Rsph4a (radial spoke head component 4A) - Rat Genome Database

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Gene: Rsph4a (radial spoke head component 4A) Rattus norvegicus
Analyze
Symbol: Rsph4a
Name: radial spoke head component 4A
RGD ID: 1307229
Description: Predicted to be involved in cilium movement and radial spoke assembly. Predicted to act upstream of or within epithelial cilium movement involved in extracellular fluid movement; establishment of localization in cell; and maintenance of ciliary planar beating movement pattern. Predicted to be located in 9+2 motile cilium. Predicted to be part of radial spoke head 1; radial spoke head 2; and radial spoke head 3. Predicted to be active in axoneme. Human ortholog(s) of this gene implicated in primary ciliary dyskinesia 11. Orthologous to human RSPH4A (radial spoke head component 4A); INTERACTS WITH lead diacetate; vinclozolin; (1->4)-beta-D-glucan (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC103689994; LOC309767; radial spoke head 4 homolog A; radial spoke head 4 homolog A (Chlamydomonas); radial spoke head protein 4 homolog A; radial spokehead-like 3; Rshl3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82031,307,102 - 31,323,263 (+)NCBIGRCr8
mRatBN7.22030,764,409 - 30,780,574 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2030,764,409 - 30,780,574 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2031,775,313 - 31,791,478 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02031,166,228 - 31,182,394 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02031,902,972 - 31,919,129 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02032,450,701 - 32,467,362 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2033,945,829 - 33,962,045 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl2032,450,733 - 32,467,194 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02034,234,611 - 34,251,002 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.02035,706,052 - 35,722,089 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42030,075,957 - 30,091,390 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12030,089,429 - 30,105,166 (+)NCBI
Celera2032,181,477 - 32,197,685 (+)NCBICelera
Cytogenetic Map20q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
3. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
4. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:19200523   PMID:23255504   PMID:26506310  


Genomics

Comparative Map Data
Rsph4a
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr82031,307,102 - 31,323,263 (+)NCBIGRCr8
mRatBN7.22030,764,409 - 30,780,574 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl2030,764,409 - 30,780,574 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx2031,775,313 - 31,791,478 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.02031,166,228 - 31,182,394 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.02031,902,972 - 31,919,129 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.02032,450,701 - 32,467,362 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl2033,945,829 - 33,962,045 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0 Ensembl2032,450,733 - 32,467,194 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.02034,234,611 - 34,251,002 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
Rnor_5.02035,706,052 - 35,722,089 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.42030,075,957 - 30,091,390 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.12030,089,429 - 30,105,166 (+)NCBI
Celera2032,181,477 - 32,197,685 (+)NCBICelera
Cytogenetic Map20q11NCBI
RSPH4A
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh386116,616,479 - 116,632,985 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl6116,616,479 - 116,632,985 (+)EnsemblGRCh38hg38GRCh38
GRCh376116,937,642 - 116,954,148 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 366117,044,343 - 117,060,834 (+)NCBINCBI36Build 36hg18NCBI36
Build 346117,044,342 - 117,060,834NCBI
Celera6117,680,709 - 117,697,215 (+)NCBICelera
Cytogenetic Map6q22.1NCBI
HuRef6114,517,217 - 114,533,724 (+)NCBIHuRef
CHM1_16117,201,269 - 117,217,765 (+)NCBICHM1_1
T2T-CHM13v2.06117,779,906 - 117,816,694 (+)NCBIT2T-CHM13v2.0
Rsph4a
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391033,781,107 - 33,792,017 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1033,781,107 - 33,792,017 (+)EnsemblGRCm39 Ensembl
GRCm381033,905,111 - 33,916,021 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1033,905,111 - 33,916,021 (+)EnsemblGRCm38mm10GRCm38
MGSCv371033,624,917 - 33,635,827 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361033,594,572 - 33,605,437 (+)NCBIMGSCv36mm8
Celera1034,815,502 - 34,826,412 (+)NCBICelera
Cytogenetic Map10B1NCBI
cM Map1018.84NCBI
Rsph4a
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495543627,902 - 43,704 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495543630,638 - 43,581 (-)NCBIChiLan1.0ChiLan1.0
RSPH4A
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v25136,615,545 - 136,649,276 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan16134,517,547 - 134,542,294 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v06114,423,322 - 114,441,199 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.16118,568,907 - 118,585,812 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl6118,568,907 - 118,585,812 (+)Ensemblpanpan1.1panPan2
RSPH4A
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1157,063,752 - 57,079,289 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl157,064,624 - 57,077,537 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha157,859,416 - 57,873,713 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0157,246,169 - 57,260,467 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl157,246,187 - 57,259,797 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1157,140,545 - 57,154,843 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0156,988,706 - 57,003,004 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0157,617,224 - 57,631,523 (+)NCBIUU_Cfam_GSD_1.0
Rsph4a
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404946107,787,394 - 107,800,190 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493706845,181 - 57,159 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493706845,105 - 59,540 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
RSPH4A
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl144,963,886 - 44,985,202 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1144,964,433 - 45,004,925 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
RSPH4A
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11357,175,100 - 57,192,184 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl1357,172,127 - 57,192,125 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604029,507,756 - 29,526,353 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Rsph4a
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462479813,023,982 - 13,046,116 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462479813,022,429 - 13,046,836 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Rsph4a
148 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:26
Count of miRNA genes:13
Interacting mature miRNAs:13
Transcripts:ENSRNOT00000036449, ENSRNOT00000064063
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 (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
6893685Bw111Body weight QTL 1112.70.004body mass (VT:0001259)body weight (CMO:0000012)20132578807Rat
7411668Foco32Food consumption QTL 3280.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)20136600972Rat
9590252Scort12Serum corticosterone level QTL 1220.460.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)20136600972Rat
2305926Iddm37Insulin dependent diabetes mellitus QTL 376blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)20152784246527842Rat
1641915Colcr9Colorectal carcinoma resistance QTL 92.970.0024intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)20153065546530655Rat
1598816Memor12Memory QTL 122.4exploratory behavior trait (VT:0010471)average horizontal distance between subject and target during voluntary locomotion in an experimental apparatus (CMO:0002674)20260683647606836Rat
7411652Foco24Food consumption QTL 240.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)201175751554435887Rat
9590092Insglur9Insulin/glucose ratio QTL 918.380.001blood insulin amount (VT:0001560)calculated plasma insulin level (CMO:0002170)201175751554435887Rat
4889610Pancm3Pancreatic morphology QTL 33.750.001pancreas mass (VT:0010144)pancreas wet weight (CMO:0000626)201761783247606836Rat
2317880Alcrsp25Alcohol response QTL 252.3response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)201769755054435887Rat
2303626Vencon10Ventilatory control QTL 100.001respiration trait (VT:0001943)respiration rate (CMO:0000289)201919072154435887Rat
2303578Gluco50Glucose level QTL 502blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)202510672254435887Rat
2303587Bw93Body weight QTL 9313body mass (VT:0001259)body weight (CMO:0000012)202510672254435887Rat
2300188Bmd68Bone mineral density QTL 686.40.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)202510672254435887Rat
1331747Hrtrt16Heart rate QTL 163.163heart pumping trait (VT:2000009)heart rate (CMO:0000002)202520973454435887Rat
1598869Memor6Memory QTL 63.1exploratory behavior trait (VT:0010471)total horizontal distance resulting from voluntary locomotion in an experimental apparatus (CMO:0001443)202924438854435887Rat


