C3h9orf78 (similar to human chromosome 9 open reading frame 78) - Rat Genome Database

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Gene: C3h9orf78 (similar to human chromosome 9 open reading frame 78) Rattus norvegicus
Analyze
Symbol: C3h9orf78
Name: similar to human chromosome 9 open reading frame 78
RGD ID: 1305178
Description: Predicted to enable U5 snRNA binding activity. Predicted to be involved in mRNA cis splicing, via spliceosome and regulation of homologous chromosome segregation. Predicted to be located in chromosome, centromeric region; cytosol; and nucleoplasm. Predicted to be part of spliceosomal complex. Orthologous to human C9orf78 (chromosome 9 open reading frame 78); INTERACTS WITH bisphenol A; thioacetamide; aristolochic acid A (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: hypothetical protein LOC311855; LOC311855; MGC108846; RGD1305178; similar to Hypothetical protein MGC11690; telomere length and silencing protein 1 homolog; uncharacterized protein C9orf78 homolog; uncharacterized protein LOC311855
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
GRCr8334,662,011 - 34,670,282 (-)NCBIGRCr8
mRatBN7.2314,264,262 - 14,272,552 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl314,264,083 - 14,272,764 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx317,336,813 - 17,345,075 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0325,921,808 - 25,930,074 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0324,169,114 - 24,177,359 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.039,813,914 - 9,822,222 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl39,813,912 - 9,822,186 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0315,172,587 - 15,180,887 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4310,039,722 - 10,047,993 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.139,935,090 - 9,943,361 (-)NCBI
Celera39,022,773 - 9,031,054 (-)NCBICelera
Cytogenetic Map3p12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

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. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932  


Genomics

Comparative Map Data
C3h9orf78
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8334,662,011 - 34,670,282 (-)NCBIGRCr8
mRatBN7.2314,264,262 - 14,272,552 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl314,264,083 - 14,272,764 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx317,336,813 - 17,345,075 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0325,921,808 - 25,930,074 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0324,169,114 - 24,177,359 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.039,813,914 - 9,822,222 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl39,813,912 - 9,822,186 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0315,172,587 - 15,180,887 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4310,039,722 - 10,047,993 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.139,935,090 - 9,943,361 (-)NCBI
Celera39,022,773 - 9,031,054 (-)NCBICelera
Cytogenetic Map3p12NCBI
C9orf78
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh389129,827,290 - 129,835,275 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl9129,827,290 - 129,835,863 (-)EnsemblGRCh38hg38GRCh38
GRCh379132,589,569 - 132,597,554 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 369131,629,385 - 131,637,393 (-)NCBINCBI36Build 36hg18NCBI36
Build 349129,669,122 - 129,677,076NCBI
Celera9103,240,592 - 103,248,602 (-)NCBICelera
Cytogenetic Map9q34.11NCBI
HuRef9102,188,390 - 102,196,399 (-)NCBIHuRef
CHM1_19132,738,592 - 132,746,596 (-)NCBICHM1_1
T2T-CHM13v2.09142,031,858 - 142,039,846 (-)NCBIT2T-CHM13v2.0
BC005624
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39230,862,845 - 30,872,225 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl230,862,189 - 30,872,213 (-)EnsemblGRCm39 Ensembl
GRCm38230,970,693 - 30,981,941 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl230,972,177 - 30,982,201 (-)EnsemblGRCm38mm10GRCm38
MGSCv37230,828,353 - 30,837,461 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36230,794,845 - 30,803,895 (-)NCBIMGSCv36mm8
Celera230,678,625 - 30,687,736 (-)NCBICelera
Cytogenetic Map2BNCBI
cM Map221.77NCBI
CUNH9orf78
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495551338,060 - 43,450 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495551338,060 - 43,450 (-)NCBIChiLan1.0ChiLan1.0
C11H9orf78
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2119,513,854 - 9,521,898 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan199,516,261 - 9,524,242 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v09100,954,771 - 100,962,794 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.19129,612,071 - 129,620,044 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl9129,612,071 - 129,620,044 (-)Ensemblpanpan1.1panPan2
C9H9orf78
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1954,009,543 - 54,016,154 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl954,009,611 - 54,015,898 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha953,206,421 - 53,213,330 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0954,907,057 - 54,913,978 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl954,907,051 - 54,913,973 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1953,684,383 - 53,691,235 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0954,006,416 - 54,013,332 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0954,099,555 - 54,106,468 (+)NCBIUU_Cfam_GSD_1.0
CUNH9orf78
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404947197,255,468 - 197,261,751 (-)NCBIHiC_Itri_2
SpeTri2.0NW_00493648717,023,993 - 17,030,275 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
C1H9orf78
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1269,986,391 - 269,995,395 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11269,986,386 - 269,995,394 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21303,883,696 - 303,892,753 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CUNH9orf78
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1128,300,869 - 8,309,620 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl128,301,195 - 8,309,900 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_0236660797,131,051 - 7,139,293 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
CUNH9orf78
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247605,594,633 - 5,599,662 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in C3h9orf78
63 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:112
Count of miRNA genes:84
Interacting mature miRNAs:102
Transcripts:ENSRNOT00000010115
Prediction methods:Miranda, Rnahybrid, Targetscan
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
70202Alc19Alcohol consumption QTL 192.5drinking behavior trait (VT:0001422)ethanol intake volume to total fluid intake volume ratio (CMO:0001591)3127494778Rat
631679Cm10Cardiac mass QTL 107.340.0001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3131158234Rat
631831Alc8Alcohol consumption QTL 82.7consumption behavior trait (VT:0002069)calculated ethanol drink intake rate (CMO:0001615)3133230976Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)diastolic blood pressure (CMO:0000005)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)systolic blood pressure (CMO:0000004)3133278763Rat
61468Bp15Blood pressure QTL 154.4blood pressure trait (VT:0000183)pulse pressure (CMO:0000292)3133278763Rat
631545Bp85Blood pressure QTL 853.1arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3133278763Rat
4889966Bss95Bone structure and strength QTL 954.4tibia area (VT:1000281)tibia-fibula cross-sectional area (CMO:0001718)3136847613Rat
2312664Scl62Serum cholesterol level QTL 620.05blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)3138710544Rat
631568Bp92Blood pressure QTL 922.20.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3139874793Rat
2290452Scl56Serum cholesterol level QTL 562.26blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)3191609953Rat
1298526Arunc3Aerobic running capacity QTL 32.2exercise endurance trait (VT:0002332)maximum distance run on treadmill (CMO:0001406)3822719433703538Rat
10401810Kidm53Kidney mass QTL 53kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3822719447233430Rat
70203Gcr2Gastric cancer resistance QTL 22.6stomach morphology trait (VT:0000470)stomach tumor susceptibility score (CMO:0002043)3865816227494778Rat
1358357Srcrtb1Stress Responsive Cort Basal QTL 16.360.002blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)3865816227494778Rat
6893355Bw101Body weight QTL 1010.40.38body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
6893363Bw105Body weight QTL 1052.60.0036body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
1558654Bw56Body weight QTL 564.50.0000171body mass (VT:0001259)body weight (CMO:0000012)31077870430357018Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)31077870450302886Rat
70191BpQTLcluster4Blood pressure QTL cluster 43arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)31077870450302886Rat
1558647Cm46Cardiac mass QTL 465.40.0000055heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1558650Cm48Cardiac mass QTL 4840.0001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)31077882330356773Rat
1558657Cm43Cardiac mass QTL 436.60.0000000293heart mass (VT:0007028)heart wet weight (CMO:0000069)31077882330356773Rat
1358905Hrtrt17Heart rate QTL 175.90.000014heart pumping trait (VT:2000009)heart rate (CMO:0000002)31086191289878372Rat

Markers in Region
RH130267  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2314,264,301 - 14,264,512 (+)MAPPERmRatBN7.2
Rnor_6.039,813,952 - 9,814,162NCBIRnor6.0
Rnor_5.0315,172,625 - 15,172,835UniSTSRnor5.0
RGSC_v3.4310,039,759 - 10,039,969UniSTSRGSC3.4
Celera39,022,810 - 9,023,020UniSTS
RH 3.4 Map345.3UniSTS
Cytogenetic Map3p12UniSTS


