CPSF4L (cleavage and polyadenylation specific factor 4 like) - Rat Genome Database

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Gene: CPSF4L (cleavage and polyadenylation specific factor 4 like) Homo sapiens
Analyze
Symbol: CPSF4L
Name: cleavage and polyadenylation specific factor 4 like
RGD ID: 2290025
HGNC Page HGNC:33632
Description: Predicted to enable RNA binding activity and metal 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.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: cleavage and polyadenylation specific factor 4-like; putative cleavage and polyadenylation specificity factor subunit 4-like protein
RGD Orthologs
Mouse
Rat
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Genes
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381773,242,101 - 73,263,778 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1773,248,449 - 73,262,352 (-)EnsemblGRCh38hg38GRCh38
GRCh371771,244,588 - 71,258,019 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361768,761,636 - 68,769,552 (-)NCBINCBI36Build 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
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

References

References - curated
# Reference Title Reference Citation
1. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12477932   PMID:16625196   PMID:20379614   PMID:21873635   PMID:26186194   PMID:28514442   PMID:33961781  


Genomics

Comparative Map Data
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 (-)EnsemblGRCh38hg38GRCh38
GRCh371771,244,588 - 71,258,019 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361768,761,636 - 68,769,552 (-)NCBINCBI36Build 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 Ensembl
GRCm3811113,698,171 - 113,710,167 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl11113,698,172 - 113,710,017 (-)EnsemblGRCm38mm10GRCm38
MGSCv3711113,559,485 - 113,571,331 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv3611113,514,261 - 113,526,107 (-)NCBIMGSCv36mm8
Celera11125,462,926 - 125,474,769 (-)NCBICelera
Cytogenetic Map11E2NCBI
cM Map1179.17NCBI
Cpsf4l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81099,241,187 - 99,255,207 (-)NCBIGRCr8
mRatBN7.21098,741,816 - 98,756,069 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1098,743,649 - 98,751,590 (-)EnsemblmRatBN7.2 Ensembl
Rnor_6.010102,213,892 - 102,227,708 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl10102,215,722 - 102,227,554 (-)NCBIRnor6.0rn6Rnor6.0
Rnor_5.010101,893,265 - 101,906,618 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.410103,327,521 - 103,339,565 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.110103,341,890 - 103,353,935 (-)NCBI
Celera1097,348,828 - 97,362,517 (-)NCBICelera
Cytogenetic Map10q32.1NCBI
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_Tasha
ROS_Cfam_1.097,595,247 - 7,602,267 (+)NCBIROS_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_1.0
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 (+)EnsemblSpeTri2.0SpeTri2.0 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

Variants

.
Variants in CPSF4L
13 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 17q24.3-25.3(chr17:69209079-83086677)x3 copy number gain See cases [RCV000052486] Chr17:69209079..83086677 [GRCh38]
Chr17:67205220..81044553 [GRCh37]
Chr17:64716815..78637842 [NCBI36]
Chr17:17q24.3-25.3
pathogenic
GRCh38/hg38 17q23.2-25.3(chr17:36449220-83086677)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000052483]|See cases [RCV000052483] Chr17:36449220..83086677 [GRCh38]
Chr17:58617905..81044553 [GRCh37]
Chr17:55972687..78637842 [NCBI36]
Chr17:17q23.2-25.3
pathogenic
GRCh38/hg38 17q23.1-25.1(chr17:36449220-75053130)x3 copy number gain See cases [RCV000137437] Chr17:36449220..75053130 [GRCh38]
Chr17:57595736..73049225 [GRCh37]
Chr17:54950518..70560820 [NCBI36]
Chr17:17q23.1-25.1
pathogenic
GRCh38/hg38 17q25.1(chr17:73031361-73264388)x3 copy number gain See cases [RCV000141363] Chr17:73031361..73264388 [GRCh38]
Chr17:71027500..71260527 [GRCh37]
Chr17:68539095..68772122 [NCBI36]
Chr17:17q25.1
uncertain significance
GRCh38/hg38 17q24.3-25.3(chr17:69916435-83102552)x3 copy number gain See cases [RCV000143342] Chr17:69916435..83102552 [GRCh38]
Chr17:67912576..81048189 [GRCh37]
Chr17:65424171..78653717 [NCBI36]
Chr17:17q24.3-25.3
pathogenic
GRCh37/hg19 17q24.2-25.3(chr17:64241326-81041938)x3 copy number gain See cases [RCV000447577] Chr17:64241326..81041938 [GRCh37]
Chr17:17q24.2-25.3
pathogenic
GRCh37/hg19 17q21.31-25.3(chr17:42580684-81085615)x3 copy number gain See cases [RCV000447823] Chr17:42580684..81085615 [GRCh37]
Chr17:17q21.31-25.3
pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:526-81041938) copy number gain See cases [RCV000511439] Chr17:526..81041938 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
NM_001129885.1(CPSF4L):c.149A>C (p.Glu50Ala) single nucleotide variant Inborn genetic diseases [RCV003287788] Chr17:73260938 [GRCh38]
Chr17:71257077 [GRCh37]
Chr17:17q25.1
uncertain significance
NM_001129885.1(CPSF4L):c.488A>C (p.Gln163Pro) single nucleotide variant Inborn genetic diseases [RCV003248980] Chr17:73252639 [GRCh38]
Chr17:71248778 [GRCh37]
Chr17:17q25.1
uncertain significance
GRCh37/hg19 17q24.2-25.3(chr17:67002415-81041938)x3 copy number gain See cases [RCV000512573] Chr17:67002415..81041938 [GRCh37]
Chr17:17q24.2-25.3
pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:526-81041938)x3 copy number gain See cases [RCV000512441] Chr17:526..81041938 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
GRCh37/hg19 17q24.1-25.3(chr17:63689671-81041938)x3 copy number gain not provided [RCV000683952] Chr17:63689671..81041938 [GRCh37]
Chr17:17q24.1-25.3
pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:8547-81060040)x3 copy number gain not provided [RCV000739324] Chr17:8547..81060040 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:7214-81058310)x3 copy number gain not provided [RCV000739320] Chr17:7214..81058310 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
GRCh37/hg19 17p13.3-q25.3(chr17:12344-81057996)x3 copy number gain not provided [RCV000739325] Chr17:12344..81057996 [GRCh37]
Chr17:17p13.3-q25.3
pathogenic
GRCh37/hg19 17q24.1-25.2(chr17:64159738-74891024)x3 copy number gain not provided [RCV000762750] Chr17:64159738..74891024 [GRCh37]
Chr17:17q24.1-25.2
likely pathogenic
GRCh37/hg19 17q24.3-25.1(chr17:70720436-73175266) copy number gain not provided [RCV000767767] Chr17:70720436..73175266 [GRCh37]
Chr17:17q24.3-25.1
pathogenic
GRCh37/hg19 17q24.1-25.3(chr17:62778720-81041938)x3 copy number gain not provided [RCV000849900] Chr17:62778720..81041938 [GRCh37]
Chr17:17q24.1-25.3
pathogenic
NM_001351264.2(C17orf80):c.1663G>A (p.Gly555Ser) single nucleotide variant Inborn genetic diseases [RCV002772236] Chr17:73242937 [GRCh38]
Chr17:71239076 [GRCh37]
Chr17:17q25.1
uncertain significance
NM_001129885.1(CPSF4L):c.130T>G (p.Phe44Val) single nucleotide variant Inborn genetic diseases [RCV002734560] Chr17:73260957 [GRCh38]
Chr17:71257096 [GRCh37]
Chr17:17q25.1
uncertain significance
NM_001129885.1(CPSF4L):c.73A>C (p.Thr25Pro) single nucleotide variant Inborn genetic diseases [RCV002777775] Chr17:73261746 [GRCh38]
Chr17:71257885 [GRCh37]
Chr17:17q25.1
uncertain significance
NM_001129885.1(CPSF4L):c.434G>A (p.Arg145Lys) single nucleotide variant Inborn genetic diseases [RCV002737117] Chr17:73252693 [GRCh38]
Chr17:71248832 [GRCh37]
Chr17:17q25.1
uncertain significance
NM_001129885.1(CPSF4L):c.332C>G (p.Ser111Cys) single nucleotide variant Inborn genetic diseases [RCV002924580] Chr17:73254002 [GRCh38]
Chr17:71250141 [GRCh37]
Chr17:17q25.1
uncertain significance
NM_001129885.1(CPSF4L):c.218G>A (p.Arg73Gln) single nucleotide variant Inborn genetic diseases [RCV002869389] Chr17:73257770 [GRCh38]
Chr17:71253909 [GRCh37]
Chr17:17q25.1
uncertain significance
NM_001351264.2(C17orf80):c.1801G>A (p.Asp601Asn) single nucleotide variant Inborn genetic diseases [RCV002868301] Chr17:73247312 [GRCh38]
Chr17:71243451 [GRCh37]
Chr17:17q25.1
uncertain significance
NM_001129885.1(CPSF4L):c.441G>A (p.Met147Ile) single nucleotide variant Inborn genetic diseases [RCV002850109] Chr17:73252686 [GRCh38]
Chr17:71248825 [GRCh37]
Chr17:17q25.1
uncertain significance
NM_001129885.1(CPSF4L):c.118G>T (p.Val40Leu) single nucleotide variant Inborn genetic diseases [RCV002804790] Chr17:73260969 [GRCh38]
Chr17:71257108 [GRCh37]
Chr17:17q25.1
uncertain significance
NM_001129885.1(CPSF4L):c.74C>A (p.Thr25Asn) single nucleotide variant Inborn genetic diseases [RCV002940383] Chr17:73261745 [GRCh38]
Chr17:71257884 [GRCh37]
Chr17:17q25.1
uncertain significance
NM_001129885.1(CPSF4L):c.424C>T (p.His142Tyr) single nucleotide variant Inborn genetic diseases [RCV002722250] Chr17:73252703 [GRCh38]
Chr17:71248842 [GRCh37]
Chr17:17q25.1
uncertain significance
GRCh37/hg19 17q24.3-25.1(chr17:69501527-71380722)x1 copy number loss not provided [RCV003483324] Chr17:69501527..71380722 [GRCh37]
Chr17:17q24.3-25.1
pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:325
Count of miRNA genes:285
Interacting mature miRNAs:301
Transcripts:ENST00000344935, ENST00000397671
Prediction methods: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.

