PSPC1 (paraspeckle component 1) - Rat Genome Database

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Gene: PSPC1 (paraspeckle component 1) Sus scrofa
Analyze
Symbol: PSPC1
Name: paraspeckle component 1
RGD ID: 14135848
Description: ENCODES a protein that exhibits RNA binding (inferred); INVOLVED IN activation of innate immune response (inferred); negative regulation of DNA-templated transcription (inferred); non-membrane-bounded organelle assembly (inferred); FOUND IN paraspeckles (ortholog)
Type: protein-coding
RefSeq Status: MODEL
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: Sscrofa11.1 - Pig Sscrofa11.1 Assembly
Position:
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl11482,564 - 572,090 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.111477,010 - 572,090 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21186,908,816 - 86,971,424 (-)NCBISscrofa10.2Sscrofa10.2susScr3
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
cytoplasm  (IEA)
fibrillar center  (IEA)
nuclear matrix  (IEA)
nuclear speck  (IEA)
nucleolus  (IEA)
nucleoplasm  (IEA)
nucleus  (IBA,IEA)
paraspeckles  (IEA,ISO)

Molecular Function
protein binding  (ISO)
RNA binding  (IBA,IEA)

References
Additional References at PubMed
PMID:22301074   PMID:30032202  


Genomics

Comparative Map Data
PSPC1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl11482,564 - 572,090 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.111477,010 - 572,090 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21186,908,816 - 86,971,424 (-)NCBISscrofa10.2Sscrofa10.2susScr3
PSPC1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381319,671,205 - 19,782,945 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1319,674,752 - 19,783,019 (-)EnsemblGRCh38hg38GRCh38
GRCh371320,248,892 - 20,357,085 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361319,146,896 - 19,255,083 (-)NCBINCBI36Build 36hg18NCBI36
Build 341319,147,527 - 19,255,082NCBI
Celera131,310,734 - 1,418,914 (-)NCBICelera
Cytogenetic Map13q12.11NCBI
HuRef131,053,841 - 1,162,259 (-)NCBIHuRef
CHM1_11320,216,795 - 20,325,586 (-)NCBICHM1_1
T2T-CHM13v2.01318,867,270 - 18,979,203 (-)NCBIT2T-CHM13v2.0
Pspc1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391456,959,898 - 57,015,775 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1456,958,167 - 57,015,773 (-)EnsemblGRCm39 Ensembl
GRCm381456,722,441 - 56,778,318 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1456,720,710 - 56,778,316 (-)EnsemblGRCm38mm10GRCm38
MGSCv371457,341,286 - 57,397,153 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361455,676,559 - 55,732,426 (-)NCBIMGSCv36mm8
Celera1454,520,204 - 54,576,103 (-)NCBICelera
Cytogenetic Map14C3NCBI
cM Map1428.4NCBI
Pspc1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81534,941,445 - 35,027,460 (-)NCBIGRCr8
mRatBN7.21530,828,617 - 30,911,315 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1530,828,626 - 30,911,202 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1532,843,198 - 32,902,554 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01533,993,854 - 34,053,213 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01532,251,952 - 32,311,317 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01536,946,914 - 37,030,273 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1536,950,257 - 37,030,281 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01540,799,244 - 40,883,016 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41535,718,357 - 35,779,139 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11535,734,056 - 35,794,839 (-)NCBI
Celera1530,565,581 - 30,624,899 (-)NCBICelera
Cytogenetic Map15p12NCBI
Pspc1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955497575,340 - 642,809 (-)EnsemblChiLan1.0
ChiLan1.0NW_004955497574,678 - 641,885 (-)NCBIChiLan1.0ChiLan1.0
PSPC1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21419,304,282 - 19,410,858 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11310,416,794 - 10,522,261 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0131,001,131 - 1,106,627 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11319,319,242 - 19,424,074 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1319,347,276 - 19,428,997 (-)Ensemblpanpan1.1panPan2
PSPC1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12518,287,827 - 18,361,801 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2518,287,899 - 18,359,553 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2518,317,277 - 18,391,326 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02518,425,772 - 18,499,922 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2518,425,958 - 18,497,672 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12518,291,628 - 18,365,647 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02518,303,745 - 18,377,811 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02518,360,192 - 18,434,592 (+)NCBIUU_Cfam_GSD_1.0
Pspc1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024404945120,329,144 - 120,422,113 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049367201,876,475 - 1,967,662 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049367201,876,726 - 1,941,705 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PSPC1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.131,160,227 - 1,232,390 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366605743,304,564 - 43,413,173 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pspc1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462477617,906,063 - 17,978,098 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462477617,906,700 - 17,978,885 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in PSPC1
2338 total Variants

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 hemolymphoid system musculoskeletal system nervous system renal system reproductive system respiratory system
High
Medium 10 4 3 5 2 23 2 3 3
Low
Below cutoff

Sequence


RefSeq Acc Id: ENSSSCT00000010490   ⟹   ENSSSCP00000010218
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl11482,564 - 572,090 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000057535   ⟹   ENSSSCP00000032237
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl11507,040 - 572,090 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000071612   ⟹   ENSSSCP00000067226
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl11528,067 - 572,090 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000077634   ⟹   ENSSSCP00000063189
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl11507,040 - 572,090 (-)Ensembl
RefSeq Acc Id: ENSSSCT00000106693   ⟹   ENSSSCP00000077432
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.1 Ensembl11522,251 - 572,090 (-)Ensembl
RefSeq Acc Id: XM_021065418   ⟹   XP_020921077
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.111507,030 - 572,090 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021065419   ⟹   XP_020921078
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.111500,594 - 572,090 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021065421   ⟹   XP_020921080
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.111477,589 - 572,090 (-)NCBI
Sequence:
RefSeq Acc Id: XM_021065422   ⟹   XP_020921081
Type: CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.111533,490 - 572,090 (-)NCBI
Sequence:
RefSeq Acc Id: XR_002336587
Type: NON-CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.111482,559 - 572,090 (-)NCBI
Sequence:
RefSeq Acc Id: XR_002336588
Type: NON-CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.111482,559 - 572,090 (-)NCBI
Sequence:
RefSeq Acc Id: XR_002336589
Type: NON-CODING
Position:
Pig AssemblyChrPosition (strand)Source
Sscrofa11.111477,010 - 572,090 (-)NCBI
Sequence:
RefSeq Acc Id: XP_020921080   ⟸   XM_021065421
- Peptide Label: isoform X3
- UniProtKB: A0A4X1TYY1 (UniProtKB/TrEMBL),   A0A8D1EZ96 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020921078   ⟸   XM_021065419
- Peptide Label: isoform X2
- UniProtKB: A0A480T8V3 (UniProtKB/TrEMBL),   A0A8D1NZC2 (UniProtKB/TrEMBL),   A0A8D1EZ96 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020921077   ⟸   XM_021065418
- Peptide Label: isoform X1
- UniProtKB: A0A286ZKW2 (UniProtKB/TrEMBL),   A0A4X1U1M1 (UniProtKB/TrEMBL),   A0A8D1EXC2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_020921081   ⟸   XM_021065422
- Peptide Label: isoform X4
- UniProtKB: A0A4X1U3Y1 (UniProtKB/TrEMBL),   A0A8D1EZ96 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSSSCP00000010218   ⟸   ENSSSCT00000010490
RefSeq Acc Id: ENSSSCP00000067226   ⟸   ENSSSCT00000071612
RefSeq Acc Id: ENSSSCP00000063189   ⟸   ENSSSCT00000077634
RefSeq Acc Id: ENSSSCP00000032237   ⟸   ENSSSCT00000057535
RefSeq Acc Id: ENSSSCP00000077432   ⟸   ENSSSCT00000106693
Protein Domains
RRM


Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSSSCG00000009569 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
  ENSSSCG00025034614 UniProtKB/TrEMBL
  ENSSSCG00030037648 UniProtKB/TrEMBL
  ENSSSCG00035021734 UniProtKB/TrEMBL
  ENSSSCG00040049758 UniProtKB/TrEMBL
  ENSSSCG00045031268 UniProtKB/TrEMBL
  ENSSSCG00050074379 UniProtKB/TrEMBL
  ENSSSCG00055003322 UniProtKB/TrEMBL
  ENSSSCG00060035379 UniProtKB/TrEMBL
  ENSSSCG00065008267 UniProtKB/TrEMBL
  ENSSSCG00070013924 UniProtKB/TrEMBL
Ensembl Transcript ENSSSCT00000010490.5 UniProtKB/TrEMBL
  ENSSSCT00000057535 ENTREZGENE
  ENSSSCT00000057535.2 UniProtKB/TrEMBL
  ENSSSCT00000077634.1 UniProtKB/TrEMBL
  ENSSSCT00000106693 ENTREZGENE
  ENSSSCT00000106693.1 UniProtKB/TrEMBL
  ENSSSCT00025047202.1 UniProtKB/TrEMBL
  ENSSSCT00025047262.1 UniProtKB/TrEMBL
  ENSSSCT00025047289.1 UniProtKB/TrEMBL
  ENSSSCT00030052404.1 UniProtKB/TrEMBL
  ENSSSCT00030052439.1 UniProtKB/TrEMBL
  ENSSSCT00030052456.1 UniProtKB/TrEMBL
  ENSSSCT00030052492.1 UniProtKB/TrEMBL
  ENSSSCT00035028362.1 UniProtKB/TrEMBL
  ENSSSCT00035028365.1 UniProtKB/TrEMBL
  ENSSSCT00035028369.1 UniProtKB/TrEMBL
  ENSSSCT00040067301.1 UniProtKB/TrEMBL
  ENSSSCT00040067401.1 UniProtKB/TrEMBL
  ENSSSCT00040067456.1 UniProtKB/TrEMBL
  ENSSSCT00045053298.1 UniProtKB/TrEMBL
  ENSSSCT00045053415.1 UniProtKB/TrEMBL
  ENSSSCT00045053529.1 UniProtKB/TrEMBL
  ENSSSCT00050101822.1 UniProtKB/TrEMBL
  ENSSSCT00050101823.1 UniProtKB/TrEMBL
  ENSSSCT00050101824.1 UniProtKB/TrEMBL
  ENSSSCT00050101829.1 UniProtKB/TrEMBL
  ENSSSCT00050101833.1 UniProtKB/TrEMBL
  ENSSSCT00050101836.1 UniProtKB/TrEMBL
  ENSSSCT00055006482.1 UniProtKB/TrEMBL
  ENSSSCT00055006505.1 UniProtKB/TrEMBL
  ENSSSCT00055006510.1 UniProtKB/TrEMBL
  ENSSSCT00060047957.1 UniProtKB/TrEMBL
  ENSSSCT00060047962.1 UniProtKB/TrEMBL
  ENSSSCT00060047964.1 UniProtKB/TrEMBL
  ENSSSCT00065011081.1 UniProtKB/TrEMBL
  ENSSSCT00065011085.1 UniProtKB/TrEMBL
  ENSSSCT00065011091.1 UniProtKB/TrEMBL
  ENSSSCT00070027254.1 UniProtKB/TrEMBL
  ENSSSCT00070027265.1 UniProtKB/TrEMBL
  ENSSSCT00070027292.1 UniProtKB/TrEMBL
  ENSSSCT00070027297.1 UniProtKB/TrEMBL
  ENSSSCT00070027304.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.330 UniProtKB/TrEMBL
  6.10.250.1170 UniProtKB/TrEMBL
InterPro NOPS UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  PSP1_RRM1 UniProtKB/TrEMBL
  PSP1_RRM2 UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  RRM_dom UniProtKB/TrEMBL
NCBI Gene PSPC1 ENTREZGENE
PANTHER PARASPECKLE COMPONENT 1 UniProtKB/TrEMBL
  RNA RECOGNITION MOTIF-CONTAINING UniProtKB/TrEMBL
Pfam NOPS UniProtKB/TrEMBL
  RRM_1 UniProtKB/TrEMBL
PROSITE RRM UniProtKB/TrEMBL
SMART RRM UniProtKB/TrEMBL
Superfamily-SCOP SSF54928 UniProtKB/TrEMBL
UniProt A0A286ZKW2 ENTREZGENE, UniProtKB/TrEMBL
  A0A480T8V3 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1TYY1 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1U1M1 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1U1Q1_PIG UniProtKB/TrEMBL
  A0A4X1U3Y1 ENTREZGENE, UniProtKB/TrEMBL
  A0A4X1U4F2_PIG UniProtKB/TrEMBL
  A0A5G2QYA0_PIG UniProtKB/TrEMBL
  A0A8D0WR24_PIG UniProtKB/TrEMBL
  A0A8D1C7H0_PIG UniProtKB/TrEMBL
  A0A8D1EWG5_PIG UniProtKB/TrEMBL
  A0A8D1EXC2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1EZ96 ENTREZGENE, UniProtKB/TrEMBL
  A0A8D1NZC2 ENTREZGENE, UniProtKB/TrEMBL
  A0A8W4FEZ2_PIG UniProtKB/TrEMBL
  F1RN28_PIG UniProtKB/TrEMBL
VGNC ID VGNC:91930 ENTREZGENE