Human Gene ABCE1 (ENST00000296577.9_4) from GENCODE V47lift37
  Description: ATP binding cassette subfamily E member 1, transcript variant 1 (from RefSeq NM_002940.3)
Gencode Transcript: ENST00000296577.9_4
Gencode Gene: ENSG00000164163.11_9
Transcript (Including UTRs)
   Position: hg19 chr4:146,019,463-146,050,676 Size: 31,214 Total Exon Count: 18 Strand: +
Coding Region
   Position: hg19 chr4:146,025,565-146,048,725 Size: 23,161 Coding Exon Count: 17 

Page IndexSequence and LinksUniProtKB CommentsPrimersMalaCardsCTD
Gene AllelesRNA-Seq ExpressionMicroarray ExpressionRNA StructureProtein StructureOther Species
GO AnnotationsmRNA DescriptionsPathwaysOther NamesModel InformationMethods
Data last updated at UCSC: 2024-08-22 23:36:26

-  Sequence and Links to Tools and Databases
 
Genomic Sequence (chr4:146,019,463-146,050,676)mRNA (may differ from genome)Protein (599 aa)
Gene SorterGenome BrowserOther Species FASTAVisiGeneGene interactionsTable Schema
AlphaFoldBioGPSEnsemblEntrez GeneExonPrimerGeneCards
HGNCMalacardsMGIOMIMPubMedReactome
UniProtKBWikipediaBioGrid CRISPR DB

-  Comments and Description Text from UniProtKB
  ID: ABCE1_HUMAN
DESCRIPTION: RecName: Full=ATP-binding cassette sub-family E member 1; AltName: Full=2'-5'-oligoadenylate-binding protein; AltName: Full=HuHP68; AltName: Full=RNase L inhibitor; AltName: Full=Ribonuclease 4 inhibitor; Short=RNS4I;
FUNCTION: Antagonizes the binding of 2-5A (5'-phosphorylated 2',5'-linked oligoadenylates) by RNase L through direct interaction with RNase L and therefore inhibits its endoribonuclease activity. May play a central role in the regulation of mRNA turnover. Antagonizes the anti-viral effect of the interferon-regulated 2-5A/RNase L pathway. May act as a chaperone for post-translational events during HIV-1 capsid assembly.
SUBUNIT: Probably heterodimerizes with RNASEL; this interaction inhibits the RNASEL. Associates with HIV-1 Vif and HIV-1, HIV-2 and SIV Gag proteins.
SUBCELLULAR LOCATION: Cytoplasm. Mitochondrion. Note=Localized to clusters of virus formation at the plasma membrane.
INDUCTION: Activated by encephalomyocarditis virus (EMCV) and HIV- 1.
MISCELLANEOUS: The ABC transporter domains seem not to be functional.
SIMILARITY: Belongs to the ABC transporter superfamily. ABCE family.
SIMILARITY: Contains 2 4Fe-4S ferredoxin-type domains.
SIMILARITY: Contains 2 ABC transporter domains.
WEB RESOURCE: Name=SeattleSNPs; URL="http://pga.gs.washington.edu/data/abce1/";
WEB RESOURCE: Name=ABCMdb; Note=Database for mutations in ABC proteins; URL="http://abcmutations.hegelab.org/proteinDetails?uniprot_id=P61221";

-  Primer design for this transcript
 

Primer3Plus can design qPCR Primers that straddle exon-exon-junctions, which amplify only cDNA, not genomic DNA.
Click here to load the transcript sequence and exon structure into Primer3Plus

Exonprimer can design one pair of Sanger sequencing primers around every exon, located in non-genic sequence.
Click here to open Exonprimer with this transcript

To design primers for a non-coding sequence, zoom to a region of interest and select from the drop-down menu: View > In External Tools > Primer3


-  MalaCards Disease Associations
  MalaCards Gene Search: ABCE1
Diseases sorted by gene-association score: cardiomyopathy, hypertrophic, 20 (6), hiv-1 (3)

-  Comparative Toxicogenomics Database (CTD)
  The following chemicals interact with this gene           more ... click here to view the complete list

+  Common Gene Haplotype Alleles
  Press "+" in the title bar above to open this section.

-  RNA-Seq Expression Data from GTEx (53 Tissues, 570 Donors)
  Highest median expression: 49.83 RPKM in Cells - EBV-transformed lymphocytes
Total median expression: 506.51 RPKM



View in GTEx track of Genome Browser    View at GTEx portal     View GTEx Body Map

+  Microarray Expression Data
  Press "+" in the title bar above to open this section.

-  mRNA Secondary Structure of 3' and 5' UTRs
 
RegionFold EnergyBasesEnergy/Base
Display As
5' UTR -41.50136-0.305 Picture PostScript Text
3' UTR -389.141951-0.199 Picture PostScript Text

The RNAfold program from the Vienna RNA Package is used to perform the secondary structure predictions and folding calculations. The estimated folding energy is in kcal/mol. The more negative the energy, the more secondary structure the RNA is likely to have.

-  Protein Domain and Structure Information
  InterPro Domains: Graphical view of domain structure
IPR001450 - 4Fe4S-bd_dom
IPR017896 - 4Fe4S_Fe-S-bd
IPR017900 - 4Fe4S_Fe_S_CS
IPR003593 - AAA+_ATPase
IPR013283 - ABC_E
IPR003439 - ABC_transporter-like
IPR017871 - ABC_transporter_CS
IPR007209 - RNaseL-inhib_metal-bd_dom

Pfam Domains:
PF00005 - ABC transporter
PF00037 - 4Fe-4S binding domain
PF04068 - Possible Fer4-like domain in RNase L inhibitor, RLI
PF12800 - 4Fe-4S binding domain

SCOP Domains:
46548 - alpha-helical ferredoxin
52540 - P-loop containing nucleoside triphosphate hydrolases
53795 - PEP carboxykinase-like
54862 - 4Fe-4S ferredoxins

ModBase Predicted Comparative 3D Structure on P61221
FrontTopSide
The pictures above may be empty if there is no ModBase structure for the protein. The ModBase structure frequently covers just a fragment of the protein. You may be asked to log onto ModBase the first time you click on the pictures. It is simplest after logging in to just click on the picture again to get to the specific info on that model.