Markers in Region
D17S1722E  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh371771,244,723 - 71,244,802UniSTSGRCh37
Build 361768,756,318 - 68,756,397RGDNCBI36
Celera1767,827,844 - 67,827,923RGD
Cytogenetic Map17q25.1UniSTS
HuRef1766,653,889 - 66,653,968UniSTS


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 sensory system adipose tissue appendage entire extraembryonic component
High
Medium 1
Low 77 2 114 29 31 27 226 5 233 13 465 107 3 122 152
Below cutoff 1945 2049 1362 465 1051 314 3310 1372 3135 226 889 1254 161 1022 1973 4

Sequence


RefSeq Acc Id: ENST00000344935   ⟹   ENSP00000343900
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1773,248,449 - 73,261,880 (-)Ensembl
RefSeq Acc Id: ENST00000397671   ⟹   ENSP00000380788
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl1773,249,793 - 73,262,352 (-)Ensembl
RefSeq Acc Id: NM_001129885   ⟹   NP_001123357
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381773,248,449 - 73,261,880 (-)NCBI
GRCh371771,244,588 - 71,258,019 (-)RGD
Celera1767,827,709 - 67,841,141 (-)RGD
HuRef1766,653,754 - 66,667,193 (-)ENTREZGENE
CHM1_11771,308,668 - 71,322,105 (-)NCBI
T2T-CHM13v2.01774,138,177 - 74,151,608 (-)NCBI
Sequence:
RefSeq Acc Id: XM_011525115   ⟹   XP_011523417
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh381773,242,101 - 73,263,778 (-)NCBI
Sequence:
RefSeq Acc Id: XM_054316905   ⟹   XP_054172880
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.01774,130,285 - 74,153,506 (-)NCBI
RefSeq Acc Id: NP_001123357   ⟸   NM_001129885
- UniProtKB: A8MU95 (UniProtKB/Swiss-Prot),   B2RXI9 (UniProtKB/Swiss-Prot),   A6NMK7 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_011523417   ⟸   XM_011525115
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSP00000380788   ⟸   ENST00000397671
RefSeq Acc Id: ENSP00000343900   ⟸   ENST00000344935
RefSeq Acc Id: XP_054172880   ⟸   XM_054316905
- Peptide Label: isoform X1
Protein Domains
C3H1-type

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A6NMK7-F1-model_v2 AlphaFold A6NMK7 1-179 view protein structure

Promoters
RGD ID:6794067
Promoter ID:HG_KWN:27011
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:NB4
Transcripts:ENST00000344935,   ENST00000397671,   NM_001129885
Position:
Human AssemblyChrPosition (strand)Source
Build 361768,769,761 - 68,770,261 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:33632 AgrOrtholog
COSMIC CPSF4L COSMIC
Ensembl Genes ENSG00000187959 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000344935 ENTREZGENE
  ENST00000344935.8 UniProtKB/Swiss-Prot
  ENST00000397671.1 UniProtKB/TrEMBL
Gene3D-CATH Zinc finger, CCCH-type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000187959 GTEx
HGNC ID HGNC:33632 ENTREZGENE
Human Proteome Map CPSF4L Human Proteome Map
InterPro CPSF4/Yth1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf-CCCH_3 UniProtKB/Swiss-Prot
  Znf_CCCH UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_CCCH_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:642843 UniProtKB/Swiss-Prot
NCBI Gene 642843 ENTREZGENE
PANTHER CLEAVAGE AND POLYADENYLATION SPECIFICITY FACTOR SUBUNIT 4-LIKE PROTEIN-RELATED UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR23102 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam zf-CCCH_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  zf-CCCH_3 UniProtKB/Swiss-Prot
  zf_CCCH_4 UniProtKB/TrEMBL
PharmGKB PA162382768 PharmGKB
PROSITE ZF_C3H1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART ZnF_C3H1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF90229 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A6NMK7 ENTREZGENE
  A8MU95 ENTREZGENE
  B2RXI9 ENTREZGENE
  CPS4L_HUMAN UniProtKB/Swiss-Prot
  H9KVA5_HUMAN UniProtKB/TrEMBL
UniProt Secondary A8MU95 UniProtKB/Swiss-Prot
  B2RXI9 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-06-28 CPSF4L  cleavage and polyadenylation specific factor 4 like    cleavage and polyadenylation specific factor 4-like  Symbol and/or name change 5135510 APPROVED