Cfap90 Gene Detail

Summary

• Symbol
  Cfap90
• Name
  cilia and flagella associated protein 90
• Synonyms
  1700001L19Rik

• Feature Type
  protein coding gene
• IDs
  MGI:1916565
  NCBI Gene: 69315
• Alliance
  gene page
• Transcription Start Sites
  2 TSS

Location &
Maps

• Sequence Map
  Chr13:68745558-68762350 bp, + strand

  From NCBI annotation of GRCm39
  

• View this region in JBrowse
  

• Genome Browsers
  Ensembl | UCSC | NCBI

• Genetic Map
  Chromosome 13, 35.55 cM, cytoband B3
• Mapping Data
  2 experiments

Strain
Comparison

• SNPs within 2kb
  466 from dbSNP Build 142
• Strain Annotations
  18

Strain	Gene Model ID	Feature Type	Coordinates
C57BL/6J	MGI_C57BL6J_1916565	protein coding gene	Chr13:68745540-68762350 (+)
129S1/SvImJ	MGP_129S1SvImJ_G0020729	protein coding gene	Chr13:68813623-68830328 (+)
A/J	MGP_AJ_G0020685	protein coding gene	Chr13:66390387-66407121 (+)
AKR/J	MGP_AKRJ_G0020660	protein coding gene	Chr13:68554254-68570896 (+)
BALB/cJ	MGP_BALBcJ_G0020682	protein coding gene	Chr13:66932601-66949248 (+)
C3H/HeJ	MGP_C3HHeJ_G0020477	protein coding gene	Chr13:68247730-68264336 (+)
C57BL/6NJ	MGP_C57BL6NJ_G0021119	protein coding gene	Chr13:71212792-71229489 (+)
CAROLI/EiJ	MGP_CAROLIEiJ_G0018687	protein coding gene	Chr13:63356249-63373278 (+)
CAST/EiJ	MGP_CASTEiJ_G0019994	protein coding gene	Chr13:67211985-67228622 (+)
CBA/J	MGP_CBAJ_G0020435	protein coding gene	Chr13:73938421-73955064 (+)
DBA/2J	MGP_DBA2J_G0020561	protein coding gene	Chr13:66284653-66301313 (+)
FVB/NJ	MGP_FVBNJ_G0020541	protein coding gene	Chr13:65296359-65312998 (+)
LP/J	MGP_LPJ_G0020633	protein coding gene	Chr13:69112467-69129032 (+)
NOD/ShiLtJ	MGP_NODShiLtJ_G0020569	protein coding gene	Chr13:72424228-72440878 (+)
NZO/HlLtJ	MGP_NZOHlLtJ_G0021158	protein coding gene	Chr13:67840349-67857051 (+)
PWK/PhJ	MGP_PWKPhJ_G0019748	protein coding gene	Chr13:64967350-64984263 (+)
SPRET/EiJ	MGP_SPRETEiJ_G0019571	protein coding gene	Chr13:64330786-64347564 (+)
WSB/EiJ	MGP_WSBEiJ_G0020051	protein coding gene	Chr13:68311085-68327648 (+)

Homology

• Human Ortholog
  CFAP90, cilia and flagella associated protein 90

• Vertebrate Orthologs
  3

Vertebrate Orthology Source

Alliance of Genome Resources

• Human Ortholog
  CFAP90, cilia and flagella associated protein 90
  
• Synonyms
  C5orf49
• Links
  HGNC:27028

  NCBI Gene ID: 134121

  neXtProt AC: NX_A4QMS7

  UniProt: A4QMS7

  
  
• Chr Location
  5p15.31; chr5:7830378-7851151 (-)  GRCh38

---

• MGI Vertebrate Homology
  Cfap90 stringent orthology
  1 human;1 mouse;1 rat;1 zebrafish
  
• HCOP
  vertebrate homology predictions: CFAP90
• Gene Tree
  Cfap90
  

Mutations,
Alleles, and
Phenotypes

• Phenotype Summary
  1 phenotype from 1 allele in 1 genetic background
  7 phenotype references
  

• All Mutations and Alleles
  4
• Chemically induced (other)
  1
• Endonuclease-mediated
  2
• Targeted
  1
• Genomic Mutations
  1 involving Cfap90
• Find Mice (IMSR)
  6 strains or lines available
• Comparison Matrix
  Gene Expression + Phenotype

Male mice for a null allele exhibit normal fertility.

Gene Ontology
(GO)
Classifications

• All GO Annotations
  6
• GO References
  4

Expression

• Assay Results
  780
• Tissues
  9
• cDNA Data
  20
• Literature Summary
  1

Images

Tissue x Stage Matrix

Comparison Matrix

Gene Expression + Phenotype

• Other Mouse Links
  Allen Institute
  GEO
  Expression Atlas

Sequences &
Gene Models

• All Sequences
  32
• RefSeq
  2
• UniProt
  1
• CCDS
  CCDS49306.1

• Ensembl
  ENSMUSG00000021534 (Evidence)
• NCBI Gene
  69315

Representative Sequences			Length	Strain/Species
genomic	69315	NCBI Gene Model | MGI Sequence Detail	16793	C57BL/6J
transcript	NM_027035	RefSeq | MGI Sequence Detail	1808	C57BL/6
polypeptide	Q9DAR0	UniProt | EBI | MGI Sequence Detail	182	Not Applicable

Protein
Information

• UniProt
  1 Sequence
• Protein Ontology
  PR:000059684 cilia- and flagella-associated protein 90
  (term hierarchy)
• PDB
  8IYJ
• InterPro Domains
  IPR027901 Cilia and flagella associated protein 90

Molecular
Reagents

• All nucleic 20

  cDNA 20

  
  

  Microarray probesets 2

Other
Accession IDs

MGI:7384807

References

• Summaries
  All 30

  Developmental Gene Expression 1

  Gene Ontology 4

  Phenotypes 7
• Earliest
  J:182573 Roderick TH, Producing and detecting paracentric chromosomal inversions in mice. Mutat Res. 1971 Jan;11(1):59-69
• Latest
  J:348435 Suzuki A, et al., Individual disruption of 12 testis-enriched genes via the CRISPR/Cas9 system does not affect the fertility of male mice. J Reprod Immunol. 2024;:104252

TSS for Cfap90:

(View these features in JBrowse)

Transcription Start Site	Location	Distance from Gene 5'-end
Tssr120270	Chr13:68745528-68745539 (+)	-24 bp
Tssr120271	Chr13:68745544-68745592 (+)	10 bp