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

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 3 35 35 21 18 21 2 74 31 40 11
Low 8 22 20 1 20 8 9 4 1 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000010115   ⟹   ENSRNOP00000010115
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl314,264,083 - 14,272,764 (-)Ensembl
Rnor_6.0 Ensembl39,813,915 - 9,822,186 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076637   ⟹   ENSRNOP00000068298
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl314,264,265 - 14,272,560 (-)Ensembl
Rnor_6.0 Ensembl39,813,912 - 9,822,182 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000076713
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl39,818,751 - 9,822,154 (-)Ensembl
RefSeq Acc Id: NM_001399581   ⟹   NP_001386510
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8334,662,011 - 34,670,282 (-)NCBI
mRatBN7.2314,264,262 - 14,272,535 (-)NCBI
RefSeq Acc Id: XM_063283961   ⟹   XP_063140031
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8334,662,014 - 34,670,279 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001386510 (Get FASTA)   NCBI Sequence Viewer  
  XP_063140031 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH91189 (Get FASTA)   NCBI Sequence Viewer  
  EDL93285 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000010115.5
  ENSRNOP00000068298
  ENSRNOP00000068298.1
Reference Protein Sequences
RefSeq Acc Id: ENSRNOP00000010115   ⟸   ENSRNOT00000010115
RefSeq Acc Id: ENSRNOP00000068298   ⟸   ENSRNOT00000076637
RefSeq Acc Id: NP_001386510   ⟸   NM_001399581
- UniProtKB: A0A096MJX5 (UniProtKB/TrEMBL),   A6JU12 (UniProtKB/TrEMBL),   D3ZKZ0 (UniProtKB/TrEMBL),   Q5BK66 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063140031   ⟸   XM_063283961
- Peptide Label: isoform X1

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A096MJX5-F1-model_v2 AlphaFold A0A096MJX5 1-289 view protein structure

Transcriptome

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

Promoters
RGD ID:13691978
Promoter ID:EPDNEW_R2496
Type:initiation region
Name:RGD1305178_1
Description:similar to Hypothetical protein MGC11690
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.039,822,180 - 9,822,240EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1305178 AgrOrtholog
BioCyc Gene G2FUF-50189 BioCyc
Ensembl Genes ENSRNOG00000007532 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000010115.7 UniProtKB/TrEMBL
  ENSRNOT00000076637 ENTREZGENE
  ENSRNOT00000076637.3 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7367873 IMAGE-MGC_LOAD
InterPro Hep_59 UniProtKB/TrEMBL
KEGG Report rno:311855 UniProtKB/TrEMBL
MGC_CLONE MGC:108846 IMAGE-MGC_LOAD
NCBI Gene 311855 ENTREZGENE
PANTHER Hep_59 UniProtKB/TrEMBL
  TELOMERE LENGTH AND SILENCING PROTEIN 1 HOMOLOG UniProtKB/TrEMBL
Pfam Hep_59 UniProtKB/TrEMBL
PhenoGen C3h9orf78 PhenoGen
RatGTEx ENSRNOG00000007532 RatGTEx
UniProt A0A096MJX5 ENTREZGENE, UniProtKB/TrEMBL
  A0A8J8YT65_RAT UniProtKB/TrEMBL
  A6JU12 ENTREZGENE, UniProtKB/TrEMBL
  D3ZKZ0 ENTREZGENE, UniProtKB/TrEMBL
  Q5BK66 ENTREZGENE
UniProt Secondary Q5BK66 UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-28 C3h9orf78  similar to human chromosome 9 open reading frame 78  RGD1305178  similar to Hypothetical protein MGC11690  Name and Symbol changed 629549 APPROVED
2005-12-06 RGD1305178  similar to Hypothetical protein MGC11690  RGD1305178_predicted  similar to Hypothetical protein MGC11690 (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1305178_predicted  similar to Hypothetical protein MGC11690 (predicted)  LOC311855_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC311855_predicted  similar to Hypothetical protein MGC11690 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL