Scgb1c1 (secretoglobin, family 1C, member 1) - Rat Genome Database

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Gene: Scgb1c1 (secretoglobin, family 1C, member 1) Mus musculus
Analyze
Symbol: Scgb1c1
Name: secretoglobin, family 1C, member 1
RGD ID: 1620445
MGI Page MGI
Description: Predicted to be located in extracellular region. Orthologous to several human genes including SCGB1C1 (secretoglobin family 1C member 1).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: ligand binding protein RYD5; Ryd; Ryd5; secretoglobin family 1C member 1; secretoglobin RYD5
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397140,425,478 - 140,426,682 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl7140,425,460 - 140,426,682 (+)EnsemblGRCm39 Ensembl
GRCm387140,845,565 - 140,846,769 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7140,845,547 - 140,846,769 (+)EnsemblGRCm38mm10GRCm38
MGSCv377148,031,464 - 148,032,668 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv367148,031,464 - 148,032,668 (+)NCBIMGSCv36mm8
Celera7140,637,851 - 140,639,055 (+)NCBICelera
Cytogenetic Map7F4NCBI
cM Map786.04NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12406855   PMID:12466851   PMID:14610273   PMID:14611657   PMID:21677750   PMID:21873635   PMID:38355793   PMID:38892470  


Genomics

Comparative Map Data
Scgb1c1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm397140,425,478 - 140,426,682 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl7140,425,460 - 140,426,682 (+)EnsemblGRCm39 Ensembl
GRCm387140,845,565 - 140,846,769 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl7140,845,547 - 140,846,769 (+)EnsemblGRCm38mm10GRCm38
MGSCv377148,031,464 - 148,032,668 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv367148,031,464 - 148,032,668 (+)NCBIMGSCv36mm8
Celera7140,637,851 - 140,639,055 (+)NCBICelera
Cytogenetic Map7F4NCBI
cM Map786.04NCBI
SCGB1C1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh3811188,050 - 194,575 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl11193,078 - 194,575 (+)EnsemblGRCh38hg38GRCh38
GRCh3711193,078 - 194,575 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3611183,080 - 184,573 (+)NCBINCBI36Build 36hg18NCBI36
Celera1787,947 - 89,440 (+)NCBICelera
Cytogenetic Map11p15.5NCBI
HuRef1112,288 - 13,781 (+)NCBIHuRef
CHM1_111191,985 - 193,478 (+)NCBICHM1_1
T2T-CHM13v2.011228,737 - 235,264 (+)NCBIT2T-CHM13v2.0
Scgb1c1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81205,352,216 - 205,354,656 (+)NCBIGRCr8
mRatBN7.21195,922,660 - 195,925,022 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1195,923,803 - 195,925,022 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1204,276,260 - 204,277,479 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01211,403,170 - 211,404,389 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01204,077,022 - 204,078,241 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01213,595,240 - 213,596,459 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1213,595,240 - 213,596,459 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01220,519,527 - 220,522,032 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41201,003,124 - 201,004,343 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera1193,567,749 - 193,568,968 (+)NCBICelera
Cytogenetic Map1q41NCBI
Scgb1c1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_00495547611,841,962 - 11,843,325 (-)NCBIChiLan1.0ChiLan1.0
SCGB1C1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v292,558,712 - 2,560,187 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1111,714,562 - 1,716,037 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v011186,794 - 188,283 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.111233,761 - 235,294 (+)NCBIpanpan1.1PanPan1.1panPan2
SCGB1C1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11825,351,393 - 25,352,893 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1825,001,375 - 25,002,870 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01825,877,969 - 25,879,464 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1825,878,083 - 25,879,463 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11825,445,995 - 25,447,490 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01825,090,777 - 25,092,272 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01825,703,585 - 25,705,080 (+)NCBIUU_Cfam_GSD_1.0
Scgb1c1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494744,999 - 46,483 (+)NCBIHiC_Itri_2
SpeTri2.0NW_00493688845,178 - 46,400 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
SCGB1C1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1217,552 - 20,717 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.22162,203,800 - 162,206,206 (-)NCBISscrofa10.2Sscrofa10.2susScr3
SCGB1C1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112,628 - 4,911 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366603897,018,567 - 97,019,562 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Scgb1c1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462476622,250,023 - 22,251,269 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Scgb1c1
9 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:97
Count of miRNA genes:96
Interacting mature miRNAs:97
Transcripts:ENSMUST00000035300
Prediction methods:Miranda, Rnahybrid
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


QTLs in Region (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
27226751Femd5_mfemur midshaft diameter 5, 10 week (mouse)753249748143153737Mouse
27095933Ulnl3_mulna length 3, 5 week (mouse)773149748143153737Mouse
11059562Lmr21b_mleishmaniasis resistance 21b (mouse)7110967235144967336Mouse
1302032Alcp12_malcohol preference locus 12 (mouse)Not determined7111166122144995196Mouse
1301590Pbwg3_mpostnatal body weight growth 3 (mouse)Not determined7127311241144995196Mouse
1300566Sluc8_msusceptibility to lung cancer 8 (mouse)Not determined7127398151144995196Mouse
14700684Civq1_mcerebral infarct volume QTL 1 (mouse)7109707335143707335Mouse
1300670Sluc19_msusceptibility to lung cancer 19 (mouse)Not determined7111166122144995196Mouse
14746988Manh63_mmandible shape 63 (mouse)7127735437144995196Mouse
14700687Civq5_mcerebral infarct volume QTL 5 (mouse)7109707335143707335Mouse
14700688Civq6_mcerebral infarct volume QTL 6 (mouse)7109707335143707335Mouse
12792978Fbmd3_mfemoral bone mineral density 3, females only (mouse)77050288142367832Mouse
4142444Femwf5_mfemur work to failure 5 (mouse)Not determined112552248144995196Mouse
1301158Eae4_msusceptibility to experimental allergic encephalomyelitis 4 (mouse)Not determined719147398141919804Mouse
1300677Bmd9_mbone mineral density 9 (mouse)Not determined7116634089144995196Mouse
1300747Skts2_mskin tumor susceptibility 2 (mouse)Not determined7112922733144995196Mouse
1301898Alcp14_malcohol preference locus 14 (mouse)Not determined7111166122144995196Mouse
1357711Adbg1_madult body growth 1 (mouse)Not determined7118693381144398314Mouse
10402499Lmr21_mleishmaniasis resistance 21 (mouse)Not determined7110967235144967336Mouse
1301773Stheal7_msoft tissue heal 7 (mouse)Not determined7119132573144995196Mouse


Sequence


Ensembl Acc Id: ENSMUST00000035300   ⟹   ENSMUSP00000048722
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl7140,425,460 - 140,426,682 (+)Ensembl
GRCm38.p6 Ensembl7140,845,547 - 140,846,769 (+)Ensembl
RefSeq Acc Id: NM_001099742   ⟹   NP_001093212
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm397140,425,478 - 140,426,682 (+)NCBI
GRCm387140,845,565 - 140,846,769 (+)ENTREZGENE
MGSCv377148,031,464 - 148,032,668 (+)RGD
Celera7140,637,851 - 140,639,055 (+)RGD
cM Map7 ENTREZGENE
Sequence:
Protein Sequences
Protein RefSeqs NP_001093212 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein DAA00357 (Get FASTA)   NCBI Sequence Viewer  
  EDL17957 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSMUSP00000048722
  ENSMUSP00000048722.6
GenBank Protein Q7M742 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_001093212   ⟸   NM_001099742
- Peptide Label: precursor
- UniProtKB: Q7M742 (UniProtKB/Swiss-Prot),   G5E8B5 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSMUSP00000048722   ⟸   ENSMUST00000035300

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q7M742-F1-model_v2 AlphaFold Q7M742 1-95 view protein structure

Promoters
RGD ID:8666025
Promoter ID:EPDNEW_M11044
Type:multiple initiation site
Name:Scgb1c1_1
Description:Mus musculus secretoglobin, family 1C, member 1 , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm387140,845,565 - 140,845,625EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:2655401 AgrOrtholog
Ensembl Genes ENSMUSG00000038801 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSMUST00000035300 ENTREZGENE
  ENSMUST00000035300.7 UniProtKB/TrEMBL
Gene3D-CATH Secretoglobin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Secretoglobin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Secretoglobin_1C-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Secretoglobin_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report mmu:338417 UniProtKB/TrEMBL
MGD MGI:2655401 ENTREZGENE
NCBI Gene 338417 ENTREZGENE
PANTHER PTHR10136 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR10136:SF8 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Uteroglobin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Scgb1c1 PhenoGen
PROSITE SCGB UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48201 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt G5E8B5 ENTREZGENE, UniProtKB/TrEMBL
  Q7M742 ENTREZGENE, UniProtKB/Swiss-Prot