Cwc22-ps1 (CWC22 spliceosome associated protein homolog, pseudogene 1) - Rat Genome Database

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Gene: Cwc22-ps1 (CWC22 spliceosome associated protein homolog, pseudogene 1) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Cwc22-ps1 (Ensembl: LOC500684)
Name: CWC22 spliceosome associated protein homolog, pseudogene 1 (Ensembl:hypothetical protein LOC500684)
RGD ID: 1562981
Description: Predicted to enable RNA binding activity. Predicted to be involved in mRNA splicing, via spliceosome. Predicted to be part of catalytic step 2 spliceosome. Orthologous to human CWC22 (CWC22 spliceosome associated protein homolog).
Type: pseudo (Ensembl: protein-coding)
RefSeq Status: INFERRED
Previously known as: hypothetical protein LOC500684; LOC102555166; LOC500684; LOC680519; LOC680829; pre-mRNA-splicing factor CWC22 homolog; similar to CG12750-PA; uncharacterized protein LOC500684
RGD Orthologs
Alliance Genes
More Info homologs ...
Related Functional Gene: Cwc22  
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr86105,396,533 - 105,399,632 (+)NCBIGRCr8
mRatBN7.2767,152,834 - 67,154,825 (-)NCBImRatBN7.2mRatBN7.2
UTH_Rnor_SHR_Utx6100,105,442 - 100,108,549 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.06100,405,137 - 100,408,244 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0699,615,862 - 99,618,977 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.06103,932,428 - 103,935,122 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl6103,932,428 - 103,935,122 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.06112,106,426 - 112,109,120 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.46104,036,871 - 104,040,819 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera764,233,794 - 64,237,336 (-)NCBICelera
Cytogenetic Map7q22NCBI
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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Variants

.
Variants in Cwc22-ps1
34 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:5
Count of miRNA genes:5
Interacting mature miRNAs:5
Transcripts:ENSRNOT00000058354
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
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)7924703115097879Rat
1643004Pain2Pain QTL 21mechanical nociception trait (VT:0002734)self mutilation severity score (CMO:0002145)7946224698011544Rat
1300132Bp182Blood pressure QTL 1823.49arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)71965431784928080Rat
1641885Alcrsp9Alcohol response QTL 9alcohol metabolism trait (VT:0015089)blood ethanol level (CMO:0000535)72409960669099606Rat
1549840Bss5Bone structure and strength QTL 59.8femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)72475184169751841Rat
10402855Bp379Blood pressure QTL 3790.21arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)72940968374409683Rat
1300127Srn1Serum renin concentration QTL 13.87blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)72940968384928080Rat
10755453Coatc12Coat color QTL 120coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)73111283276112832Rat
7411605Foco14Food consumption QTL 1424.10.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)73429328279293282Rat
631534Lnnr1Liver neoplastic nodule remodeling QTL 13.850.001liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)73429328279293282Rat
631513Scl7Serum cholesterol level QTL 74.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)73796056982960569Rat
61357Bp38Blood pressure QTL 381.60.052arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)741333674119109060Rat
634326Hc3Hypercalciuria QTL 32.1urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)74278731487787314Rat
10053722Scort27Serum corticosterone level QTL 272.410.0083blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)74322875088228750Rat
1358361Sradr5Stress Responsive Adrenal Weight QTL 55.55adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)743747012108555253Rat
1300179Kidm5Kidney mass QTL 53.51kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)743747012135012528Rat
1300149Cm6Cardiac mass QTL 64.09heart mass (VT:0007028)heart left ventricle weight to body weight ratio (CMO:0000530)743747099102228765Rat
631504Cm27Cardiac mass QTL 273.45heart left ventricle mass (VT:0007031)heart left ventricle wet weight (CMO:0000071)744421311118198041Rat
61428Scl3Serum cholesterol level QTL 33.2blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)74486753389867533Rat
738030Anxrr8Anxiety related response QTL 84.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)74659007091590070Rat
2293696Bmd32Bone mineral density QTL 325.10.0001femur strength trait (VT:0010010)femoral neck polar moment of inertia (CMO:0001670)74765143992651439Rat
2293707Bss32Bone structure and strength QTL 327.640.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)74765143992651439Rat
2300178Bmd54Bone mineral density QTL 545.30.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)74765143992651439Rat
2293644Bmd29Bone mineral density QTL 295.40.0001femur size trait (VT:1000369)femoral neck cross-sectional area (CMO:0001697)74765143992651439Rat
2293667Bss42Bone structure and strength QTL 427.250.0001lumbar vertebra size trait (VT:0010518)lumbar vertebra cross-sectional area (CMO:0001689)74765143992651439Rat
2293678Bss24Bone structure and strength QTL 246.710.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)74765143992651439Rat
2293685Bmd21Bone mineral density QTL 214.20.0003femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)74765143992651439Rat
1300151Bp181Blood pressure QTL 1813.36arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)753612714103945643Rat
2317035Aia16Adjuvant induced arthritis QTL 162.71joint integrity trait (VT:0010548)right rear ankle joint diameter (CMO:0002150)759238038104238038Rat
1298528Bp169Blood pressure QTL 1690.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)761074194106074194Rat
1559283Emca4Estrogen-induced mammary cancer QTL 43.7mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)762004452101773158Rat
1576303Ept7Estrogen-induced pituitary tumorigenesis QTL 73.7pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)762004452101773158Rat
70173Niddm19Non-insulin dependent diabetes mellitus QTL 194.330.00005blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)764002457135012528Rat

