.1

Conserved Domains (1) summary

pfam04505
Location:177 → 206

CD225; Interferon-induced transmembrane protein
XM_047440496.1 → XP_047296452.1 synapse differentiation-inducing gene protein 1 isoform X1
XM_011529347.4 → XP_011527649.1 synapse differentiation-inducing gene protein 1 isoform X1

See identical proteins and their annotated locations for XP_011527649.1

Conserved Domains (1) summary

pfam04505
Location:177 → 206

CD225; Interferon-induced transmembrane protein
XM_011529348.4 → XP_011527650.1 synapse differentiation-inducing gene protein 1 isoform X1

See identical proteins and their annotated locations for XP_011527650.1

Conserved Domains (1) summary

pfam04505
Location:177 → 206

CD225; Interferon-induced transmembrane protein
XM_017028069.3 → XP_016883558.1 synapse differentiation-inducing gene protein 1 isoform X6
XM_017028066.3 → XP_016883555.1 synapse differentiation-inducing gene protein 1 isoform X2

UniProtKB/Swiss-Prot

Q6IA30, Q9H514, Q9H7V2

Conserved Domains (1) summary

pfam04505
Location:177 → 242

CD225; Interferon-induced transmembrane protein
XM_017028067.3 → XP_016883556.1 synapse differentiation-inducing gene protein 1 isoform X2

UniProtKB/Swiss-Prot

Q6IA30, Q9H514, Q9H7V2

Conserved Domains (1) summary

pfam04505
Location:177 → 242

CD225; Interferon-induced transmembrane protein
XM_017028065.2 → XP_016883554.1 synapse differentiation-inducing gene protein 1 isoform X2

UniProtKB/Swiss-Prot

Q6IA30, Q9H514, Q9H7V2

Conserved Domains (1) summary

pfam04505
Location:177 → 242

CD225; Interferon-induced transmembrane protein
XM_011529353.3 → XP_011527655.1 synapse differentiation-inducing gene protein 1 isoform X1

See identical proteins and their annotated locations for XP_011527655.1

Conserved Domains (1) summary

pfam04505
Location:177 → 206

CD225; Interferon-induced transmembrane protein
XM_011529354.3 → XP_011527656.1 synapse differentiation-inducing gene protein 1 isoform X1

See identical proteins and their annotated locations for XP_011527656.1

Conserved Domains (1) summary

pfam04505
Location:177 → 206

CD225; Interferon-induced transmembrane protein
XM_011529351.2 → XP_011527653.1 synapse differentiation-inducing gene protein 1 isoform X1

See identical proteins and their annotated locations for XP_011527653.1

Conserved Domains (1) summary

pfam04505
Location:177 → 206

CD225; Interferon-induced transmembrane protein
XM_047440497.1 → XP_047296453.1 synapse differentiation-inducing gene protein 1 isoform X1
XM_047440498.1 → XP_047296454.1 synapse differentiation-inducing gene protein 1 isoform X1
XM_047440500.1 → XP_047296456.1 synapse differentiation-inducing gene protein 1 isoform X6
XM_017028064.2 → XP_016883553.1 synapse differentiation-inducing gene protein 1 isoform X1

Conserved Domains (1) summary

pfam04505
Location:177 → 206

CD225; Interferon-induced transmembrane protein
XM_017028068.2 → XP_016883557.1 synapse differentiation-inducing gene protein 1 isoform X2

UniProtKB/Swiss-Prot

Q6IA30, Q9H514, Q9H7V2

Conserved Domains (1) summary

pfam04505
Location:177 → 242

CD225; Interferon-induced transmembrane protein

Alternate T2T-CHM13v2.0

Genomic

NC_060944.1 Alternate T2T-CHM13v2.0

Range

24531610..24729659

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054324030.1 → XP_054180005.1 synapse differentiation-inducing gene protein 1 isoform X3
XM_054324031.1 → XP_054180006.1 synapse differentiation-inducing gene protein 1 isoform X4
XM_054324032.1 → XP_054180007.1 synapse differentiation-inducing gene protein 1 isoform X5
XM_054324017.1 → XP_054179992.1 synapse differentiation-inducing gene protein 1 isoform X1
XM_054324018.1 → XP_054179993.1 synapse differentiation-inducing gene protein 1 isoform X1
XM_054324015.1 → XP_054179990.1 synapse differentiation-inducing gene protein 1 isoform X1
XM_054324016.1 → XP_054179991.1 synapse differentiation-inducing gene protein 1 isoform X1
XM_054324033.1 → XP_054180008.1 synapse differentiation-inducing gene protein 1 isoform X6
XM_054324027.1 → XP_054180002.1 synapse differentiation-inducing gene protein 1 isoform X2

UniProtKB/Swiss-Prot

Q6IA30, Q9H514, Q9H7V2
XM_054324026.1 → XP_054180001.1 synapse differentiation-inducing gene protein 1 isoform X2

UniProtKB/Swiss-Prot

Q6IA30, Q9H514, Q9H7V2
XM_054324024.1 → XP_054179999.1 synapse differentiation-inducing gene protein 1 isoform X1
XM_054324019.1 → XP_054179994.1 synapse differentiation-inducing gene protein 1 isoform X1
XM_054324020.1 → XP_054179995.1 synapse differentiation-inducing gene protein 1 isoform X1
XM_054324021.1 → XP_054179996.1 synapse differentiation-inducing gene protein 1 isoform X1
XM_054324022.1 → XP_054179997.1 synapse differentiation-inducing gene protein 1 isoform X1
XM_054324034.1 → XP_054180009.1 synapse differentiation-inducing gene protein 1 isoform X6
XM_054324029.1 → XP_054180004.1 synapse differentiation-inducing gene protein 1 isoform X2

UniProtKB/Swiss-Prot

Q6IA30, Q9H514, Q9H7V2
XM_054324023.1 → XP_054179998.1 synapse differentiation-inducing gene protein 1 isoform X1
XM_054324025.1 → XP_054180000.1 synapse differentiation-inducing gene protein 1 isoform X1
XM_054324028.1 → XP_054180003.1 synapse differentiation-inducing gene protein 1 isoform X2

UniProtKB/Swiss-Prot

Q6IA30, Q9H514, Q9H7V2