IGF2BP2-AS1 (IGF2BP2 antisense RNA 1) - Rat Genome Database

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Gene: IGF2BP2-AS1 (IGF2BP2 antisense RNA 1) Homo sapiens
Analyze
Symbol: IGF2BP2-AS1
Name: IGF2BP2 antisense RNA 1
RGD ID: 1602599
HGNC Page HGNC:32674
Description: ASSOCIATED WITH Currarino syndrome; INTERACTS WITH 2-hydroxypropanoic acid; DDE; propofol
Type: ncrna (Ensembl: lncRNA)
RefSeq Status: VALIDATED
Previously known as: C3orf65; FLJ32900
Allele / Splice: See ClinVar data
Latest Assembly: GRCh38 - Human Genome Assembly GRCh38
Position:
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh383185,713,252 - 185,729,787 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl3185,712,528 - 185,729,787 (+)EnsemblGRCh38hg38GRCh38
GRCh373185,431,040 - 185,447,575 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 363186,913,774 - 186,918,649 (+)NCBINCBI36Build 36hg18NCBI36
Celera3183,868,956 - 183,873,871 (+)NCBICelera
Cytogenetic Map3q27.2NCBI
HuRef3182,841,421 - 182,846,336 (+)NCBIHuRef
CHM1_13185,394,000 - 185,398,915 (+)NCBICHM1_1
T2T-CHM13v2.03188,529,170 - 188,545,707 (+)NCBIT2T-CHM13v2.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
References
Additional References at PubMed
PMID:12477932   PMID:14702039   PMID:34637162  


Genomics

Variants

.
Variants in IGF2BP2-AS1
2 total Variants

Clinical Variants
Name Type Condition(s) Position(s) Clinical significance
GRCh38/hg38 3q27.2(chr3:185506271-185977882)x1 copy number loss See cases [RCV000133801] Chr3:185506271..185977882 [GRCh38]
Chr3:185224059..185695671 [GRCh37]
Chr3:186706753..187178365 [NCBI36]
Chr3:3q27.2		 pathogenic
GRCh38/hg38 3q13.11-29(chr3:103426882-198110178)x3 copy number gain See cases [RCV000134948] Chr3:103426882..198110178 [GRCh38]
Chr3:103145726..197837049 [GRCh37]
Chr3:104628416..199321446 [NCBI36]
Chr3:3q13.11-29		 pathogenic
GRCh38/hg38 3q26.2-29(chr3:168167568-198110178)x3 copy number gain See cases [RCV000137106] Chr3:168167568..198110178 [GRCh38]
Chr3:167885356..197837049 [GRCh37]
Chr3:169368050..199321446 [NCBI36]
Chr3:3q26.2-29		 pathogenic
GRCh38/hg38 3q26.32-29(chr3:176439911-198118383)x3 copy number gain See cases [RCV000138009] Chr3:176439911..198118383 [GRCh38]
Chr3:176157699..197845254 [GRCh37]
Chr3:177640393..199329651 [NCBI36]
Chr3:3q26.32-29		 pathogenic|likely benign
GRCh38/hg38 3q26.32-29(chr3:176168525-198118383)x3 copy number gain See cases [RCV000138662] Chr3:176168525..198118383 [GRCh38]
Chr3:175886313..197845254 [GRCh37]
Chr3:177369007..199329651 [NCBI36]
Chr3:3q26.32-29		 pathogenic
GRCh38/hg38 3q25.1-29(chr3:152100512-198118383)x3 copy number gain See cases [RCV000139435] Chr3:152100512..198118383 [GRCh38]
Chr3:151818301..197845254 [GRCh37]
Chr3:153300991..199329651 [NCBI36]
Chr3:3q25.1-29		 pathogenic
GRCh38/hg38 3q27.2-27.3(chr3:184843627-187461008)x3 copy number gain See cases [RCV000139009] Chr3:184843627..187461008 [GRCh38]
Chr3:184561415..187178796 [GRCh37]
Chr3:186044109..188661490 [NCBI36]
Chr3:3q27.2-27.3		 pathogenic
GRCh38/hg38 3q27.1-27.2(chr3:184010704-186288926)x1 copy number loss See cases [RCV000139917] Chr3:184010704..186288926 [GRCh38]
Chr3:183728492..186006715 [GRCh37]
Chr3:185211186..187489409 [NCBI36]
Chr3:3q27.1-27.2		 likely pathogenic
GRCh38/hg38 3q25.31-29(chr3:156321878-198113452)x3 copy number gain See cases [RCV000140849] Chr3:156321878..198113452 [GRCh38]
Chr3:156039667..197840323 [GRCh37]
Chr3:157522361..199324720 [NCBI36]
Chr3:3q25.31-29		 pathogenic
GRCh38/hg38 3q25.31-29(chr3:156118441-198125115)x3 copy number gain See cases [RCV000142310] Chr3:156118441..198125115 [GRCh38]
Chr3:155836230..197851986 [GRCh37]
Chr3:157318924..199336383 [NCBI36]
Chr3:3q25.31-29		 pathogenic
GRCh38/hg38 3q26.33-27.3(chr3:182319764-186443121)x1 copy number loss See cases [RCV000142154] Chr3:182319764..186443121 [GRCh38]
Chr3:182037552..186160910 [GRCh37]
Chr3:183520246..187643604 [NCBI36]
Chr3:3q26.33-27.3		 likely pathogenic
GRCh38/hg38 3q26.1-28(chr3:167717962-188365272)x3 copy number gain See cases [RCV000142107] Chr3:167717962..188365272 [GRCh38]
Chr3:167435750..188083060 [GRCh37]
Chr3:168918444..189565754 [NCBI36]
Chr3:3q26.1-28		 likely pathogenic
GRCh38/hg38 3q26.33-28(chr3:181138664-192512023)x1 copy number loss See cases [RCV000142019] Chr3:181138664..192512023 [GRCh38]
Chr3:180856452..192229812 [GRCh37]
Chr3:182339146..193712506 [NCBI36]
Chr3:3q26.33-28		 pathogenic
GRCh38/hg38 3q26.1-29(chr3:166137209-198125115)x3 copy number gain See cases [RCV000143694] Chr3:166137209..198125115 [GRCh38]
Chr3:165854997..197851986 [GRCh37]
Chr3:167337691..199336383 [NCBI36]
Chr3:3q26.1-29		 pathogenic
GRCh38/hg38 3q26.33-28(chr3:182678453-188418928)x1 copy number loss See cases [RCV000051607] Chr3:182678453..188418928 [GRCh38]
Chr3:182396241..188136716 [GRCh37]
Chr3:183878935..189619410 [NCBI36]
Chr3:3q26.33-28		 pathogenic
GRCh38/hg38 3q26.32-29(chr3:178411707-198110319)x3 copy number gain See cases [RCV000051736] Chr3:178411707..198110319 [GRCh38]
Chr3:178129495..197837190 [GRCh37]
Chr3:179612189..199321587 [NCBI36]
Chr3:3q26.32-29		 pathogenic
GRCh38/hg38 3q27.2-29(chr3:185485849-198110178)x1 copy number loss See cases [RCV000051608] Chr3:185485849..198110178 [GRCh38]
Chr3:185203637..197837049 [GRCh37]
Chr3:186686331..199321446 [NCBI36]
Chr3:3q27.2-29		 pathogenic
GRCh38/hg38 3q22.3-29(chr3:137126982-198110178)x3 copy number gain Developmental Delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051723]|Developmental delay and additional significant developmental and morphological phenotypes referred for genetic testing [RCV000051723]|See cases [RCV000051723] Chr3:137126982..198110178 [GRCh38]
Chr3:136845824..197837049 [GRCh37]
Chr3:138328514..199321446 [NCBI36]
Chr3:3q22.3-29		 pathogenic
GRCh38/hg38 3q24-29(chr3:147521892-198096565)x3 copy number gain See cases [RCV000051725] Chr3:147521892..198096565 [GRCh38]
Chr3:147239679..197823436 [GRCh37]
Chr3:148722369..199307833 [NCBI36]
Chr3:3q24-29		 pathogenic
GRCh38/hg38 3q25.31-29(chr3:157293378-198134727)x3 copy number gain See cases [RCV000051726] Chr3:157293378..198134727 [GRCh38]
Chr3:157011167..197861598 [GRCh37]
Chr3:158493861..199345995 [NCBI36]
Chr3:3q25.31-29		 pathogenic
NC_000003.12:g.177772523_185716872dup duplication Currarino triad [RCV000417195] Chr3:177772523..185716872 [GRCh38]
Chr3:3q26.32-27.2		 likely pathogenic
GRCh38/hg38 3q27.1-27.2(chr3:183020090-185760128)x1 copy number loss Fetal growth restriction [RCV004574943] Chr3:183020090..185760128 [GRCh38]
Chr3:3q27.1-27.2		 pathogenic
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:1256
Count of miRNA genes:743
Interacting mature miRNAs:830
Transcripts:ENST00000296270, ENST00000456447, ENST00000465364, ENST00000470754, ENST00000496717
Prediction methods:Microtar, 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 (GRCh38)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
597297576GWAS1393650_HBMI-adjusted hip circumference QTL GWAS1393650 (human)2e-14BMI-adjusted hip circumferencehip circumference (CMO:0000014)3185715651185715652Human
597537444GWAS1633518_Hbody height QTL GWAS1633518 (human)1e-09body height (VT:0001253)body height (CMO:0000106)3185729250185729251Human
597063354GWAS1159428_Hbody height QTL GWAS1159428 (human)0.000006body height (VT:0001253)body height (CMO:0000106)3185727297185727298Human


Expression

RNA-SEQ Expression

adipose tissue
alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
entire extraembryonic component
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
676 1133 1216 626 2044 877 1326 1 299 624 178 1452 2419 2322 15 1320 404 1048 1042 128

Sequence


Ensembl Acc Id: ENST00000296270
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3185,713,292 - 185,718,167 (+)Ensembl
Ensembl Acc Id: ENST00000456447
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3185,713,252 - 185,729,787 (+)Ensembl
Ensembl Acc Id: ENST00000465364
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3185,728,244 - 185,728,587 (+)Ensembl
Ensembl Acc Id: ENST00000470754
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3185,712,528 - 185,716,892 (+)Ensembl
Ensembl Acc Id: ENST00000496717
Type: CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh38.p14 Ensembl3185,722,464 - 185,729,787 (+)Ensembl
RefSeq Acc Id: NR_126326
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Human AssemblyChrPosition (strand)Source
GRCh383185,713,252 - 185,729,787 (+)NCBI
CHM1_13185,394,000 - 185,410,509 (+)NCBI
T2T-CHM13v2.03188,529,170 - 188,545,707 (+)NCBI
Sequence:
Protein Sequences
GenBank Protein BAB71499 (Get FASTA)   NCBI Sequence Viewer  
  EAW78212 (Get FASTA)   NCBI Sequence Viewer  
  Q96M15 (Get FASTA)   NCBI Sequence Viewer  

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q96M15-F1-model_v2 AlphaFold Q96M15 1-143 view protein structure

Promoters
RGD ID:15095732
Promoter ID:EPDNEWNC_H546
Type:initiation region
Name:IGF2BP2-AS1_1
Description:IGF2BP2 antisense RNA 1 [Source:HGNC Symbol;Acc:HGNC:32674]
SO ACC ID:SO:0000170
Source:EPDNEWNC (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.; Paired-end sequencing.
Position:
Human AssemblyChrPosition (strand)Source
GRCh383185,728,209 - 185,728,269EPDNEWNC

Additional Information

Database Acc Id Source(s)
COSMIC IGF2BP2-AS1 COSMIC
Ensembl Genes ENSG00000163915 Ensembl, ENTREZGENE
Ensembl Transcript ENST00000456447 ENTREZGENE
GTEx ENSG00000163915 GTEx
HGNC ID HGNC:32674 ENTREZGENE
Human Proteome Map IGF2BP2-AS1 Human Proteome Map
NCBI Gene 646600 ENTREZGENE
RNAcentral URS00007BD98E RNACentral
  URS00007C08DD RNACentral
  URS00007C2D64 RNACentral
  URS00007C5419 RNACentral
  URS00007DBB01 RNACentral
  URS00007E38D8 RNACentral
UniProt IFAS1_HUMAN UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-10-07 IGF2BP2-AS1  IGF2BP2 antisense RNA 1  C3orf65  chromosome 3 open reading frame 65  Symbol and/or name change 5135510 APPROVED