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

nervous system reproductive system respiratory system
High
Medium
Low
Below cutoff 2 1 11

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000036449   ⟹   ENSRNOP00000033479
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl2030,764,409 - 30,780,574 (+)Ensembl
Rnor_6.0 Ensembl2032,450,733 - 32,467,194 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000064063   ⟹   ENSRNOP00000059088
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl2033,945,829 - 33,962,045 (+)Ensembl
RefSeq Acc Id: NM_001107629   ⟹   NP_001101099
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr82031,307,102 - 31,323,263 (+)NCBI
mRatBN7.22030,764,409 - 30,780,574 (+)NCBI
Protein Sequences
Protein RefSeqs NP_001101099 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL92954 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000033479
  ENSRNOP00000033479.3
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000033479   ⟸   ENSRNOT00000036449
RefSeq Acc Id: ENSRNOP00000059088   ⟸   ENSRNOT00000064063
RefSeq Acc Id: NP_001101099   ⟸   NM_001107629
- UniProtKB: D4AE52 (UniProtKB/TrEMBL),   D4A8S8 (UniProtKB/TrEMBL)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A8S8-F1-model_v2 AlphaFold D4A8S8 1-711 view protein structure

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1307229 AgrOrtholog
BioCyc Gene G2FUF-3669 BioCyc
Ensembl Genes ENSRNOG00000047471 Ensembl
  ENSRNOG00000049696 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000036449 ENTREZGENE
  ENSRNOT00000036449.6 UniProtKB/TrEMBL
InterPro Radial_spoke UniProtKB/TrEMBL
NCBI Gene 309767 ENTREZGENE
PANTHER RADIAL SPOKE HEAD PROTEIN 4 HOMOLOG A UniProtKB/TrEMBL
  Radial_spoke UniProtKB/TrEMBL
Pfam Radial_spoke UniProtKB/TrEMBL
PhenoGen Rsph4a PhenoGen
RatGTEx ENSRNOG00000047471 RatGTEx
  ENSRNOG00000049696 RatGTEx
UniProt D4A8S8 ENTREZGENE, UniProtKB/TrEMBL
  D4AE52 ENTREZGENE
UniProt Secondary D4AE52 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2021-03-09 Rsph4a  radial spoke head component 4A  LOC103689994  radial spoke head protein 4 homolog A  Data merged from RGD:9339057 737654 PROVISIONAL
2018-08-17 Rsph4a  radial spoke head component 4A  Rsph4a  radial spoke head 4 homolog A  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-04-13 Rsph4a  radial spoke head 4 homolog A  Rsph4a  radial spoke head 4 homolog A (Chlamydomonas)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2014-08-25 LOC103689994  radial spoke head protein 4 homolog A      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-05-25 Rsph4a  radial spoke head 4 homolog A (Chlamydomonas)  Rshl3  radial spokehead-like 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Rshl3  radial spokehead-like 3   Rshl3_predicted  radial spokehead-like 3 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Rshl3_predicted  radial spokehead-like 3 (predicted)      Symbol and Name status set to approved 70820 APPROVED