SCYL3 SCY1 like pseudokinase 3 [Homo sapiens (human)] - Gene

Summary

Official Symbol: SCYL3provided by HGNC
Official Full Name: SCY1 like pseudokinase 3provided by HGNC
Primary source: HGNC:HGNC:19285
See related: Ensembl:ENSG00000000457 MIM:608192; AllianceGenome:HGNC:19285
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: PACE1; PACE-1
Summary: This gene encodes a protein with a kinase domain and four HEAT repeats. The encoded protein interacts with the C-terminal domain of ezrin, an ERM protein, and may play a role in cell adhesion and migration. Alternative splicing results in multiple transcript variants encoding multiple isoforms. [provided by RefSeq, Jun 2012]
Expression: Ubiquitous expression in lymph node (RPKM 4.6), testis (RPKM 4.3) and 25 other tissues See more
Orthologs: mouse all
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Genomic context

Location:: 1q24.2

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2023_10	current	GRCh38.p14 (GCF_000001405.40)	1	NC_000001.11 (169849631..169894268, complement)
RS_2023_10	current	T2T-CHM13v2.0 (GCF_009914755.1)	1	NC_060925.1 (169205381..169249993, complement)
105.20220307	previous assembly	GRCh37.p13 (GCF_000001405.25)	1	NC_000001.10 (169818772..169863037, complement)

Chromosome 1 - NC_000001.11 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: 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?

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.
Observational study of gene-disease association. (HuGE Navigator)
Title: Pre-B-cell leukemia homeobox 1 (PBX1) shows functional and possible genetic association with bone mineral density variation.

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

SHGC-106696 (e-PCR)
- UniSTS:169986

SHGC-75868 (e-PCR)
- UniSTS:80456

RH103578 (e-PCR)
- UniSTS:97903

SHGC-75871 (e-PCR)
- UniSTS:16040

Gene Ontology Provided by GOA

Function	Evidence Code	Pubs
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
NOT enables kinase activity	IDA Inferred from Direct Assay more info	PubMed
enables protein binding	IPI Inferred from Physical Interaction more info	PubMed

Process	Evidence Code	Pubs
involved_in cell migration	NAS Non-traceable Author Statement more info	PubMed
involved_in inflammatory response	IEA Inferred from Electronic Annotation more info
involved_in neuron development	IEA Inferred from Electronic Annotation more info
involved_in protein localization	IEA Inferred from Electronic Annotation more info
involved_in spinal cord motor neuron differentiation	IEA Inferred from Electronic Annotation more info

Component	Evidence Code	Pubs
located_in Golgi apparatus	IDA Inferred from Direct Assay more info	PubMed
located_in Golgi membrane	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	IDA Inferred from Direct Assay more info	PubMed
located_in cytosol	IDA Inferred from Direct Assay more info
located_in endoplasmic reticulum	IDA Inferred from Direct Assay more info
located_in lamellipodium	IDA Inferred from Direct Assay more info	PubMed

General protein information

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Preferred Names: protein-associating with the carboxyl-terminal domain of ezrin

Names: SCY1-like 3; SCY1-like protein 3; SCY1-like, kinase-like 3; ezrin-binding partner PACE-1 (PACE-1); ezrin-binding protein PACE-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_020423.7 → NP_065156.5 protein-associating with the carboxyl-terminal domain of ezrin isoform 1

See identical proteins and their annotated locations for NP_065156.5

Status: REVIEWED

Description

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

Source sequence(s)

AL031297, AL117233, DA449356

Consensus CDS

CCDS1286.1

UniProtKB/TrEMBL

X6RHX1

Related

ENSP00000356745.5, ENST00000367771.11

Conserved Domains (3) summary

cd14011
Location:9 → 247

PK_SCY1_like; Pseudokinase domain of Scy1-like proteins

pfam00069
Location:26 → 245

Pkinase; Protein kinase domain

sd00044
Location:294 → 319

HEAT; HEAT repeat [structural motif]
NM_181093.4 → NP_851607.2 protein-associating with the carboxyl-terminal domain of ezrin isoform 2

See identical proteins and their annotated locations for NP_851607.2

Status: REVIEWED

Description

Transcript Variant: This variant (2) contains an alternate in-frame exon in the 3' coding region compared to variant 1. It encodes isoform 2, which is longer than isoform 1.

Source sequence(s)

AK292507, AL031297, AL117233

Consensus CDS

CCDS1287.1

UniProtKB/Swiss-Prot

A8K8Z2, Q5THA6, Q5THA8, Q8IZE3, Q8IZN9, Q96C56, Q9UBK6

Related

ENSP00000356746.4, ENST00000367772.8

Conserved Domains (3) summary

cd14011
Location:9 → 247

PK_SCY1_like; Pseudokinase domain of Scy1-like proteins

pfam00069
Location:26 → 245

Pkinase; Protein kinase domain

sd00044
Location:294 → 319

HEAT; HEAT repeat [structural motif]

RefSeqs of Annotated Genomes: GCF_000001405.40-RS_2023_10

The following sections contain reference sequences that belong to a specific genome build. Explain

Reference GRCh38.p14 Primary Assembly

Genomic

NC_000001.11 Reference GRCh38.p14 Primary Assembly

Range

169849631..169894268 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_017001863.2 → XP_016857352.1 protein-associating with the carboxyl-terminal domain of ezrin isoform X2

UniProtKB/TrEMBL

X6RHX1

Related

ENSP00000407993.1, ENST00000423670.1

Conserved Domains (3) summary

cd14011
Location:9 → 247

PK_SCY1_like; Pseudokinase domain of Scy1-like proteins

pfam00069
Location:26 → 245

Pkinase; Protein kinase domain

sd00044
Location:294 → 319

HEAT; HEAT repeat [structural motif]
XM_011509801.2 → XP_011508103.1 protein-associating with the carboxyl-terminal domain of ezrin isoform X1

See identical proteins and their annotated locations for XP_011508103.1

UniProtKB/Swiss-Prot

A8K8Z2, Q5THA6, Q5THA8, Q8IZE3, Q8IZN9, Q96C56, Q9UBK6

Conserved Domains (3) summary

cd14011
Location:9 → 247

PK_SCY1_like; Pseudokinase domain of Scy1-like proteins

pfam00069
Location:26 → 245

Pkinase; Protein kinase domain

sd00044
Location:294 → 319

HEAT; HEAT repeat [structural motif]
XM_017001862.2 → XP_016857351.1 protein-associating with the carboxyl-terminal domain of ezrin isoform X2

UniProtKB/TrEMBL

X6RHX1

Conserved Domains (3) summary

cd14011
Location:9 → 247

PK_SCY1_like; Pseudokinase domain of Scy1-like proteins

pfam00069
Location:26 → 245

Pkinase; Protein kinase domain

sd00044
Location:294 → 319

HEAT; HEAT repeat [structural motif]
XM_006711465.2 → XP_006711528.1 protein-associating with the carboxyl-terminal domain of ezrin isoform X1

See identical proteins and their annotated locations for XP_006711528.1

UniProtKB/Swiss-Prot

A8K8Z2, Q5THA6, Q5THA8, Q8IZE3, Q8IZN9, Q96C56, Q9UBK6

Conserved Domains (3) summary

cd14011
Location:9 → 247

PK_SCY1_like; Pseudokinase domain of Scy1-like proteins

pfam00069
Location:26 → 245

Pkinase; Protein kinase domain

sd00044
Location:294 → 319

HEAT; HEAT repeat [structural motif]
XM_011509802.2 → XP_011508104.1 protein-associating with the carboxyl-terminal domain of ezrin isoform X3

See identical proteins and their annotated locations for XP_011508104.1

Conserved Domains (2) summary

sd00044
Location:152 → 177

HEAT; HEAT repeat [structural motif]

cl21453
Location:1 → 105

PKc_like; Protein Kinases, catalytic domain
XM_047425909.1 → XP_047281865.1 protein-associating with the carboxyl-terminal domain of ezrin isoform X4

Alternate T2T-CHM13v2.0

Genomic

NC_060925.1 Alternate T2T-CHM13v2.0

Range

169205381..169249993 complement

Download

GenBank, FASTA, Sequence Viewer (Graphics)

mRNA and Protein(s)

XM_054337795.1 → XP_054193770.1 protein-associating with the carboxyl-terminal domain of ezrin isoform X2
XM_054337793.1 → XP_054193768.1 protein-associating with the carboxyl-terminal domain of ezrin isoform X1
XM_054337792.1 → XP_054193767.1 protein-associating with the carboxyl-terminal domain of ezrin isoform X1
XM_054337794.1 → XP_054193769.1 protein-associating with the carboxyl-terminal domain of ezrin isoform X2
XM_054337796.1 → XP_054193771.1 protein-associating with the carboxyl-terminal domain of ezrin isoform X3
XM_054337797.1 → XP_054193772.1 protein-associating with the carboxyl-terminal domain of ezrin isoform X4