PCIF1 (phosphorylated CTD interacting factor 1) - Rat Genome Database

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Gene: PCIF1 (phosphorylated CTD interacting factor 1) Homo sapiens
Analyze
Symbol: PCIF1
Name: phosphorylated CTD interacting factor 1
RGD ID: 1321911
HGNC Page HGNC:16200
Description: Enables RNA polymerase II C-terminal domain phosphoserine binding activity; S-adenosyl-L-methionine binding activity; and mRNA (2'-O-methyladenosine-N6-)-methyltransferase activity. Involved in negative regulation of translation and positive regulation of translation. Located in intercellular bridge; microtubule cytoskeleton; and nucleoplasm.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: C20orf67; cap-specific adenosine methyltransferase; CAPAM; hCAPAM; hPCIF1; mRNA (2'-O-methyladenosine-N(6)-)-methyltransferase; MT-A70; PDX-1 C terminus-interacting factor 1; PDX1 C-terminal inhibiting factor 1; phosphorylated CTD-interacting factor 1; PPP1R121
RGD Orthologs
Mouse
Rat
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382045,934,683 - 45,948,020 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2045,934,683 - 45,948,023 (+)EnsemblGRCh38hg38GRCh38
GRCh372044,563,322 - 44,576,659 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362043,996,724 - 44,010,069 (+)NCBINCBI36Build 36hg18NCBI36
Build 342043,996,723 - 44,010,067NCBI
Celera2041,274,773 - 41,288,119 (+)NCBICelera
Cytogenetic Map20q13.12NCBI
HuRef2041,304,981 - 41,318,131 (+)NCBIHuRef
CHM1_12044,466,000 - 44,479,319 (+)NCBICHM1_1
T2T-CHM13v2.02047,670,740 - 47,684,073 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Phenotype Annotations     Click to see Annotation Detail View

Human Phenotype
References

References - curated
# Reference Title Reference Citation
1. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
2. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:11780052   PMID:12477932   PMID:12565871   PMID:14702039   PMID:15121856   PMID:15489334   PMID:17126328   PMID:18029348   PMID:18294453   PMID:19060906   PMID:19389623   PMID:19682092  
PMID:21832049   PMID:21873635   PMID:26496610   PMID:28036027   PMID:29395067   PMID:29676528   PMID:30467178   PMID:30487554   PMID:31279658   PMID:31279659   PMID:31822664   PMID:32814042  
PMID:33428944   PMID:33961781   PMID:34079125   PMID:34266951   PMID:34545078   PMID:34634806   PMID:35189146   PMID:35868483   PMID:35944360   PMID:36215168   PMID:36514940   PMID:37643007  
PMID:37689310   PMID:38526325  


Genomics

Comparative Map Data
PCIF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382045,934,683 - 45,948,020 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2045,934,683 - 45,948,023 (+)EnsemblGRCh38hg38GRCh38
GRCh372044,563,322 - 44,576,659 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 362043,996,724 - 44,010,069 (+)NCBINCBI36Build 36hg18NCBI36
Build 342043,996,723 - 44,010,067NCBI
Celera2041,274,773 - 41,288,119 (+)NCBICelera
Cytogenetic Map20q13.12NCBI
HuRef2041,304,981 - 41,318,131 (+)NCBIHuRef
CHM1_12044,466,000 - 44,479,319 (+)NCBICHM1_1
T2T-CHM13v2.02047,670,740 - 47,684,073 (+)NCBIT2T-CHM13v2.0
Pcif1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392164,721,288 - 164,733,360 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl2164,721,224 - 164,736,374 (+)EnsemblGRCm39 Ensembl
GRCm382164,879,368 - 164,891,440 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2164,879,304 - 164,894,454 (+)EnsemblGRCm38mm10GRCm38
MGSCv372164,704,868 - 164,716,937 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv362164,570,573 - 164,582,642 (+)NCBIMGSCv36mm8
Celera2170,816,601 - 170,828,684 (+)NCBICelera
Cytogenetic Map2H3NCBI
cM Map285.27NCBI
Pcif1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83174,033,471 - 174,046,403 (+)NCBIGRCr8
mRatBN7.23153,614,147 - 153,627,079 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3153,614,147 - 153,627,079 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx3157,422,576 - 157,435,503 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03165,921,550 - 165,934,477 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03163,665,323 - 163,678,250 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.03161,343,883 - 161,356,815 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3161,343,883 - 161,356,815 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.03167,528,503 - 167,541,435 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43155,914,227 - 155,927,159 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.13155,821,464 - 155,833,176 (+)NCBI
Celera3152,219,717 - 152,232,649 (+)NCBICelera
Cytogenetic Map3q42NCBI
Pcif1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495544511,355,227 - 11,368,392 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495544511,355,227 - 11,368,392 (-)NCBIChiLan1.0ChiLan1.0
PCIF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v22151,676,010 - 51,689,424 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan12051,669,169 - 51,682,535 (+)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v02042,273,443 - 42,286,885 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.12043,360,219 - 43,373,956 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2043,360,219 - 43,374,593 (+)Ensemblpanpan1.1panPan2
PCIF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12433,214,370 - 33,225,922 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2433,214,419 - 33,226,732 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2432,740,403 - 32,752,784 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02433,923,867 - 33,936,241 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2433,924,726 - 33,936,276 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12433,182,148 - 33,194,524 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02433,297,465 - 33,309,839 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02433,836,439 - 33,848,821 (+)NCBIUU_Cfam_GSD_1.0
Pcif1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024408640191,636,744 - 191,645,564 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365147,091,140 - 7,103,124 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365147,090,367 - 7,103,124 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
PCIF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1748,120,599 - 48,132,620 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11748,120,263 - 48,132,003 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21753,760,285 - 53,771,889 (+)NCBISscrofa10.2Sscrofa10.2susScr3
PCIF1
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1217,938,156 - 17,953,289 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl217,938,423 - 17,948,425 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366605066,573,899 - 66,586,931 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Pcif1
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046247908,647,317 - 8,660,080 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046247908,647,292 - 8,660,138 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in PCIF1
33 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 20q13.12-13.33(chr20:44787704-64277321)x3 copy number gain See cases [RCV000053035] Chr20:44787704..64277321 [GRCh38]
Chr20:43416345..62908674 [GRCh37]
Chr20:42849759..62379118 [NCBI36]
Chr20:20q13.12-13.33		 pathogenic
NM_022104.3(PCIF1):c.1693G>T (p.Val565Phe) single nucleotide variant Malignant melanoma [RCV000063757] Chr20:45947152 [GRCh38]
Chr20:44575791 [GRCh37]
Chr20:44009198 [NCBI36]
Chr20:20q13.12		 not provided
NM_022095.3(ZNF335):c.3992G>A (p.Gly1331Asp) single nucleotide variant Malignant melanoma [RCV000063758] Chr20:45948990 [GRCh38]
Chr20:44577629 [GRCh37]
Chr20:44011036 [NCBI36]
Chr20:20q13.12		 not provided
NM_022095.3(ZNF335):c.3991G>A (p.Gly1331Ser) single nucleotide variant Malignant melanoma [RCV000063759] Chr20:45948991 [GRCh38]
Chr20:44577630 [GRCh37]
Chr20:44011037 [NCBI36]
Chr20:20q13.12		 not provided
NM_022095.3(ZNF335):c.3664A>T (p.Asn1222Tyr) single nucleotide variant Malignant melanoma [RCV000063760] Chr20:45949805 [GRCh38]
Chr20:44578444 [GRCh37]
Chr20:44011851 [NCBI36]
Chr20:20q13.12		 not provided
GRCh38/hg38 20p13-q13.33(chr20:99557-64277321)x3 copy number gain See cases [RCV000135859] Chr20:99557..64277321 [GRCh38]
Chr20:80198..62908674 [GRCh37]
Chr20:28198..62379118 [NCBI36]
Chr20:20p13-q13.33		 pathogenic
GRCh38/hg38 20q11.22-13.12(chr20:35237946-47631818)x1 copy number loss See cases [RCV000140816] Chr20:35237946..47631818 [GRCh38]
Chr20:33825749..46260562 [GRCh37]
Chr20:33289165..45693969 [NCBI36]
