Scgb3a1 Gene Detail

Summary

• Symbol
  Scgb3a1
• Name
  secretoglobin, family 3A, member 1
• Synonyms
  1110030K16Rik, HIN-1, LuLeu2, UGRP2

• Feature Type
  protein coding gene
• IDs
  MGI:1915912
  NCBI Gene: 68662
• Alliance
  gene page
• Transcription Start Sites
  2 TSS
• Candidate for QTL
  1 QTL

Location &
Maps

• Sequence Map
  Chr11:49554437-49555945 bp, + strand

  From Ensembl annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 11, 29.75 cM, cytoband B1.2
• Mapping Data
  4 experiments

Strain
Comparison

• SNPs within 2kb
  123 from dbSNP Build 142
• Strain Annotations
  18
• RFLP
  1

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1915912	protein coding gene	Chr11:49554422-49555945 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0018235	protein coding gene	Chr11:48802787-48804295 (+)
A/J	MGP_AJ_G0018203	protein coding gene	Chr11:46921109-46922617 (+)
AKR/J	MGP_AKRJ_G0018173	protein coding gene	Chr11:48426539-48428047 (+)
BALB/cJ	MGP_BALBcJ_G0018173	protein coding gene	Chr11:47206024-47207532 (+)
C3H/HeJ	MGP_C3HHeJ_G0017986	protein coding gene	Chr11:48424623-48426131 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0018624	protein coding gene	Chr11:50256309-50257817 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0016276	protein coding gene	Chr11:44546796-44548299 (+)
CAST/EiJ	MGP_CASTEiJ_G0017548	protein coding gene	Chr11:48388242-48389742 (+)
CBA/J	MGP_CBAJ_G0017961	protein coding gene	Chr11:52592782-52594290 (+)
DBA/2J	MGP_DBA2J_G0018068	protein coding gene	Chr11:46737376-46738884 (+)
FVB/NJ	MGP_FVBNJ_G0018062	protein coding gene	Chr11:46353258-46354766 (+)
LP/J	MGP_LPJ_G0018143	protein coding gene	Chr11:49131613-49133121 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0018087	protein coding gene	Chr11:54136702-54138210 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0018668	protein coding gene	Chr11:48526996-48528504 (+)
PWK/PhJ	MGP_PWKPhJ_G0017326	protein coding gene	Chr11:47121082-47122649 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0017121	protein coding gene	Chr11:48225720-48227219 (+)
WSB/EiJ	MGP_WSBEiJ_G0017601	protein coding gene	Chr11:48171348-48172856 (+)

Homology

• Human Ortholog
  SCGB3A1, secretoglobin family 3A member 1

• Vertebrate Orthologs
  2

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  SCGB3A1, secretoglobin family 3A member 1
  
• Synonyms
  HIN-1, HIN1, LU105, PnSP-2, UGRP2
• Links
  HGNC:18384

  NCBI Gene ID: 92304

  neXtProt AC: NX_Q96QR1

  UniProt: Q96QR1

  
  
• Chr Location
  5q35.3; chr5:180590105-180591499 (-)  GRCh38

---

• MGI Vertebrate Homology
  Scgb3a1 stringent orthology
  1 human;1 mouse;1 rat
  
• HCOP
  vertebrate homology predictions: SCGB3A1
• Gene Tree
  Scgb3a1
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  2 phenotypes from 1 allele in 2 genetic backgrounds
  16 phenotype references
  

• All Mutations and Alleles
  11
• Chemically induced (other)
  1
• Endonuclease-mediated
  4
• Gene trapped
  2
• Targeted
  4
• Genomic Mutations
  1 involving Scgb3a1
• Find Mice (IMSR)
  9 strains or lines available

Mice homozygous for a null allele exhibit reduced ciliated cells in the lungs.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  7
• GO References
  6

Expression

• Assay Results
  816
• Tissues
  56
• cDNA Data
  17
• Literature Summary
  11

Images

Tissue x Stage Matrix

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  39
• RefSeq
  4
• UniProt
  3
• CCDS
  CCDS24619.1, CCDS36145.1

• Ensembl
  ENSMUSG00000064057 (Evidence)
• NCBI Gene
  68662

Representative Sequences			Length	Strain/Species
genomic	ENSMUSG00000064057	Ensembl Gene Model | MGI Sequence Detail	1509	C57BL/6J
transcript	ENSMUST00000043873	Ensembl | MGI Sequence Detail	493	Not Applicable
polypeptide	ENSMUSP00000043325	Ensembl | MGI Sequence Detail	104	Not Applicable

Protein
Information

• UniProt
  3 Sequences
• Protein Ontology
  PR:000014511 secretoglobin family 3A member 1
  (term hierarchy)
• InterPro Domains
  IPR040301 Secretoglobin 3A

Molecular
Reagents

• All nucleic 23

  cDNA 17

  Primer pair 6

  
  

  Microarray probesets 3

References

• Summaries
  All 53

  Developmental Gene Expression 11

  Gene Ontology 6

  Phenotypes 16
• Earliest
  J:137335 Roderick TH, Chromosomal inversions in studies of mammalian mutagenesis. Genetics. 1979 May;92(1 Pt 1 Suppl):s121-6
• Latest
  J:345621 Adams DJ, et al., Genetic determinants of micronucleus formation in vivo. Nature. 2024 Mar;627(8002):130-136

TSS for Scgb3a1:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr101190	Chr11:49554430-49554448 (+)	2 bp
Tssr101191	Chr11:49554474-49554485 (+)	43 bp

Scgb3a1 is Candidate Gene for:

QTL	Genetic Location*	Genome Location (GRCm39)	Reference	QTL Note
Blmpf2	Chr11, 32.13 cM	Chr11:54065670-67078411	J:100369	Gene expression analysis was used to identify candidate genes for bleomycin-induced pulmonary fibrorsis QTLs Blmpf1 and Blmpf2. These loci were previously mapped in an F2 cross between susceptible strain C57BL/6J and resistant strain C3Hf/Kam. Blmpf1 maps to 17.4 cM on mouse Chromosome 17 and Blmpf2 maps to 28 cM on mouse Chromosome 11. Genes mapping to the Blmpf1 interval on mouse Chromosome 17 were evaluated for lung mRNA expression in C57BL/6J and C3Hf/Kam animals with and without bleomycin treatment. Genes showing significant expression differences with P<0.001 are H2-D1 (19.09 cM), C4 (18.8 cM), Glo1 (16 cM), H2-Q7 (19.19 cM), H2-K (18.65 cM), Gabbr1 (20.4 cM), Tff2 (17 cM), Notch4 (18.72 cM), and Fkbp5 (13 cM). Genes mapping to the Blmpf2 interval on mouse Chromosome 11 were evaluated for lung mRNA expression in C57BL/6J and C3Hf/Kam animals with and without bleomycin treatment. Genes showing significant expression differences with P<0.001 are Scgb3a1 (25 cM), Trim16, Pttg1, and Gria1 (31 cM).

*cM position of peak correlated region/marker