Cstf2t (cleavage stimulation factor, 3' pre-RNA subunit 2, tau) - Rat Genome Database

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Gene: Cstf2t (cleavage stimulation factor, 3' pre-RNA subunit 2, tau) Mus musculus
Analyze
Symbol: Cstf2t
Name: cleavage stimulation factor, 3' pre-RNA subunit 2, tau
RGD ID: 1320691
MGI Page MGI
Description: Enables RNA binding activity. Predicted to act upstream of or within mRNA 3'-end processing. Predicted to be located in nucleoplasm. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex. Is expressed in brain and spinal cord. Orthologous to human CSTF2T (cleavage stimulation factor subunit 2 tau variant).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: 64kD; 64kDa; C77975; CF-1 64 kDa subunit tau; CF-1 64 kDa subunit, tau; cleavage stimulation factor 64 kDa subunit tau; cleavage stimulation factor 64 kDa subunit, tau; cleavage stimulation factor subunit 2 tau; cleavage stimulation factor subunit 2 tau variant; cleavage stimulation factor, 3' pre-RNA subunit 2, 64 kDa, tau; CSTF 64 kDa subunit tau; CSTF 64 kDa subunit, tau; tauCstF-64; tCstF-6; tCstF-64
RGD Orthologs
Human
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: GRCm39 - Mouse Genome Assembly GRCm39
Position:
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391931,060,241 - 31,063,992 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1931,060,237 - 31,064,469 (+)EnsemblGRCm39 Ensembl
GRCm381931,082,841 - 31,086,592 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1931,082,837 - 31,087,069 (+)EnsemblGRCm38mm10GRCm38
MGSCv371931,157,331 - 31,161,082 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361931,149,001 - 31,152,589 (+)NCBIMGSCv36mm8
Celera1931,867,444 - 31,871,195 (+)NCBICelera
Cytogenetic Map19C1NCBI
cM Map1925.94NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
Phenotype Annotations     Click to see Annotation Detail View

Mammalian Phenotype
References

References - curated
# Reference Title Reference Citation
1. Pre-mRNA 3'-end processing complex assembly and function. Chan S, etal., Wiley Interdiscip Rev RNA. 2011 May-Jun;2(3):321-35. doi: 10.1002/wrna.54. Epub 2010 Oct 18.
2. Means to an end: mechanisms of alternative polyadenylation of messenger RNA precursors. Gruber AR, etal., Wiley Interdiscip Rev RNA. 2014 Mar-Apr;5(2):183-96. doi: 10.1002/wrna.1206. Epub 2013 Nov 14.
3. Large-scale cDNA analysis reveals phased gene expression patterns during preimplantation mouse development. Ko MS, etal., Development 2000 Apr;127(8):1737-49.
4. MGDs mouse GO annotations MGD data from the GO Consortium
5. Analysis of the mouse transcriptome based on functional annotation of 60,770 full-length cDNAs. Okazaki Y, etal., Nature. 2002 Dec 5;420(6915):563-73.
6. KEGG Annotation Import Pipeline Pipeline to import KEGG annotations from KEGG into RGD
7. Mouse MP Annotation Import Pipeline RGD automated import pipeline
8. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:8889548   PMID:10349636   PMID:10922068   PMID:11042159   PMID:11076861   PMID:11113135   PMID:11217851   PMID:12408968   PMID:12477932   PMID:14681198   PMID:15368895   PMID:15489334  
PMID:16033648   PMID:16141072   PMID:16141073   PMID:16207706   PMID:16467265   PMID:17029590   PMID:18077340   PMID:19284619   PMID:20463354   PMID:21267068   PMID:21489638   PMID:21873635  
PMID:23110235   PMID:26700942   PMID:27812195   PMID:29673127   PMID:30196744   PMID:32325033   PMID:34133714  