Markers in Region
RH136821  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2362,815,442 - 62,815,644 (+)MAPPERmRatBN7.2
mRatBN7.2362,815,442 - 62,815,645 (+)MAPPERmRatBN7.2
Rnor_6.0364,731,358 - 64,731,560NCBIRnor6.0
Rnor_6.06103,932,405 - 103,932,607NCBIRnor6.0
Rnor_5.06112,106,403 - 112,106,605UniSTSRnor5.0
Rnor_5.0371,298,303 - 71,298,505UniSTSRnor5.0
Celera362,293,835 - 62,294,037UniSTS
Cytogenetic Map3q24UniSTS
Cytogenetic Map6q24UniSTS


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 1
Low 3 30 48 32 19 32 1 2 74 34 38 11 1
Below cutoff 13 9 9 9 7 9 1 2 7

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000058354   ⟹   ENSRNOP00000055154
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl6103,932,428 - 103,935,122 (-)Ensembl
RefSeq Acc Id: NM_001047959   ⟹   NP_001041424
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.06103,932,428 - 103,935,122 (-)NCBI
Rnor_5.06112,106,426 - 112,109,120 (-)NCBI
RGSC_v3.46104,036,871 - 104,040,819 (+)RGD
Sequence:
Protein Sequences
Reference Protein Sequences
RefSeq Acc Id: NP_001041424   ⟸   NM_001047959
- Sequence:
RefSeq Acc Id: ENSRNOP00000055154   ⟸   ENSRNOT00000058354
Protein Domains
MI

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D3ZEL0-F1-model_v2 AlphaFold D3ZEL0 1-873 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:1562981 AgrOrtholog
BioCyc Gene G2FUF-33656 BioCyc
Ensembl Genes ENSRNOG00000038322 Ensembl
Gene3D-CATH 1.25.40.180 UniProtKB/TrEMBL
InterPro ARM-type_fold UniProtKB/TrEMBL
  Initiation_fac_eIF4g_MI UniProtKB/TrEMBL
  MIF4G-like_typ-3 UniProtKB/TrEMBL
NCBI Gene 500684 ENTREZGENE
PANTHER CELL CYCLE CONTROL PROTEIN CWF22-RELATED UniProtKB/TrEMBL
  PRE-MRNA-SPLICING FACTOR CWC22 HOMOLOG UniProtKB/TrEMBL
Pfam MA3 UniProtKB/TrEMBL
  MIF4G UniProtKB/TrEMBL
PhenoGen Cwc22-ps1 PhenoGen
PROSITE PS51366 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000038322 RatGTEx
SMART MA3 UniProtKB/TrEMBL
  MIF4G UniProtKB/TrEMBL
Superfamily-SCOP ARM-type_fold UniProtKB/TrEMBL
UniProt Q7TP30_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-10 Cwc22-ps1  CWC22 spliceosome associated protein homolog, pseudogene 1  LOC500684  hypothetical protein LOC500684  Symbol and Name Changed 1299863 APPROVED
2021-03-09 LOC500684  hypothetical protein LOC500684  LOC102555166  pre-mRNA-splicing factor CWC22 homolog  Data merged from RGD:7593830 737654 PROVISIONAL
2015-07-29 LOC500684  hypothetical protein LOC500684  LOC680829  similar to CG12750-PA  Data merged from RGD:1587054 737654 PROVISIONAL
2015-07-29 LOC500684  hypothetical protein LOC500684  LOC680519  similar to CG12750-PA  Data merged from RGD:1590641 737654 PROVISIONAL
2013-12-18 LOC102555166  pre-mRNA-splicing factor CWC22 homolog      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-20 LOC680519  similar to CG12750-PA      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-11-19 LOC680829  similar to CG12750-PA      Symbol and Name status set to provisional 70820 PROVISIONAL
2006-02-09 LOC500684  hypothetical protein LOC500684      Symbol and Name status set to provisional 70820 PROVISIONAL