C1h15orf40-ps2 (similar to human chromosome 15 open reading frame 40, pseudogene 2) - Rat Genome Database

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Gene: C1h15orf40-ps2 (similar to human chromosome 15 open reading frame 40, pseudogene 2) Rattus norvegicus
Analyze
No known orthologs.
Symbol: C1h15orf40-ps2 (Ensembl: LOC100363116)
Name: similar to human chromosome 15 open reading frame 40, pseudogene 2 (Ensembl:RIKEN cDNA 3110040N11 gene)
RGD ID: 2324773
Description: Orthologous to human C15orf40 (chromosome 15 open reading frame 40).
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: INFERRED
Previously known as: hypothetical protein LOC100363116; LOC100363116; UPF0235 protein C15orf40 homolog
RGD Orthologs
Alliance Genes
More Info homologs ...
Related Functional Gene: C1h15orf40  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86136,786,988 - 136,788,580 (+)NCBIGRCr8
mRatBN7.26130,965,834 - 130,967,426 (+)NCBImRatBN7.2mRatBN7.2
Rnor_6.06136,473,683 - 136,475,156 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1143,601,014 - 143,607,170 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06145,482,165 - 145,483,777 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46136,686,622 - 136,695,726 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera6128,518,951 - 128,520,424 (+)NCBICelera
Cytogenetic Map6q32NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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

Genomics

Variants

.
Variants in C1h15orf40-ps2
4 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731173Uae22Urinary albumin excretion QTL 2210.1urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
2290393Uae37Urinary albumin excretion QTL 370.0001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)665531555140994061Rat
724513Uae14Urinary albumin excretion QTL 146.5urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)685311061133478515Rat
1300076Glom8Glomerulus QTL 870.000000009kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)686894788131894788Rat
2303624Vencon5Ventilatory control QTL 54.45respiration trait (VT:0001943)minute ventilation (CMO:0000132)688047916133047916Rat
61414Pia3Pristane induced arthritis QTL 34.5joint integrity trait (VT:0010548)post-insult time to onset of experimental arthritis (CMO:0001450)694968928137848904Rat
12801411Schws8Schwannoma susceptibility QTL 8nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)694968928139968928Rat
8552796Vie3Viral induced encephalitis QTL 32.6brain integrity trait (VT:0010579)encephalitis incidence/prevalence measurement (CMO:0002361)696833997140994061Rat
1358355Srcrt4Stress Responsive Cort QTL 46.39blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)6100364669140994061Rat
2313399Anxrr28Anxiety related response QTL 28aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)6100671796132340886Rat
71111Iddm8Insulin dependent diabetes mellitus QTL 81.90.002blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)6105156861140994061Rat
4145118Mcs26Mammary carcinoma susceptibility QTL 260.0001mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6106752656132339866Rat
737976Pia24Pristane induced arthritis QTL 24joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)6112636280140994061Rat
1641917Colcr5Colorectal carcinoma resistance QTL 53.180.0009intestine integrity trait (VT:0010554)benign colorectal tumor number (CMO:0001795)6122549046137801795Rat
2293085Iddm29Insulin dependent diabetes mellitus QTL 297.66blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)6122549046140286318Rat
61329Eae9Experimental allergic encephalomyelitis QTL 93.7body mass (VT:0001259)change in body weight (CMO:0002045)6122549046140994061Rat
2312560Pur20Proteinuria QTL 202.10.005urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)6125628133137801795Rat

Markers in Region
RH141012  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.26130,967,169 - 130,967,352 (+)MAPPERmRatBN7.2
mRatBN7.21135,726,256 - 135,726,439 (-)MAPPERmRatBN7.2
mRatBN7.26130,967,169 - 130,967,352 (-)MAPPERmRatBN7.2
mRatBN7.21135,726,256 - 135,726,439 (+)MAPPERmRatBN7.2
Rnor_6.01143,601,399 - 143,601,581NCBIRnor6.0
Rnor_6.06136,475,242 - 136,475,424NCBIRnor6.0
Rnor_5.06145,483,725 - 145,483,907UniSTSRnor5.0
Rnor_5.01144,544,949 - 144,545,131UniSTSRnor5.0
RGSC_v3.46136,696,535 - 136,696,717UniSTSRGSC3.4
Celera6128,520,510 - 128,520,692UniSTS
Celera1127,777,100 - 127,777,282UniSTS
Cytogenetic Map1q31UniSTS


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 34 30 16 19 16 74 31 34 11
Low 9 27 25 25 8 11 4 7 8
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000079643   ⟹   ENSRNOP00000070531
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1135,717,545 - 135,732,039 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000098314   ⟹   ENSRNOP00000091584
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl1135,725,872 - 135,732,020 (-)Ensembl
RefSeq Acc Id: XM_003750235   ⟹   XP_003750283
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.26130,965,834 - 130,967,084 (+)NCBI
Rnor_6.06136,473,683 - 136,475,156 (+)NCBI
Rnor_5.06145,482,165 - 145,483,777 (+)NCBI
Sequence:
Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q505I4-F1-model_v2 AlphaFold Q505I4 1-126 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:2324773 AgrOrtholog
BioCyc Gene G2FUF-35823 BioCyc
Ensembl Genes ENSRNOG00000052273 Ensembl
NCBI Gene 100363116 ENTREZGENE
PhenoGen C1h15orf40-ps2 PhenoGen
RatGTEx ENSRNOG00000052273 RatGTEx


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-07-15 C1h15orf40-ps2  similar to human chromosome 15 open reading frame 40, pseudogene 2  LOC100363116  hypothetical protein LOC100363116  Name and Symbol and Type changed (type changed from [protein-coding] to [pseudo]) 629549 APPROVED
2010-05-12 LOC100363116  hypothetical protein LOC100363116      Symbol and Name status set to provisional 70820 PROVISIONAL