Ighmbp2 immunoglobulin mu DNA binding protein 2 [Rattus norvegicus (Norway rat)] - Gene

Summary

Official Symbol: Ighmbp2provided by RGD
Official Full Name: immunoglobulin mu DNA binding protein 2provided by RGD
Primary source: RGD:68325
See related: Ensembl:ENSRNOG00000013456 AllianceGenome:RGD:68325
Gene type: protein coding
RefSeq status: PROVISIONAL
Organism: Rattus norvegicus
Lineage: Eukaryota; Metazoa; Chordata; Craniata; Vertebrata; Euteleostomi; Mammalia; Eutheria; Euarchontoglires; Glires; Rodentia; Myomorpha; Muroidea; Muridae; Murinae; Rattus
Also known as: AEP
Summary: Enables RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Involved in negative regulation of transcription by RNA polymerase II. Predicted to be located in several cellular components, including growth cone; neuronal cell body; and nuclear body. Predicted to be part of ribonucleoprotein complex. Predicted to be active in cytoplasm and nucleus. Human ortholog(s) of this gene implicated in Charcot-Marie-Tooth disease axonal type 2S and distal spinal muscular atrophy 1. Orthologous to human IGHMBP2 (immunoglobulin mu DNA binding protein 2). [provided by Alliance of Genome Resources, Apr 2022]
Expression: Biased expression in Brain (RPKM 55.0), Thymus (RPKM 49.5) and 9 other tissues See more
Orthologs: human mouse all
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Genomic context

Location:: 1q42

Exon count:: 15

Annotation release	Status	Assembly	Chr	Location
RS_2024_02	current	GRCr8 (GCF_036323735.1)	1	NC_086019.1 (209935922..209958570, complement)
RS_2023_06	previous assembly	mRatBN7.2 (GCF_015227675.2)	1	NC_051336.1 (200506641..200529293, complement)
106	previous assembly	Rnor_6.0 (GCF_000001895.5)	1	NC_005100.4 (218509274..218531922, complement)

Chromosome 1 - NC_086019.1 Genomic Context describing neighboring genes

Genomic regions, transcripts, and products

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Genomic Sequence:

Go to nucleotide: Graphics FASTA GenBank

Expression

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See details

Project title: A rat RNA-Seq transcriptomic BodyMap across 11 organs and 4 developmental stages
Description: 320 RNA samples isolated from 11 organs (adrenal gland, brain, heart, kidney, liver, lung, muscle, spleen, thymus, and testes or uterus) from both sexes of Fischer 344 rats across four developmental stages (2-, 6-, 21-, and 104-weeks-old)
BioProject: PRJNA238328
Publication: PMID 24510058
Analysis date: Mon Jun 6 17:44:12 2016

Bibliography

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GeneRIFs: Gene References Into Functions

What's a GeneRIF?

results suggest that the negative transcriptional effect of Smubp-2 arises from its binding to the 50-bp element located in the MMTV promoter region
Title: Characterization of Smubp-2 as a mouse mammary tumor virus promoter-binding protein.

Submit: New GeneRIF Correction

General gene information

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Markers

BF390296 (e-PCR)
- UniSTS:249426

RH139495 (e-PCR)
- UniSTS:221581

Gene Ontology Provided by RGD

Function	Evidence Code	Pubs
enables 5'-3' DNA helicase activity	IBA Inferred from Biological aspect of Ancestor more info
enables 5'-3' DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables 5'-3' DNA helicase activity	ISO Inferred from Sequence Orthology more info
enables 5'-3' DNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables 5'-3' RNA helicase activity	IEA Inferred from Electronic Annotation more info
enables 5'-3' RNA helicase activity	ISO Inferred from Sequence Orthology more info
enables 5'-3' RNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables ATP binding	IEA Inferred from Electronic Annotation more info
enables ATP binding	ISO Inferred from Sequence Orthology more info
enables ATP binding	ISS Inferred from Sequence or Structural Similarity more info
enables ATP hydrolysis activity	IEA Inferred from Electronic Annotation more info
enables ATP hydrolysis activity	ISO Inferred from Sequence Orthology more info
enables ATP hydrolysis activity	ISS Inferred from Sequence or Structural Similarity more info
enables ATP-dependent activity, acting on DNA	ISO Inferred from Sequence Orthology more info
enables ATP-dependent activity, acting on DNA	ISS Inferred from Sequence or Structural Similarity more info
enables ATP-dependent activity, acting on RNA	ISO Inferred from Sequence Orthology more info
enables ATP-dependent activity, acting on RNA	ISS Inferred from Sequence or Structural Similarity more info
enables DNA binding	IDA Inferred from Direct Assay more info	PubMed
enables DNA binding	IEA Inferred from Electronic Annotation more info
enables DNA binding	ISO Inferred from Sequence Orthology more info
enables G-rich single-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	IEA Inferred from Electronic Annotation more info
enables RNA binding	ISO Inferred from Sequence Orthology more info
enables RNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables double-stranded DNA helicase activity	IEA Inferred from Electronic Annotation more info
enables double-stranded DNA helicase activity	ISO Inferred from Sequence Orthology more info
enables double-stranded DNA helicase activity	ISS Inferred from Sequence or Structural Similarity more info
enables helicase activity	IEA Inferred from Electronic Annotation more info
enables identical protein binding	IEA Inferred from Electronic Annotation more info
enables identical protein binding	ISO Inferred from Sequence Orthology more info
enables ribosome binding	IEA Inferred from Electronic Annotation more info
enables ribosome binding	ISO Inferred from Sequence Orthology more info
enables ribosome binding	ISS Inferred from Sequence or Structural Similarity more info
enables single-stranded DNA binding	IEA Inferred from Electronic Annotation more info
enables single-stranded DNA binding	ISO Inferred from Sequence Orthology more info
enables single-stranded DNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables single-stranded RNA binding	IEA Inferred from Electronic Annotation more info
enables single-stranded RNA binding	ISO Inferred from Sequence Orthology more info
enables single-stranded RNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables tRNA binding	IEA Inferred from Electronic Annotation more info
enables tRNA binding	ISO Inferred from Sequence Orthology more info
enables tRNA binding	ISS Inferred from Sequence or Structural Similarity more info
enables zinc ion binding	IEA Inferred from Electronic Annotation more info

Process	Evidence Code	Pubs
involved_in DNA duplex unwinding	IEA Inferred from Electronic Annotation more info
involved_in DNA duplex unwinding	ISO Inferred from Sequence Orthology more info
involved_in DNA duplex unwinding	ISS Inferred from Sequence or Structural Similarity more info
involved_in RNA secondary structure unwinding	IEA Inferred from Electronic Annotation more info
involved_in RNA secondary structure unwinding	ISO Inferred from Sequence Orthology more info
involved_in negative regulation of transcription by RNA polymerase II	IDA Inferred from Direct Assay more info	PubMed
acts_upstream_of_or_within negative regulation of transcription by RNA polymerase II	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within neuromuscular process	ISO Inferred from Sequence Orthology more info
acts_upstream_of_or_within spinal cord motor neuron differentiation	ISO Inferred from Sequence Orthology more info

Component	Evidence Code	Pubs
located_in axon	ISO Inferred from Sequence Orthology more info
is_active_in cytoplasm	IBA Inferred from Biological aspect of Ancestor more info
located_in cytoplasm	IEA Inferred from Electronic Annotation more info
located_in cytoplasm	ISO Inferred from Sequence Orthology more info
located_in cytoplasm	ISS Inferred from Sequence or Structural Similarity more info
located_in growth cone	ISO Inferred from Sequence Orthology more info
located_in neuronal cell body	ISO Inferred from Sequence Orthology more info
located_in nuclear body	IEA Inferred from Electronic Annotation more info
located_in nuclear body	ISO Inferred from Sequence Orthology more info
located_in nucleoplasm	ISO Inferred from Sequence Orthology more info
is_active_in nucleus	IBA Inferred from Biological aspect of Ancestor more info
located_in nucleus	IEA Inferred from Electronic Annotation more info
located_in nucleus	ISO Inferred from Sequence Orthology more info
located_in nucleus	ISS Inferred from Sequence or Structural Similarity more info
located_in perinuclear region of cytoplasm	ISO Inferred from Sequence Orthology more info
part_of ribonucleoprotein complex	ISO Inferred from Sequence Orthology more info

General protein information

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Preferred Names: DNA-binding protein SMUBP-2

Names: ATP-dependent helicase IGHMBP2; antifreeze enhancer-binding protein ortholog; immunoglobulin S mu binding protein 2; immunoglobulin mu binding protein 2

NP_113774.2

EC 3.6.4.12

EC 3.6.4.13

NCBI Reference Sequences (RefSeq)

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RefSeqs maintained independently of Annotated Genomes

These reference sequences exist independently of genome builds. Explain

These reference sequences are curated independently of the genome annotation cycle, so their versions may not match the RefSeq versions in the current genome build. Identify version mismatches by comparing the version of the RefSeq in this section to the one reported in Genomic regions, transcripts, and products above.

mRNA and Protein(s)

NM_031586.2 → NP_113774.2 DNA-binding protein SMUBP-2

Status: PROVISIONAL

Source sequence(s)

JAXUCZ010000001

UniProtKB/Swiss-Prot

Q9EQN5

Related

ENSRNOP00000018487.4, ENSRNOT00000018487.5

Conserved Domains (3) summary

cd02641
Location:724 → 782

R3H_Smubp-2_like; R3H domain of Smubp-2_like proteins. Smubp-2_like proteins also contain a helicase_like and an AN1-like Zinc finger domain and have been shown to bind single-stranded DNA. The name of the R3H domain comes from the characteristic spacing of the most ...

smart00154
Location:890 → 930

ZnF_AN1; AN1-like Zinc finger

TIGR00376
Location:19 → 640

TIGR00376; DNA helicase, putative