PRAMENP (PRAME N-terminal like, pseudogene) - Rat Genome Database

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Gene: PRAMENP (PRAME N-terminal like, pseudogene) Homo sapiens
Analyze
Symbol: PRAMENP
Name: PRAME N-terminal like, pseudogene
RGD ID: 2293902
HGNC Page HGNC:34302
Description: INTERACTS WITH benzo[a]pyrene; all-trans-retinoic acid (ortholog); mono(2-ethylhexyl) phthalate (ortholog)
Type: pseudo (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: FLJ16327; PRAME N-terminal-like, pseudogene; PRAMEF24P; PRAMEL
RGD Orthologs
Mouse
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
GRCh382221,991,099 - 22,043,934 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2221,991,236 - 21,995,428 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p14 Ensembl2221,991,099 - 22,043,934 (-)EnsemblGRCh38hg38GRCh38
GRCh372222,345,496 - 22,398,332 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362220,675,496 - 20,728,256 (-)NCBINCBI36Build 36hg18NCBI36
Celera226,163,012 - 6,202,911 (-)NCBICelera
Cytogenetic Map22q11.22NCBI
HuRef225,302,547 - 5,355,145 (-)NCBIHuRef
CHM1_12222,345,569 - 22,398,404 (-)NCBICHM1_1
T2T-CHM13v2.02222,404,651 - 22,457,485 (-)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References

Genomics

Comparative Map Data
PRAMENP
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh382221,991,099 - 22,043,934 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl2221,991,236 - 21,995,428 (-)EnsemblGRCh38hg38GRCh38
GRCh38.p14 Ensembl2221,991,099 - 22,043,934 (-)EnsemblGRCh38hg38GRCh38
GRCh372222,345,496 - 22,398,332 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362220,675,496 - 20,728,256 (-)NCBINCBI36Build 36hg18NCBI36
Celera226,163,012 - 6,202,911 (-)NCBICelera
Cytogenetic Map22q11.22NCBI
HuRef225,302,547 - 5,355,145 (-)NCBIHuRef
CHM1_12222,345,569 - 22,398,404 (-)NCBICHM1_1
T2T-CHM13v2.02222,404,651 - 22,457,485 (-)NCBIT2T-CHM13v2.0
Pramel3e
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X134,395,314 - 134,405,504 (+)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX134,395,337 - 134,405,343 (+)EnsemblGRCm39 Ensembl
GRCm38X135,494,554 - 135,504,755 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX135,494,588 - 135,504,594 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X132,029,127 - 132,039,133 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36X130,840,952 - 130,851,118 (+)NCBIMGSCv36mm8
CeleraX118,818,073 - 118,828,076 (+)NCBICelera
Cytogenetic MapXF1NCBI
cM MapX57.12NCBI

Variants

.
Variants in PRAMENP
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 22q11.21-11.23(chr22:21454661-23414686)x3 copy number gain See cases [RCV000148078] Chr22:21454661..23414686 [GRCh38]
Chr22:21808950..23756873 [GRCh37]
Chr22:20138950..22086873 [NCBI36]
Chr22:22q11.21-11.23
uncertain significance
GRCh38/hg38 22q11.21-11.22(chr22:21454661-22562663)x1 copy number loss See cases [RCV000148145] Chr22:21454661..22562663 [GRCh38]
Chr22:21808950..22905068 [GRCh37]
Chr22:20138950..21235068 [NCBI36]
Chr22:22q11.21-11.22
pathogenic
GRCh38/hg38 22q11.21-11.23(chr22:20726772-23135971)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053061]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053061]|See cases [RCV000053061] Chr22:20726772..23135971 [GRCh38]
Chr22:21081060..23478158 [GRCh37]
Chr22:19411060..21808158 [NCBI36]
Chr22:22q11.21-11.23
pathogenic
GRCh38/hg38 22q11.21-11.23(chr22:21454661-24289119)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053079]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053079]|See cases [RCV000053079] Chr22:21454661..24289119 [GRCh38]
Chr22:21808950..24685087 [GRCh37]
Chr22:20138950..23015087 [NCBI36]
Chr22:22q11.21-11.23
pathogenic
GRCh38/hg38 22q11.21-11.23(chr22:21454661-24197852)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053084]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053084]|See cases [RCV000053084] Chr22:21454661..24197852 [GRCh38]
Chr22:21808950..24593820 [GRCh37]
Chr22:20138950..22923820 [NCBI36]
Chr22:22q11.21-11.23
pathogenic
GRCh38/hg38 22q11.21-11.23(chr22:21454661-23301036)x1 copy number loss Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053085]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053085]|See cases [RCV000053085] Chr22:21454661..23301036 [GRCh38]
Chr22:21808950..23643223 [GRCh37]
Chr22:20138950..21973223 [NCBI36]
Chr22:22q11.21-11.23
pathogenic
GRCh38/hg38 22q11.21-11.22(chr22:21150869-22562804)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053157]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000053157]|See cases [RCV000053157] Chr22:21150869..22562804 [GRCh38]
Chr22:21505158..22905209 [GRCh37]
Chr22:19835158..21235209 [NCBI36]
Chr22:22q11.21-11.22
uncertain significance
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:884
Count of miRNA genes:375
Interacting mature miRNAs:403
Transcripts:ENST00000337471, ENST00000419303, ENST00000546598, ENST00000548391
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.

Markers in Region
RH48655  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372222,354,859 - 22,354,980UniSTSGRCh37
Build 362220,684,859 - 20,684,980RGDNCBI36
Celera226,172,375 - 6,172,496RGD
Cytogenetic Map22q11.22UniSTS
HuRef225,311,857 - 5,311,978UniSTS
GeneMap99-GB4 RH Map2237.68UniSTS
NCBI RH Map2249.4UniSTS
UniSTS:146579  
Human AssemblyChrPosition (strand)SourceJBrowse
GRCh372222,398,379 - 22,398,729UniSTSGRCh37
Build 362220,728,379 - 20,728,729RGDNCBI36
Celera226,215,896 - 6,216,246RGD
HuRef225,355,192 - 5,355,542UniSTS


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
High
Medium 5 1 114 1 2 1 1
Low 132 97 88 56 786 56 2 2 34 362 50 6
Below cutoff 745 976 590 390 821 275 660 281 621 145 305 582 115 330 428

Sequence


RefSeq Acc Id: ENST00000337471
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2221,991,100 - 22,043,934 (-)Ensembl
RefSeq Acc Id: ENST00000419303
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2221,991,099 - 22,043,858 (-)Ensembl
RefSeq Acc Id: ENST00000548391
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl2221,991,236 - 21,995,428 (-)Ensembl
RefSeq Acc Id: NR_135291
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh382221,991,099 - 22,043,934 (-)NCBI
CHM1_12222,345,569 - 22,398,404 (-)NCBI
T2T-CHM13v2.02222,404,651 - 22,457,485 (-)NCBI
Sequence:
Protein Sequences
GenBank Protein BAD18485 (Get FASTA)   NCBI Sequence Viewer  

Promoters
RGD ID:6800094
Promoter ID:HG_KWN:41802
Type:Non-CpG
SO ACC ID:SO:0000170
Source:MPROMDB
Tissues & Cell Lines:K562,   Lymphoblastoid
Transcripts:ENST00000337471,   OTTHUMT00000320277
Position:
Human AssemblyChrPosition (strand)Source
Build 362220,728,056 - 20,728,556 (-)MPROMDB

Additional Information

Database Acc Id Source(s)
AGR Gene HGNC:34302 AgrOrtholog
COSMIC PRAMENP COSMIC
Ensembl Genes ENSG00000197549 Ensembl
  ENSG00000290847 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000337471 ENTREZGENE
GTEx ENSG00000197549 GTEx
  ENSG00000290847 GTEx
HGNC ID HGNC:34302 ENTREZGENE
Human Proteome Map PRAMENP Human Proteome Map
NCBI Gene 649179 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-02-26 PRAMENP  PRAME N-terminal like, pseudogene    PRAME N-terminal-like, pseudogene  Symbol and/or name change 5135510 APPROVED
2016-02-29 PRAMENP  PRAME N-terminal-like, pseudogene  PRAMEL  preferentially expressed antigen in melanoma-like  Symbol and/or name change 5135510 APPROVED