Cpsf4l (cleavage and polyadenylation specific factor 4-like) - Rat Genome Database

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Gene: Cpsf4l (cleavage and polyadenylation specific factor 4-like) Rattus norvegicus
Analyze
Symbol: Cpsf4l
Name: cleavage and polyadenylation specific factor 4-like
RGD ID: 1306397
Description: Predicted to enable RNA binding activity and zinc ion binding activity. Predicted to be involved in mRNA 3'-end processing. Predicted to be located in nucleus. Predicted to be part of mRNA cleavage and polyadenylation specificity factor complex. Orthologous to human CPSF4L (cleavage and polyadenylation specific factor 4 like); INTERACTS WITH 1,2,4-trichloro-5-(2,5-dichlorophenyl)benzene (ortholog); 1,2-dichloroethane (ortholog); 17beta-estradiol (ortholog).
Type: protein-coding
RefSeq Status: MODEL
Previously known as: AC096468.1; LOC287799; putative cleavage and polyadenylation specificity factor subunit 4-like protein; RGD1306397; similar to hypothetical protein D11Ertd636e
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81099,241,187 - 99,255,207 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1099,242,794 - 99,257,172 (-)EnsemblGRCr8
mRatBN7.21098,741,816 - 98,756,069 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1098,743,649 - 98,751,590 (-)EnsemblmRatBN7.2
Rnor_6.010102,213,892 - 102,227,708 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10102,215,722 - 102,227,554 (-)NCBIrn6Rnor6.0
Rnor_5.010101,893,265 - 101,906,618 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.410103,327,521 - 103,339,565 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1097,348,828 - 97,362,517 (-)NCBICelera
RGSC_v3.110103,341,890 - 103,353,935 (-)NCBI
Cytogenetic Map10q32.1NCBI
JBrowse:




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. GOA pipeline RGD automated data pipeline
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions

Genomics

Comparative Map Data
Cpsf4l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81099,241,187 - 99,255,207 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl1099,242,794 - 99,257,172 (-)EnsemblGRCr8
mRatBN7.21098,741,816 - 98,756,069 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1098,743,649 - 98,751,590 (-)EnsemblmRatBN7.2
Rnor_6.010102,213,892 - 102,227,708 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10102,215,722 - 102,227,554 (-)NCBIrn6Rnor6.0
Rnor_5.010101,893,265 - 101,906,618 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.410103,327,521 - 103,339,565 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera1097,348,828 - 97,362,517 (-)NCBICelera
RGSC_v3.110103,341,890 - 103,353,935 (-)NCBI
Cytogenetic Map10q32.1NCBI
CPSF4L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381773,242,101 - 73,263,778 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1773,248,449 - 73,262,352 (-)Ensemblhg38GRCh38
GRCh371771,244,588 - 71,258,019 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361768,761,636 - 68,769,552 (-)NCBIBuild 36Build 36hg18NCBI36
Celera1767,827,709 - 67,841,141 (-)NCBICelera
Cytogenetic Map17q25.1NCBI
HuRef1766,653,754 - 66,667,193 (-)NCBIHuRef
CHM1_11771,308,668 - 71,322,105 (-)NCBICHM1_1
T2T-CHM13v2.01774,130,285 - 74,153,506 (-)NCBIT2T-CHM13v2.0
Cpsf4l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm3911113,588,997 - 113,601,125 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl11113,588,998 - 113,600,843 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm3811113,698,171 - 113,710,167 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11113,698,172 - 113,710,017 (-)Ensemblmm10GRCm38
MGSCv3711113,559,485 - 113,571,331 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv3611113,514,261 - 113,526,107 (-)NCBIMGSCv36mm8
Celera11125,462,926 - 125,474,769 (-)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1179.17NCBI
CPSF4L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21989,258,090 - 89,285,785 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11794,085,195 - 94,110,375 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01767,170,897 - 67,192,519 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11772,632,536 - 72,645,845 (-)NCBIPanPan1.1PanPan1.1panPan2
CPSF4L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.196,924,334 - 6,929,076 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha97,543,932 - 7,550,993 (+)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.097,595,247 - 7,602,267 (+)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.197,635,657 - 7,642,718 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.097,738,553 - 7,745,614 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.097,799,311 - 7,806,372 (+)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Cpsf4l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244056027,479,199 - 7,489,426 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936655977,469 - 983,241 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936655977,413 - 985,067 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CPSF4L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1127,669,819 - 7,697,532 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2127,951,162 - 7,965,164 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CPSF4L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.11648,358,899 - 48,394,504 (+)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_02366607719,196,035 - 19,215,983 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Cpsf4l
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v1975,596,060 - 75,608,484 (+)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Cpsf4l
62 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:106
Count of miRNA genes:90
Interacting mature miRNAs:95
Transcripts:ENSRNOT00000052406
Prediction methods:Microtar, 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 (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354641Bvd2Brain ventricular dilatation QTL 26.360.001brain ventricle morphology trait (VT:0000822)hydrocephalus severity score (CMO:0001881)1093723381107556066Rat
8657410Bp374Blood pressure QTL 374heart left ventricle size trait (VT:0002753)heart left ventricle end-diastolic diameter (CMO:0000982)1067476608107713808Rat
61449Ciaa2CIA Autoantibody QTL 27.1blood autoantibody amount (VT:0003725)calculated serum anti-type 2 collagen antibody titer (CMO:0001279)1063719161107713808Rat
61325Aia5Adjuvant induced arthritis QTL 50.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
1298078Stresp5Stress response QTL 52.990.00025blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1042546145107713808Rat
1549831Bss6Bone structure and strength QTL 64lumbar vertebra strength trait (VT:0010574)vertebra ultimate force (CMO:0001678)1058073360103073360Rat
12903252Cm113Cardiac mass QTL 1130.047heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
70164Bw21Body weight QTL 214.360.00005body mass (VT:0001259)body weight (CMO:0000012)105429633699451733Rat
2298548Neuinf7Neuroinflammation QTL 73.4nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)1064939013107713808Rat
1302404Cia27Collagen induced arthritis QTL 272.60.0045joint integrity trait (VT:0010548)experimental arthritis severity measurement (CMO:0001459)1076951790107713808Rat
1300107Rf18Renal function QTL 183.41urine output (VT:0003620)timed urine volume (CMO:0000260)1079272424102982300Rat
70168Eae12Experimental allergic encephalomyelitis QTL 120.0009nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1073599825107713808Rat
70171Cari1Carrageenan-induced inflammation QTL 14.90.0005hypodermis integrity trait (VT:0010550)inflammatory exudate volume (CMO:0001429)1054296227107713808Rat
12903269Am15Aortic mass QTL 150.042aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
12903266Cm114Cardiac mass QTL 1140.02heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)1066817119107713808Rat
1578672Bmd16Bone mineral density QTL 166.2femur mineral mass (VT:0010011)compact volumetric bone mineral density (CMO:0001730)1097202388107556066Rat
61354Pia10Pristane induced arthritis QTL 100.01joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
2313103Bss80Bone structure and strength QTL 8020.0001tibia strength trait (VT:1000284)tibia midshaft endosteal cross-sectional area (CMO:0001716)1062556066107556066Rat
70193Mcs7Mammary carcinoma susceptibility QTL 72.38mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
12880372Am12Aortic mass QTL 120.003aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)1066817119107713808Rat
2313105Bss79Bone structure and strength QTL 791.80.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)1062556066107556066Rat
61363Oia3Oil induced arthritis QTL 30.001joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1087807758107713808Rat
12880375Kidm66Kidney mass QTL 660.009kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
2316949Gluco60Glucose level QTL 603.7blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1014991535107556066Rat
12880370Cm105Cardiac mass QTL 1050.008heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
12880371Cm106Cardiac mass QTL 1060.007heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)1066817119107713808Rat
1300137Bp186Blood pressure QTL 1863.57arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)1091127270107556066Rat
11565453Kidm58Kidney mass QTL 580.002kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)1066817119107713808Rat
1578663Bss18Bone structure and strength QTL 183.6femur width (VT:1000666)femoral neck width (CMO:0001695)1097202388107556066Rat
7387312Bw125Body weight QTL 12530.0047retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight (CMO:0000356)1065390777107713808Rat
6893357Bw102Body weight QTL 1020.50.36body mass (VT:0001259)body weight (CMO:0000012)1081012077101828297Rat
61387Bp1Blood pressure QTL 15.1arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)1052269185107713808Rat
61396Bp9Blood pressure QTL 94.80.0001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1068920187107713808Rat
1358915Stresp7Stress response QTL 73.52blood norepinephrine amount (VT:0005663)plasma norepinephrine level (CMO:0001010)1065307813107713808Rat
634320Niddm49Non-insulin dependent diabetes mellitus QTL 494.41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1089039175107713808Rat
70363Bp71Blood pressure QTL 710.04arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1061843496106843496Rat
6893366Bw106Body weight QTL 1060.30.47body mass (VT:0001259)body weight (CMO:0000012)1070698731107713808Rat
1576313Pia25Pristane induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096620293107713808Rat
1558643Cm44Cardiac mass QTL 444.80.0000368heart mass (VT:0007028)heart wet weight (CMO:0000069)1061843496100198886Rat
631267Cia20Collagen induced arthritis QTL 203.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1023948641107713808Rat
1576307Cia28Collagen induced arthritis QTL 28joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1096620293107713808Rat
631269Cia22Collagen induced arthritis QTL 228.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1576308Schws1Schwannoma susceptibility QTL 10.0041nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)1040535708107713808Rat
631268Cia21Collagen induced arthritis QTL 213.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1014991535107713808Rat
631270Cia23Collagen induced arthritis QTL 233.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1040535708107713808Rat
1581559Eae18Experimental allergic encephalomyelitis QTL 180.00002nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis severity score (CMO:0001419)1066108888107555881Rat
6893336Cm75Cardiac mass QTL 750.10.87heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)1061843496100198886Rat
1600367Mcs15Mammary carcinoma susceptibility QTL 154.5mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)1072724423107713808Rat
631537Oia4Oil induced arthritis QTL 4joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1076128947107713808Rat
634354Rends3Renal damage susceptibility QTL 30.05kidney blood vessel morphology trait (VT:0000530)organ lesion measurement (CMO:0000677)1061997479106997479Rat
61436Cia5Collagen induced arthritis QTL 54.9joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)1091727883107713808Rat
2301405Cm69Cardiac mass QTL 690.031heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)1066817119107713808Rat
631542Bp82Blood pressure QTL 826.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)102702353599451848Rat


Expression

RNA-SEQ Expression

circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
sensory system
visual system
7 10 33 58 40 16 18 15 3 3

Sequence


Ensembl Acc Id: ENSRNOT00000080066   ⟹   ENSRNOP00000074846
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1099,242,794 - 99,257,172 (-)Ensembl
mRatBN7.2 Ensembl1098,743,649 - 98,751,590 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000163225   ⟹   ENSRNOP00000110895
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl1099,242,794 - 99,254,848 (-)Ensembl
RefSeq Acc Id: XM_063270168   ⟹   XP_063126238
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81099,241,187 - 99,251,866 (-)NCBI
RefSeq Acc Id: XM_063270169   ⟹   XP_063126239
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr81099,241,187 - 99,255,207 (-)NCBI
Ensembl Acc Id: ENSRNOP00000074846   ⟸   ENSRNOT00000080066
RefSeq Acc Id: XP_063126239   ⟸   XM_063270169
- Peptide Label: isoform X2
- UniProtKB: A6HKG9 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063126238   ⟸   XM_063270168
- Peptide Label: isoform X1
- UniProtKB: A6HKH0 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000110895   ⟸   ENSRNOT00000163225
Protein Domains
C3H1-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2K937-F1-model_v2 AlphaFold A0A0G2K937 1-164 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:1306397 AgrOrtholog
BioCyc Gene G2FUF-22757 BioCyc
Ensembl Genes ENSRNOG00000056582 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000080066 ENTREZGENE
  ENSRNOT00000080066.3 UniProtKB/TrEMBL
  ENSRNOT00000163225 ENTREZGENE
  ENSRNOT00000163225.1 UniProtKB/TrEMBL
Gene3D-CATH Zinc finger, CCCH-type UniProtKB/TrEMBL
InterPro CPSF4/Yth1 UniProtKB/TrEMBL
  Znf_CCCH UniProtKB/TrEMBL
  Znf_CCCH_sf UniProtKB/TrEMBL
NCBI Gene 287799 ENTREZGENE
PANTHER CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4-LIKE PROTEIN-RELATED UniProtKB/TrEMBL
  PTHR23102 UniProtKB/TrEMBL
Pfam zf-CCCH UniProtKB/TrEMBL
  zf-CCCH_2 UniProtKB/TrEMBL
PhenoGen Cpsf4l PhenoGen
PROSITE ZF_C3H1 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000056582 RatGTEx
SMART ZnF_C3H1 UniProtKB/TrEMBL
Superfamily-SCOP SSF90229 UniProtKB/TrEMBL
UniProt A0A0G2K937_RAT UniProtKB/TrEMBL
  A0ABK0LZV4_RAT UniProtKB/TrEMBL
  A6HKG9 ENTREZGENE, UniProtKB/TrEMBL
  A6HKH0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Cpsf4l  cleavage and polyadenylation specific factor 4-like  AC096468.1    Data merged from RGD:15010361 737654 PROVISIONAL
2021-09-02 AC096468.1    Cpsf4l  cleavage and polyadenylation specific factor 4-like  Symbol and/or name change 19259462 PROVISIONAL
2021-08-09 Cpsf4l  cleavage and polyadenylation specific factor 4-like  AC096468.1    Symbol and/or name change 19259462 PROVISIONAL
2019-11-08 AC096468.1        Symbol and Name status set to provisional 45752 PROVISIONAL
2008-03-11 Cpsf4l  cleavage and polyadenylation specific factor 4-like  RGD1306397_predicted  similar to hypothetical protein D11Ertd636e (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-01-20 RGD1306397_predicted  similar to hypothetical protein D11Ertd636e (predicted)  LOC287799_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC287799_predicted  similar to hypothetical protein D11Ertd636e (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL