Scg2 MGI Mouse Gene Detail - MGI:103033 - secretogranin II

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Scg2 Gene Detail

Symbol

Scg2
Name

secretogranin II
Synonyms

Chgc, SgII

Feature Type

protein coding gene
IDs

MGI:103033
NCBI Gene: 20254
Alliance

genome feature page
Transcription Start Sites

6 TSS
Candidate for QTL

8 QTL

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Sequence Map

Chr1:79412386-79417837 bp, - strand
From Ensembl annotation of GRCm39
View this region in JBrowse
Genome Browsers

Ensembl | UCSC | NCBI

Genetic Map

Chromosome 1, 40.89 cM
Mapping Data

5 experiments

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SNPs within 2kb

157 from dbSNP Build 142
Strain Annotations

19
PCR

1
RFLP

1

For selected strains:

Strain	Gene Model ID	Feature Type	Coordinates	Select Strains
C57BL/6J	MGI_C57BL6J_103033	protein coding gene	Chr1:79412083-79417837 (-)
129S1/SvImJ	ENSMUSG00200034046	protein coding gene	Chr1:77091517-77096969 (-)
A/J	ENSMUSG00195010069	protein coding gene	Chr1:76502855-76508307 (-)
AKR/J	ENSMUSG00220010198	protein coding gene	Chr1:76674296-76679747 (-)
BALB/cJ	ENSMUSG00180019236	protein coding gene	Chr1:76765355-76770808 (-)
C3H/HeJ	ENSMUSG00175016886	protein coding gene	Chr1:76909353-76914805 (-)
C57BL/6NJ	ENSMUSG00215012620	protein coding gene	Chr1:76814817-76820268 (-)
CAROLI/EiJ	MGP_CAROLIEiJ_G0014315	protein coding gene	Chr1:72717772-72723216 (-)
CAST/EiJ	ENSTCUG00005025090	protein coding gene	Chr1:76485072-76490527 (-)
CBA/J	ENSMUSG00210036561	protein coding gene	Chr1:76685006-76690457 (-)
DBA/2J	ENSMUSG00185031785	protein coding gene	Chr1:77731156-77736607 (-)
FVB/NJ	ENSMUSG00205018762	protein coding gene	Chr1:76225681-76231133 (-)
JF1/MsJ	ENSUMUG00000003561	protein coding gene	Chr1:76536400-76541849 (-)
LP/J	ENSMUSG00230008615	protein coding gene	Chr1:77666807-77672259 (-)
NOD/ShiLtJ	ENSMUSG00190034764	protein coding gene	Chr1:76888683-76894134 (-)
NZO/HlLtJ	ENSMUSG00225039309	protein coding gene	Chr1:80902155-80907607 (-)
PWK/PhJ	ENSLUMG00010013414	protein coding gene	Chr1:76151518-76156967 (-)
SPRET/EiJ	ENSMSPG00010019606	protein coding gene	Chr1:78312145-78317592 (-)
WSB/EiJ	ENSIUOG00005012804	protein coding gene	Chr1:76432543-76437994 (-)

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Human Ortholog

SCG2, secretogranin II

Vertebrate Orthologs

4

Vertebrate Orthology Source

Alliance of Genome Resources

Human Ortholog

SCG2, secretogranin II
Synonyms

CHGC, EM66, SgII, SN
Links

HGNC:10575

NCBI Gene ID: 7857

UniProt: P13521
Chr Location

2q36.1; chr2:223596940-223602361 (-) GRCh38

MGI Vertebrate Homology

Scg2 stringent orthology
1 human;1 mouse;1 rat;2 zebrafish
HCOP

vertebrate homology predictions: SCG2
Gene Tree

Scg2

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Phenotype Summary

1 phenotype from 1 allele in 1 genetic background
12 phenotype references

Phenotype Overview

Phenotype Overview

Blue squares indicate phenotypes directly attributed to mutations/alleles of this gene.

adipose tissue	behavior/neurological	cardiovascular system	cellular	craniofacial	digestive/alimentary system	embryo	endocrine/exocrine glands	growth/size/body	hearing/vestibular/ear	hematopoietic system	homeostasis/metabolism	integument	immune system	limbs/digits/tail	liver/biliary system	mortality/aging	muscle	nervous system	pigmentation	renal/urinary system	reproductive system	respiratory system	skeleton	taste/olfaction	neoplasm	vision/eye

Click cells to view annotations.

All Mutations and Alleles

9
Chemically induced (other)

1
Endonuclease-mediated

5
Radiation induced

1
Targeted

2
Genomic Mutations

2 involving Scg2
Incidental Mutations

Mutagenetix , APF , CvDC
Find Mice (IMSR)

37 strains or lines available

Mice homozygous for a conditional alleles activated in CA1 hippocampal neurons exhibit altered gamma rhythms and pyramidal cell coupling to theta phase.

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All GO Annotations

46
GO References

11

Molecular Function

carbohydrate derivative binding	cytoskeletal protein binding	DNA binding	enzyme regulator	hydrolase	ligase	lipid binding	oxidoreductase	RNA binding	signaling receptor activity	signaling receptor binding	transcription	transferase	transporter

Biological Process

carbohydrate derivative metabolism	cell differentiation	cell population proliferation	cellular component organization	DNA-templated transcription	establishment of localization	homeostatic process	immune system process	lipid metabolic process	programmed cell death	protein metabolic process	response to stimulus	signaling	system development

Cellular Component

cell projection	cytoplasmic vesicle	cytoskeleton	cytosol	endoplasmic reticulum	endosome	extracellular region	Golgi apparatus	mitochondrion	membraneless organelle	nucleus	organelle envelope	organelle lumen	plasma membrane	protein-containing complex	synapse	vacuole

Click cells to view annotations.

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Expression Overview

Expression Overview

GXD's primary emphasis is on endogenous gene expression during development. Click on grid cells to view annotations.

Blue cells = expressed in wild-type.
Gray triangles = other expression annotations only
(e.g. absence of expression or data from mutants).

early conceptus	embryo ectoderm	embryo endoderm	embryo mesoderm	embryo mesenchyme	extraembryonic component	alimentary system	auditory system	branchial arches	cardiovascular system	connective tissue	endocrine system	exocrine system	hemolymphoid system	integumental system	limbs	liver and biliary system	musculoskeletal system	nervous system	olfactory system	reproductive system	respiratory system	urinary system	visual system

Click cells to view annotations.

Assay Results

1061
Tissues

199
cDNA Data

56
Literature Summary

18

Tissue x Stage Matrix

Other Mouse Links

Allen Institute

GENSAT

GEO

Expression Atlas
Other Vertebrate Links

Xenbase scg2

ZFIN scg2a, scg2b

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All Sequences

40
RefSeq

4
UniProt

3
CCDS

CCDS15089.1, CCDS78625.1

Ensembl

ENSMUSG00000050711 (Evidence)
NCBI Gene

20254

Representative Sequences				Length	Strain/Species	Flank
	genomic	ENSMUSG00000050711	Ensembl Gene Model \| MGI Sequence Detail	5452	C57BL/6J	± kb
	transcript	ENSMUST00000049972	Ensembl \| MGI Sequence Detail	2515	Not Applicable
	polypeptide	ENSMUSP00000062556	Ensembl \| MGI Sequence Detail	617	Not Applicable

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UniProt

3 Sequences
Protein Ontology

PR:000014502 secretogranin-2

(term hierarchy)
InterPro Domains

IPR001990 Chromogranin A/B/C

IPR038858 Secretogranin-2

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All nucleic 66

Genomic 1

cDNA 58

Primer pair 4

Other 3

Antibodies 3

Microarray probesets 3

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MGD-MRK-1971, MGD-MRK-23870

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Summaries

All 70

Developmental Gene Expression 18

Gene Ontology 11

Phenotypes 12
Earliest

J:134667 Roderick TH, et al., Two radiation-induced chromosomal inversions in mice (Mus musculus). Proc Natl Acad Sci U S A. 1970 Oct;67(2):961-7
Latest

J:376344 Yang X, et al., Secretogranin 2 binds LILRB4 resulting in immunosuppression. Nat Immunol. 2025 Sep;26(9):1567-1580

TSS for Scg2:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr12438	Chr1:79417820-79417825 (-)	14 bp
Tssr12437	Chr1:79417756-79417797 (-)	60 bp
Tssr12436	Chr1:79417732-79417752 (-)	95 bp
Tssr12435	Chr1:79417720-79417731 (-)	111 bp
Tssr12434	Chr1:79414046-79414065 (-)	3,781 bp
Tssr12433	Chr1:79413969-79413982 (-)	3,861 bp

Scg2 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Insq2	Chr1, syntenic		J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. A potential candidate gene for Obq2 at 15 cM on mouse Chromosome 1 as identified by ExQuest is Gsta3. For QTLs Obq7 (28.7 cM), Wt6q1 (27 cM), Insq2 (36cM), and Insq6 (37 cM), potential candidate genes Aox1 (23.2 cM), Fn1 (36.1 cM), Pecr, Igfbp2 (36.1 cM), Plcd4 (39.2 cM), Scg2 (43.6 cM), Irs1, and Inpp5d (57 cM) were identified. For QTL Nidd6 (77 cM), potential candidate gene Qscn6 was identified. For QTL Obq9 (88.4 cM), potential candidate genes Fmo1, Fmo3, and Apoa2 (92.6 cM) were identified. For QTL Wt6q2 (108 cM), potential candidate gene Hsd11b1 was identified.
Insq6	Chr1, 38.01 cM	Chr1:73726922-73727077	J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. A potential candidate gene for Obq2 at 15 cM on mouse Chromosome 1 as identified by ExQuest is Gsta3. For QTLs Obq7 (28.7 cM), Wt6q1 (27 cM), Insq2 (36cM), and Insq6 (37 cM), potential candidate genes Aox1 (23.2 cM), Fn1 (36.1 cM), Pecr, Igfbp2 (36.1 cM), Plcd4 (39.2 cM), Scg2 (43.6 cM), Irs1, and Inpp5d (57 cM) were identified. For QTL Nidd6 (77 cM), potential candidate gene Qscn6 was identified. For QTL Obq9 (88.4 cM), potential candidate genes Fmo1, Fmo3, and Apoa2 (92.6 cM) were identified. For QTL Wt6q2 (108 cM), potential candidate gene Hsd11b1 was identified.
Nidd6	Chr1, 65.11 cM		J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. A potential candidate gene for Obq2 at 15 cM on mouse Chromosome 1 as identified by ExQuest is Gsta3. For QTLs Obq7 (28.7 cM), Wt6q1 (27 cM), Insq2 (36cM), and Insq6 (37 cM), potential candidate genes Aox1 (23.2 cM), Fn1 (36.1 cM), Pecr, Igfbp2 (36.1 cM), Plcd4 (39.2 cM), Scg2 (43.6 cM), Irs1, and Inpp5d (57 cM) were identified. For QTL Nidd6 (77 cM), potential candidate gene Qscn6 was identified. For QTL Obq9 (88.4 cM), potential candidate genes Fmo1, Fmo3, and Apoa2 (92.6 cM) were identified. For QTL Wt6q2 (108 cM), potential candidate gene Hsd11b1 was identified.
Obq2	Chr1, 6.50 cM	Chr1:20941620-20941887	J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. A potential candidate gene for Obq2 at 15 cM on mouse Chromosome 1 as identified by ExQuest is Gsta3. For QTLs Obq7 (28.7 cM), Wt6q1 (27 cM), Insq2 (36cM), and Insq6 (37 cM), potential candidate genes Aox1 (23.2 cM), Fn1 (36.1 cM), Pecr, Igfbp2 (36.1 cM), Plcd4 (39.2 cM), Scg2 (43.6 cM), Irs1, and Inpp5d (57 cM) were identified. For QTL Nidd6 (77 cM), potential candidate gene Qscn6 was identified. For QTL Obq9 (88.4 cM), potential candidate genes Fmo1, Fmo3, and Apoa2 (92.6 cM) were identified. For QTL Wt6q2 (108 cM), potential candidate gene Hsd11b1 was identified.
Obq7	Chr1, 33.31 cM		J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. A potential candidate gene for Obq2 at 15 cM on mouse Chromosome 1 as identified by ExQuest is Gsta3. For QTLs Obq7 (28.7 cM), Wt6q1 (27 cM), Insq2 (36cM), and Insq6 (37 cM), potential candidate genes Aox1 (23.2 cM), Fn1 (36.1 cM), Pecr, Igfbp2 (36.1 cM), Plcd4 (39.2 cM), Scg2 (43.6 cM), Irs1, and Inpp5d (57 cM) were identified. For QTL Nidd6 (77 cM), potential candidate gene Qscn6 was identified. For QTL Obq9 (88.4 cM), potential candidate genes Fmo1, Fmo3, and Apoa2 (92.6 cM) were identified. For QTL Wt6q2 (108 cM), potential candidate gene Hsd11b1 was identified.
Obq9	Chr1, 74.68 cM		J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. A potential candidate gene for Obq2 at 15 cM on mouse Chromosome 1 as identified by ExQuest is Gsta3. For QTLs Obq7 (28.7 cM), Wt6q1 (27 cM), Insq2 (36cM), and Insq6 (37 cM), potential candidate genes Aox1 (23.2 cM), Fn1 (36.1 cM), Pecr, Igfbp2 (36.1 cM), Plcd4 (39.2 cM), Scg2 (43.6 cM), Irs1, and Inpp5d (57 cM) were identified. For QTL Nidd6 (77 cM), potential candidate gene Qscn6 was identified. For QTL Obq9 (88.4 cM), potential candidate genes Fmo1, Fmo3, and Apoa2 (92.6 cM) were identified. For QTL Wt6q2 (108 cM), potential candidate gene Hsd11b1 was identified.
Wt6q1	Chr1, syntenic		J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. A potential candidate gene for Obq2 at 15 cM on mouse Chromosome 1 as identified by ExQuest is Gsta3. For QTLs Obq7 (28.7 cM), Wt6q1 (27 cM), Insq2 (36cM), and Insq6 (37 cM), potential candidate genes Aox1 (23.2 cM), Fn1 (36.1 cM), Pecr, Igfbp2 (36.1 cM), Plcd4 (39.2 cM), Scg2 (43.6 cM), Irs1, and Inpp5d (57 cM) were identified. For QTL Nidd6 (77 cM), potential candidate gene Qscn6 was identified. For QTL Obq9 (88.4 cM), potential candidate genes Fmo1, Fmo3, and Apoa2 (92.6 cM) were identified. For QTL Wt6q2 (108 cM), potential candidate gene Hsd11b1 was identified.
Wt6q2	Chr1, syntenic		J:99477	Authors used novel data mining tool ExQuest to identify novel candidate genes for existing diabesity QTLs. Next, candidate gene expression in the liver, adipose, and pancreas of diabesity-prone Tally Ho mice and diabesity-resistant C57BL/6J mice was assessed by quantitative PCR analysis. Several potential candidate genes, some with no previous association to diabesity QTLs, were identified. Since QTL intervals may be large and could contain hundreds or thousands of potential candidate genes, this method allows researchers to focus on those with strong potential as well as identify novel candidate genes. A potential candidate gene for Obq2 at 15 cM on mouse Chromosome 1 as identified by ExQuest is Gsta3. For QTLs Obq7 (28.7 cM), Wt6q1 (27 cM), Insq2 (36cM), and Insq6 (37 cM), potential candidate genes Aox1 (23.2 cM), Fn1 (36.1 cM), Pecr, Igfbp2 (36.1 cM), Plcd4 (39.2 cM), Scg2 (43.6 cM), Irs1, and Inpp5d (57 cM) were identified. For QTL Nidd6 (77 cM), potential candidate gene Qscn6 was identified. For QTL Obq9 (88.4 cM), potential candidate genes Fmo1, Fmo3, and Apoa2 (92.6 cM) were identified. For QTL Wt6q2 (108 cM), potential candidate gene Hsd11b1 was identified.

*cM position of peak correlated region/marker

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