Genomics

Comparative Map Data
Cstf2t
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391931,060,241 - 31,063,992 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1931,060,237 - 31,064,469 (+)EnsemblGRCm39 Ensembl
GRCm381931,082,841 - 31,086,592 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1931,082,837 - 31,087,069 (+)EnsemblGRCm38mm10GRCm38
MGSCv371931,157,331 - 31,161,082 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361931,149,001 - 31,152,589 (+)NCBIMGSCv36mm8
Celera1931,867,444 - 31,871,195 (+)NCBICelera
Cytogenetic Map19C1NCBI
cM Map1925.94NCBI
CSTF2T
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381051,695,486 - 51,699,595 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1051,695,486 - 51,699,595 (-)EnsemblGRCh38hg38GRCh38
GRCh371053,455,246 - 53,459,355 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361053,125,252 - 53,129,361 (-)NCBINCBI36Build 36hg18NCBI36
Build 341053,125,251 - 53,129,361NCBI
Celera1046,718,008 - 46,722,117 (-)NCBICelera
Cytogenetic Map10q21.1NCBI
HuRef1047,433,327 - 47,437,436 (-)NCBIHuRef
CHM1_11053,737,028 - 53,741,141 (-)NCBICHM1_1
T2T-CHM13v2.01052,544,505 - 52,548,614 (-)NCBIT2T-CHM13v2.0
Cstf2t
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81238,366,042 - 238,369,608 (+)NCBIGRCr8
mRatBN7.21228,952,617 - 228,956,183 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1228,952,504 - 228,955,873 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1237,310,067 - 237,313,633 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01244,239,783 - 244,243,349 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01237,077,535 - 237,081,100 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01249,574,954 - 249,578,520 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1249,574,954 - 249,578,520 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01256,813,751 - 256,817,317 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41235,060,489 - 235,064,055 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11235,224,192 - 235,226,470 (+)NCBI
Celera1226,077,478 - 226,081,044 (+)NCBICelera
Cytogenetic Map1q52NCBI
Cstf2t
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554256,832,580 - 6,834,499 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554256,830,775 - 6,834,799 (-)NCBIChiLan1.0ChiLan1.0
CSTF2T
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2864,004,122 - 64,015,913 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11064,007,666 - 64,012,290 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01048,342,491 - 48,346,810 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11050,477,193 - 50,481,591 (-)NCBIpanpan1.1PanPan1.1panPan2
CSTF2T
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Dog10K_Boxer_Tasha2636,151,251 - 36,153,709 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02637,797,337 - 37,799,769 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2637,797,408 - 37,799,309 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12635,699,493 - 35,701,917 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02635,288,227 - 35,290,664 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02636,528,531 - 36,530,957 (+)NCBIUU_Cfam_GSD_1.0
Cstf2t
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721375,816,561 - 75,820,484 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936787838,485 - 840,353 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_004936787838,153 - 842,118 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CSTF2T
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1498,105,772 - 98,110,358 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11498,104,957 - 98,109,479 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214106,806,097 - 106,809,854 (+)NCBISscrofa10.2Sscrofa10.2susScr3
Cstf2t
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462479111,925,197 - 11,927,188 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462479111,924,945 - 11,929,106 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Cstf2t
116 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:389
Count of miRNA genes:302
Interacting mature miRNAs:322
Transcripts:ENSMUST00000066039
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 (GRCm39)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1300904Chab5_mcholesterol absorption 5 (mouse)Not determined19165376435653927Mouse
4142406Pbctlp1_mperipheral blood cytotoxic T lymphocyte percentage 1 (mouse)Not determined132875174Mouse
1302126Skull26_mskull morphology 26 (mouse)Not determined19332321637323348Mouse
1302019Pgia23_mproteoglycan induced arthritis 23 (mouse)Not determined19978745343787602Mouse
13506250Renmq1_mrenal mercury accumulation QTL 1 (mouse)192738559461385705Mouse
1301228Iba4_minduction of brown adipocytes 4 (mouse)Not determined19930571543305821Mouse
1300683Fembm7_mfemoral bone morphometry 7 (mouse)Not determined193014122461420004Mouse
26884385Skwq14_mskull length QTL 14, 16 week (mouse)19325000035877400Mouse
14928311Manh85_mmandible shape 85 (mouse)191191478945914789Mouse
10412251Mnp_mmodifier of Niemann Pick type C1 (mouse)Not determined192023431454234461Mouse
4141659Pbwg20_mpostnatal body weight growth 20 (mouse)Not determined192137870555378928Mouse
4141138Femwf11_mfemur work to failure 11 (mouse)Not determined2814034861420004Mouse
12790634Ebm1_mEpidermolysis Bullosa modifier 1 (mouse)192498843958988439Mouse
1302123Tlsr8_mthymic lymphoma suppressor region 8 (mouse)Not determined192513600242388916Mouse
1357568Tgct4_mtesticular germ cell tumor 4 (mouse)Not determined192777198535295381Mouse
1301336Alcp23_malcohol preference locus 23 (mouse)Not determined191591260749912719Mouse
1301633Alcp24_malcohol preference locus 24 (mouse)Not determined191591260749912719Mouse
1301410Cd8mts6_mCD8 memory T cell subset 6 (mouse)Not determined193014123161420004Mouse
11039522Tbbr4_mTrypanosoma brucei brucei response 4 (mouse)19531332639313470Mouse
1301451Ath16_matherosclerosis 16 (mouse)Not determined192542691759427005Mouse
1302063Eae19_mexperimental allergic encephalomyelitis 19 (mouse)Not determined191829516252295381Mouse
4142343Moen2_mmodifier of engrailed QTL 2 (mouse)Not determined192023431454234461Mouse
1357596Tgct3_mtesticular germ cell tumor 3 (mouse)Not determined192198409132912719Mouse
1301271Datd_mdopamine transporter density (mouse)Not determined19132340234Mouse
1300923Bits4_mbitterness sensitivity 4 (mouse)Not determined19332321637323348Mouse
1300856Nobq2_mNew Zealand obese QTL 2 (mouse)Not determined193089788061420004Mouse
10413881Moe2_mmodifier of epilepsy 2 (mouse)191492301648923138Mouse
1558876W3q14_mweight 3 weeks QTL 14 (mouse)Not determined192231332653911504Mouse
1301800Faq10_mfluctuating asymmetry QTL 10 (mouse)Not determined19332321637323348Mouse
1300591Pas3_mpulmonary adenoma susceptibility 3 (mouse)Not determined19332321637323348Mouse
1302004Lfp2_mlong free running period 2 (mouse)Not determined191829516252295381Mouse
1301942Pas13_mpulmonary adenoma susceptibility 13 (mouse)Not determined193014123161420004Mouse

Markers in Region
Cstf2t  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381931,084,316 - 31,084,915UniSTSGRCm38
MGSCv371931,158,806 - 31,159,405UniSTSGRCm37
Celera1931,868,919 - 31,869,518UniSTS
Cytogenetic Map19C2UniSTS
Cytogenetic Map19C1UniSTS
cM Map19 UniSTS
RH126283  
Mouse AssemblyChrPosition (strand)SourceJBrowse
GRCm381931,085,644 - 31,085,859UniSTSGRCm38
MGSCv371931,160,134 - 31,160,349UniSTSGRCm37
Celera1931,870,247 - 31,870,462UniSTS
Cytogenetic Map19C1UniSTS
Cytogenetic Map19C2UniSTS
Whitehead/MRC_RH19306.86UniSTS


Expression


Sequence


RefSeq Acc Id: ENSMUST00000066039   ⟹   ENSMUSP00000093831
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm39 Ensembl1931,060,237 - 31,064,469 (+)Ensembl
GRCm38.p6 Ensembl1931,082,837 - 31,087,069 (+)Ensembl
RefSeq Acc Id: NM_031249   ⟹   NP_112539
RefSeq Status: VALIDATED
Type: CODING
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm391931,060,241 - 31,063,992 (+)NCBI
GRCm381931,082,841 - 31,086,592 (+)ENTREZGENE
MGSCv371931,157,331 - 31,161,082 (+)RGD
Celera1931,867,444 - 31,871,195 (+)RGD
cM Map19 ENTREZGENE
Sequence:
RefSeq Acc Id: NP_112539   ⟸   NM_031249
- UniProtKB: Q8R2Y1 (UniProtKB/Swiss-Prot),   Q8C3W7 (UniProtKB/Swiss-Prot),   Q8BHH7 (UniProtKB/Swiss-Prot),   Q6A016 (UniProtKB/Swiss-Prot),   Q9EPU3 (UniProtKB/Swiss-Prot),   Q8C7E9 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSMUSP00000093831   ⟸   ENSMUST00000066039
Protein Domains
RRM

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q8C7E9-F1-model_v2 AlphaFold Q8C7E9 1-632 view protein structure

Promoters
RGD ID:13679254
Promoter ID:EPDNEW_M23775
Type:initiation region
Name:Cstf2t_1
Description:Mus musculus cleavage stimulation factor, 3' pre-RNA subunit2, tau , mRNA.
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Mouse AssemblyChrPosition (strand)Source
GRCm381931,083,011 - 31,083,071EPDNEW
RGD ID:6829932
Promoter ID:MM_KWN:26830
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:3T3L1_Day0,   3T3L1_Day1,   3T3L1_Day2,   3T3L1_Day3,   3T3L1_Day4,   3T3L1_Day6,   BoneMarrow_0Hour,   BoneMarrow_2Hour,   BoneMarrow_4Hour,   Brain,   ES_Cell,   Kidney,   Liver,   Lung,   MEF_B4,   MEF_B6,   Spleen
Transcripts:NM_031249
Position:
Mouse AssemblyChrPosition (strand)Source
MGSCv361931,157,196 - 31,159,152 (+)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene MGI:1932622 AgrOrtholog
Ensembl Genes ENSMUSG00000053536 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSMUST00000066039 ENTREZGENE
  ENSMUST00000066039.8 UniProtKB/Swiss-Prot
Gene3D-CATH 1.10.20.70 UniProtKB/Swiss-Prot
  1.25.40.630 UniProtKB/Swiss-Prot
  3.30.70.330 UniProtKB/Swiss-Prot
InterPro CSTF2_C_sf UniProtKB/Swiss-Prot
  CSTF2_hinge UniProtKB/Swiss-Prot
  CSTF_C UniProtKB/Swiss-Prot
  Nucleotide-bd_a/b_plait_sf UniProtKB/Swiss-Prot
  RBD_domain_sf UniProtKB/Swiss-Prot
  RRM_dom UniProtKB/Swiss-Prot
KEGG Report mmu:83410 UniProtKB/Swiss-Prot
MGD MGI:1932622 ENTREZGENE
NCBI Gene 83410 ENTREZGENE
PANTHER CLEAVAGE STIMULATION FACTOR SUBUNIT 2 UniProtKB/Swiss-Prot
  CLEAVAGE STIMULATION FACTOR SUBUNIT 2 TAU VARIANT UniProtKB/Swiss-Prot
Pfam CSTF2_hinge UniProtKB/Swiss-Prot
  CSTF_C UniProtKB/Swiss-Prot
  RRM_1 UniProtKB/Swiss-Prot
PhenoGen Cstf2t PhenoGen
PROSITE RRM UniProtKB/Swiss-Prot
SMART RRM UniProtKB/Swiss-Prot
Superfamily-SCOP SSF54928 UniProtKB/Swiss-Prot
UniProt CSTFT_MOUSE UniProtKB/Swiss-Prot
  Q6A016 ENTREZGENE
  Q8BHH7 ENTREZGENE
  Q8C3W7 ENTREZGENE
  Q8C7E9 ENTREZGENE
  Q8R2Y1 ENTREZGENE
  Q9EPU3 ENTREZGENE
UniProt Secondary Q6A016 UniProtKB/Swiss-Prot
  Q8BHH7 UniProtKB/Swiss-Prot
  Q8C3W7 UniProtKB/Swiss-Prot
  Q8R2Y1 UniProtKB/Swiss-Prot
  Q9EPU3 UniProtKB/Swiss-Prot