Chr20:20q11.22-13.12		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:61569-62915555)x3 copy number gain See cases [RCV000510832] Chr20:61569..62915555 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
NM_022104.4(PCIF1):c.979C>T (p.His327Tyr) single nucleotide variant not specified [RCV004312127] Chr20:45943739 [GRCh38]
Chr20:44572378 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.2065C>T (p.Arg689Trp) single nucleotide variant not specified [RCV004296460] Chr20:45947705 [GRCh38]
Chr20:44576344 [GRCh37]
Chr20:20q13.12		 uncertain significance
GRCh37/hg19 20p13-q13.33(chr20:61569-62915555) copy number gain See cases [RCV000512450] Chr20:61569..62915555 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62961294)x3 copy number gain not provided [RCV000741059] Chr20:63244..62961294 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62912463)x3 copy number gain not provided [RCV000741057] Chr20:63244..62912463 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
GRCh37/hg19 20p13-q13.33(chr20:63244-62948788)x3 copy number gain not provided [RCV000741058] Chr20:63244..62948788 [GRCh37]
Chr20:20p13-q13.33		 pathogenic
NM_022104.4(PCIF1):c.1582C>T (p.Pro528Ser) single nucleotide variant not specified [RCV004301867] Chr20:45946353 [GRCh38]
Chr20:44574992 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.2082G>C (p.Glu694Asp) single nucleotide variant not specified [RCV004315822] Chr20:45947722 [GRCh38]
Chr20:44576361 [GRCh37]
Chr20:20q13.12		 uncertain significance
Single allele deletion Focal-onset seizure [RCV001004039] Chr20:34980430..46806549 [GRCh37]
Chr20:20q11.23-13.13		 likely pathogenic
GRCh37/hg19 20q13.12-13.13(chr20:42985044-48599046)x1 copy number loss Developmental and epileptic encephalopathy, 26 [RCV001801198] Chr20:42985044..48599046 [GRCh37]
Chr20:20q13.12-13.13		 pathogenic
NC_000020.10:g.(?_42223339)_(44638757_?)del deletion Combined immunodeficiency due to STK4 deficiency [RCV003109483] Chr20:42223339..44638757 [GRCh37]
Chr20:20q13.12		 pathogenic
NM_022104.4(PCIF1):c.2051C>T (p.Ser684Leu) single nucleotide variant not specified [RCV004100981] Chr20:45947691 [GRCh38]
Chr20:44576330 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.307A>C (p.Thr103Pro) single nucleotide variant not specified [RCV004108621] Chr20:45940532 [GRCh38]
Chr20:44569171 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.644A>G (p.His215Arg) single nucleotide variant not specified [RCV004121308] Chr20:45941178 [GRCh38]
Chr20:44569817 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.616T>G (p.Ser206Ala) single nucleotide variant not specified [RCV004112076] Chr20:45941150 [GRCh38]
Chr20:44569789 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.916C>T (p.Pro306Ser) single nucleotide variant not specified [RCV004100301] Chr20:45943676 [GRCh38]
Chr20:44572315 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.1882A>C (p.Lys628Gln) single nucleotide variant not specified [RCV004167677] Chr20:45947437 [GRCh38]
Chr20:44576076 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.1964C>T (p.Pro655Leu) single nucleotide variant not specified [RCV004099816] Chr20:45947604 [GRCh38]
Chr20:44576243 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.1808G>A (p.Arg603His) single nucleotide variant not specified [RCV004114031] Chr20:45947363 [GRCh38]
Chr20:44576002 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.59C>T (p.Pro20Leu) single nucleotide variant not specified [RCV004148565] Chr20:45939058 [GRCh38]
Chr20:44567697 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.2014C>T (p.Arg672Cys) single nucleotide variant not specified [RCV004198573] Chr20:45947654 [GRCh38]
Chr20:44576293 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.1045G>A (p.Val349Ile) single nucleotide variant not specified [RCV004157759] Chr20:45944907 [GRCh38]
Chr20:44573546 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.24C>G (p.Ser8Arg) single nucleotide variant not specified [RCV004203225] Chr20:45939023 [GRCh38]
Chr20:44567662 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.1537G>A (p.Ala513Thr) single nucleotide variant not specified [RCV004176288] Chr20:45946308 [GRCh38]
Chr20:44574947 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.1697C>T (p.Ser566Phe) single nucleotide variant not specified [RCV004089326] Chr20:45947156 [GRCh38]
Chr20:44575795 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.1322G>A (p.Arg441His) single nucleotide variant not specified [RCV004310155] Chr20:45945864 [GRCh38]
Chr20:44574503 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.1727C>T (p.Pro576Leu) single nucleotide variant not specified [RCV004259696] Chr20:45947282 [GRCh38]
Chr20:44575921 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.1269G>A (p.Met423Ile) single nucleotide variant not specified [RCV004277071] Chr20:45945811 [GRCh38]
Chr20:44574450 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.505C>A (p.Leu169Ile) single nucleotide variant not specified [RCV004309833] Chr20:45940926 [GRCh38]
Chr20:44569565 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.1939G>A (p.Asp647Asn) single nucleotide variant not specified [RCV004334382] Chr20:45947579 [GRCh38]
Chr20:44576218 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.112C>G (p.Gln38Glu) single nucleotide variant not specified [RCV004347581] Chr20:45939111 [GRCh38]
Chr20:44567750 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.31G>A (p.Glu11Lys) single nucleotide variant not specified [RCV004353553] Chr20:45939030 [GRCh38]
Chr20:44567669 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.560A>G (p.Lys187Arg) single nucleotide variant not specified [RCV004335973] Chr20:45941094 [GRCh38]
Chr20:44569733 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.1418G>A (p.Arg473Gln) single nucleotide variant not specified [RCV004500631] Chr20:45946105 [GRCh38]
Chr20:44574744 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.1796T>C (p.Met599Thr) single nucleotide variant not specified [RCV004500632] Chr20:45947351 [GRCh38]
Chr20:44575990 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.226G>A (p.Val76Met) single nucleotide variant not specified [RCV004500635] Chr20:45939316 [GRCh38]
Chr20:44567955 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.1049C>T (p.Ser350Leu) single nucleotide variant not specified [RCV004500628] Chr20:45944911 [GRCh38]
Chr20:44573550 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.2018G>A (p.Ser673Asn) single nucleotide variant not specified [RCV004500634] Chr20:45947658 [GRCh38]
Chr20:44576297 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.1295A>G (p.Tyr432Cys) single nucleotide variant not specified [RCV004500630] Chr20:45945837 [GRCh38]
Chr20:44574476 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.454A>C (p.Thr152Pro) single nucleotide variant not specified [RCV004500637] Chr20:45940875 [GRCh38]
Chr20:44569514 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.649C>T (p.Arg217Trp) single nucleotide variant not specified [RCV004500639] Chr20:45941183 [GRCh38]
Chr20:44569822 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.625A>G (p.Ile209Val) single nucleotide variant not specified [RCV004500638] Chr20:45941159 [GRCh38]
Chr20:44569798 [GRCh37]
Chr20:20q13.12		 uncertain significance
NM_022104.4(PCIF1):c.8A>G (p.Asn3Ser) single nucleotide variant not specified [RCV004500640] Chr20:45939007 [GRCh38]
Chr20:44567646 [GRCh37]
Chr20:20q13.12		 uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:714
Count of miRNA genes:488
Interacting mature miRNAs:541
Transcripts:ENST00000372409, ENST00000479348
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
SHGC-78139  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372044,565,871 - 44,566,211UniSTSGRCh37
Build 362043,999,278 - 43,999,618RGDNCBI36
Celera2041,277,328 - 41,277,668RGD
Cytogenetic Map20q13.12UniSTS
HuRef2041,307,345 - 41,307,685UniSTS
TNG Radiation Hybrid Map2020878.0UniSTS
STS-Z40713  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372044,576,547 - 44,576,638UniSTSGRCh37
Build 362044,009,954 - 44,010,045RGDNCBI36
Celera2041,288,004 - 41,288,095RGD
Cytogenetic Map20q13.12UniSTS
HuRef2041,318,016 - 41,318,107UniSTS
GeneMap99-GB4 RH Map20291.19UniSTS
NCBI RH Map20463.6UniSTS


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 2427 2853 1550 450 1922 292 4353 2093 3324 404 1447 1608 171 1204 2787 3
Low 5 131 173 172 26 172 2 100 384 14 1 1 1
Below cutoff

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_022104 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011528980 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_011528981 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017028013 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017028014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_047440368 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054323822 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054323823 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054323824 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_054323825 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_008485291 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_936605 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AB050014 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK056553 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AK299435 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL137473 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  AL162458 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC010005 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC013365 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BQ020621 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BQ684226 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH471077 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CP068258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENST00000372409   ⟹   ENSP00000361486
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2045,934,683 - 45,948,020 (+)Ensembl
RefSeq Acc Id: ENST00000479348   ⟹   ENSP00000480607
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2045,945,007 - 45,948,023 (+)Ensembl
RefSeq Acc Id: ENST00000616084
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2045,934,733 - 45,937,972 (+)Ensembl
RefSeq Acc Id: NM_022104   ⟹   NP_071387
RefSeq Status: VALIDATED
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382045,934,683 - 45,948,020 (+)NCBI
GRCh372044,563,313 - 44,576,732 (+)NCBI
Build 362043,996,724 - 44,010,069 (+)NCBI Archive
Celera2041,274,773 - 41,288,119 (+)RGD
HuRef2041,304,981 - 41,318,131 (+)RGD
CHM1_12044,466,000 - 44,479,319 (+)NCBI
T2T-CHM13v2.02047,670,740 - 47,684,073 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011528980   ⟹   XP_011527282
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382045,934,683 - 45,948,020 (+)NCBI
Sequence:
RefSeq Acc Id: XM_011528981   ⟹   XP_011527283
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382045,935,282 - 45,948,020 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017028013   ⟹   XP_016883502
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382045,935,199 - 45,948,020 (+)NCBI
Sequence:
RefSeq Acc Id: XM_047440368   ⟹   XP_047296324
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382045,943,209 - 45,948,020 (+)NCBI
RefSeq Acc Id: XM_054323822   ⟹   XP_054179797
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.02047,670,740 - 47,684,073 (+)NCBI
RefSeq Acc Id: XM_054323823   ⟹   XP_054179798
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.02047,671,339 - 47,684,073 (+)NCBI
RefSeq Acc Id: XM_054323824   ⟹   XP_054179799
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.02047,671,256 - 47,684,073 (+)NCBI
RefSeq Acc Id: XM_054323825   ⟹   XP_054179800
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.02047,679,266 - 47,684,073 (+)NCBI
RefSeq Acc Id: XR_008485291
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
T2T-CHM13v2.02047,670,740 - 47,682,356 (+)NCBI
RefSeq Acc Id: XR_936605
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382045,934,683 - 45,946,299 (+)NCBI
Sequence:
Reference Protein Sequences
RefSeq Acc Id: NP_071387   ⟸   NM_022104
- UniProtKB: Q54AB9 (UniProtKB/Swiss-Prot),   E1P5P1 (UniProtKB/Swiss-Prot),   Q9NT85 (UniProtKB/Swiss-Prot),   Q9H4Z3 (UniProtKB/Swiss-Prot),   B7Z5U5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011527282   ⟸   XM_011528980
- Peptide Label: isoform X1
- UniProtKB: Q54AB9 (UniProtKB/Swiss-Prot),   E1P5P1 (UniProtKB/Swiss-Prot),   Q9NT85 (UniProtKB/Swiss-Prot),   Q9H4Z3 (UniProtKB/Swiss-Prot),   B7Z5U5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_011527283   ⟸   XM_011528981
- Peptide Label: isoform X1
- UniProtKB: Q54AB9 (UniProtKB/Swiss-Prot),   E1P5P1 (UniProtKB/Swiss-Prot),   Q9NT85 (UniProtKB/Swiss-Prot),   Q9H4Z3 (UniProtKB/Swiss-Prot),   B7Z5U5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_016883502   ⟸   XM_017028013
- Peptide Label: isoform X1
- UniProtKB: Q54AB9 (UniProtKB/Swiss-Prot),   E1P5P1 (UniProtKB/Swiss-Prot),   Q9NT85 (UniProtKB/Swiss-Prot),   Q9H4Z3 (UniProtKB/Swiss-Prot),   B7Z5U5 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSP00000361486   ⟸   ENST00000372409
RefSeq Acc Id: ENSP00000480607   ⟸   ENST00000479348
RefSeq Acc Id: XP_047296324   ⟸   XM_047440368
- Peptide Label: isoform X2
RefSeq Acc Id: XP_054179797   ⟸   XM_054323822
- Peptide Label: isoform X1
- UniProtKB: Q9H4Z3 (UniProtKB/Swiss-Prot),   Q54AB9 (UniProtKB/Swiss-Prot),   E1P5P1 (UniProtKB/Swiss-Prot),   Q9NT85 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_054179799   ⟸   XM_054323824
- Peptide Label: isoform X1
- UniProtKB: Q9H4Z3 (UniProtKB/Swiss-Prot),   Q54AB9 (UniProtKB/Swiss-Prot),   E1P5P1 (UniProtKB/Swiss-Prot),   Q9NT85 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_054179798   ⟸   XM_054323823
- Peptide Label: isoform X1
- UniProtKB: Q9H4Z3 (UniProtKB/Swiss-Prot),   Q54AB9 (UniProtKB/Swiss-Prot),   E1P5P1 (UniProtKB/Swiss-Prot),   Q9NT85 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: XP_054179800   ⟸   XM_054323825
- Peptide Label: isoform X2
Protein Domains
PCIF1 WW   WW

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q9H4Z3-F1-model_v2 AlphaFold Q9H4Z3 1-704 view protein structure

Promoters
RGD ID:6798885
Promoter ID:HG_KWN:39642
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   CD4+TCell_2Hour,   HeLa_S3,   Jurkat,   K562,   Lymphoblastoid,   NB4
Transcripts:OTTHUMT00000079550
Position:
Human AssemblyChrPosition (strand)Source
Build 362043,995,911 - 43,996,697 (+)MPROMDB
RGD ID:6798886
Promoter ID:HG_KWN:39643
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   K562,   Lymphoblastoid,   NB4
Transcripts:UC002XQT.2
Position:
Human AssemblyChrPosition (strand)Source
Build 362044,005,991 - 44,007,412 (+)MPROMDB
RGD ID:6798887
Promoter ID:HG_KWN:39644
Type:CpG-Island
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:CD4+TCell,   CD4+TCell_12Hour,   HeLa_S3,   K562,   Lymphoblastoid,   NB4
Transcripts:UC002XQU.1
Position:
Human AssemblyChrPosition (strand)Source
Build 362044,008,171 - 44,009,562 (+)MPROMDB
RGD ID:13207135
Promoter ID:EPDNEW_H27148
Type:initiation region
Name:PCIF1_1
Description:PDX1 C-terminal inhibiting factor 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh382045,934,698 - 45,934,758EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:16200 AgrOrtholog
COSMIC PCIF1 COSMIC
Ensembl Genes ENSG00000100982 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENST00000372409 ENTREZGENE
  ENST00000372409.8 UniProtKB/Swiss-Prot
  ENST00000479348.2 UniProtKB/TrEMBL
Gene3D-CATH 1.20.1270.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  2.20.70.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
GTEx ENSG00000100982 GTEx
HGNC ID HGNC:16200 ENTREZGENE
Human Proteome Map PCIF1 Human Proteome Map
InterPro HSP70_C_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PCIF1-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PCIF1_WW UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WW_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  WW_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report hsa:63935 UniProtKB/Swiss-Prot
NCBI Gene 63935 ENTREZGENE
OMIM 618626 OMIM
PANTHER MRNA (2'-O-METHYLADENOSINE-N(6)-)-METHYLTRANSFERASE UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR21727 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PCIF1_WW UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PF00397 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PharmGKB PA162398977 PharmGKB
PROSITE WW_DOMAIN_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART SM00456 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF51045 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A087WWZ2_HUMAN UniProtKB/TrEMBL
  B7Z5U5 ENTREZGENE, UniProtKB/TrEMBL
  CAPAM_HUMAN UniProtKB/Swiss-Prot
  E1P5P1 ENTREZGENE
  Q54AB9 ENTREZGENE
  Q9H4Z3 ENTREZGENE
  Q9NT85 ENTREZGENE
UniProt Secondary E1P5P1 UniProtKB/Swiss-Prot
  Q54AB9 UniProtKB/Swiss-Prot
  Q9NT85 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2020-08-31 PCIF1  phosphorylated CTD interacting factor 1  PCIF1  PDX1 C-terminal inhibiting factor 1  Symbol and/or name change 19259463 PROVISIONAL