-  Orthologous Genes in Other Species
  Orthologies between human, mouse, and rat are computed by taking the best BLASTP hit, and filtering out non-syntenic hits. For more distant species reciprocal-best BLASTP hits are used. Note that the absence of an ortholog in the table below may reflect incomplete annotations in the other species rather than a true absence of the orthologous gene.
MouseRatZebrafishD. melanogasterC. elegansS. cerevisiae
No orthologNo orthologNo orthologNo orthologNo orthologGenome Browser
Gene DetailsGene Details Gene Details Gene Details
Gene SorterGene Sorter Gene Sorter Gene Sorter
 RGDEnsembl  SGD
     Protein Sequence
     Alignment

-  Gene Ontology (GO) Annotations with Structured Vocabulary
  Molecular Function:
GO:0000166 nucleotide binding
GO:0005506 iron ion binding
GO:0005515 protein binding
GO:0005524 ATP binding
GO:0016887 ATPase activity
GO:0043024 ribosomal small subunit binding
GO:0060698 endoribonuclease inhibitor activity

Biological Process:
GO:0000054 ribosomal subunit export from nucleus
GO:0006413 translational initiation
GO:0006415 translational termination
GO:0016032 viral process
GO:0060338 regulation of type I interferon-mediated signaling pathway
GO:0060702 negative regulation of endoribonuclease activity

Cellular Component:
GO:0005737 cytoplasm
GO:0005739 mitochondrion
GO:0005759 mitochondrial matrix
GO:0005829 cytosol
GO:0016020 membrane
GO:0005852 eukaryotic translation initiation factor 3 complex


-  Descriptions from all associated GenBank mRNAs
  LF208162 - JP 2014500723-A/15665: Polycomb-Associated Non-Coding RNAs.
AK315198 - Homo sapiens cDNA, FLJ96183.
AB062293 - Homo sapiens OK/SW-cl.40 mRNA for ATP-binding cassette sub-family E member 1, complete cds.
JD168692 - Sequence 149716 from Patent EP1572962.
X76388 - H.sapiens mRNA for 2-5A binding protein.
BC016283 - Homo sapiens ATP-binding cassette, sub-family E (OABP), member 1, mRNA (cDNA clone MGC:9023 IMAGE:3909151), complete cds.
KJ892016 - Synthetic construct Homo sapiens clone ccsbBroadEn_01410 ABCE1 gene, encodes complete protein.
CU677591 - Synthetic construct Homo sapiens gateway clone IMAGE:100023271 5' read ABCE1 mRNA.
AB528026 - Synthetic construct DNA, clone: pF1KB6161, Homo sapiens ABCE1 gene for ATP-binding cassette, sub-family E (OABP), member 1, without stop codon, in Flexi system.
BT009779 - Homo sapiens ATP-binding cassette, sub-family E (OABP), member 1 mRNA, complete cds.
LF373112 - JP 2014500723-A/180615: Polycomb-Associated Non-Coding RNAs.
X74987 - H.sapiens mRNA for 2'-5' oligoadenylate binding protein.
BC016988 - Homo sapiens, clone IMAGE:4396587, mRNA, partial cds.
LF373108 - JP 2014500723-A/180611: Polycomb-Associated Non-Coding RNAs.
LF373107 - JP 2014500723-A/180610: Polycomb-Associated Non-Coding RNAs.
LF373105 - JP 2014500723-A/180608: Polycomb-Associated Non-Coding RNAs.
AK123593 - Homo sapiens cDNA FLJ41599 fis, clone CTONG2025513, highly similar to Mus musculus ATP-binding cassette, sub-family E (OABP), member 1 (Abce1).
LF373104 - JP 2014500723-A/180607: Polycomb-Associated Non-Coding RNAs.
JD236118 - Sequence 217142 from Patent EP1572962.
LF373103 - JP 2014500723-A/180606: Polycomb-Associated Non-Coding RNAs.
JD106276 - Sequence 87300 from Patent EP1572962.
LF373102 - JP 2014500723-A/180605: Polycomb-Associated Non-Coding RNAs.
LF338862 - JP 2014500723-A/146365: Polycomb-Associated Non-Coding RNAs.
LF373099 - JP 2014500723-A/180602: Polycomb-Associated Non-Coding RNAs.
JD244863 - Sequence 225887 from Patent EP1572962.
JD302951 - Sequence 283975 from Patent EP1572962.
JD302952 - Sequence 283976 from Patent EP1572962.
JD296785 - Sequence 277809 from Patent EP1572962.
LF373098 - JP 2014500723-A/180601: Polycomb-Associated Non-Coding RNAs.
JD235986 - Sequence 217010 from Patent EP1572962.
JD551195 - Sequence 532219 from Patent EP1572962.
JD377569 - Sequence 358593 from Patent EP1572962.
JD565305 - Sequence 546329 from Patent EP1572962.
JD391118 - Sequence 372142 from Patent EP1572962.
JD300546 - Sequence 281570 from Patent EP1572962.
JD285936 - Sequence 266960 from Patent EP1572962.
LF373097 - JP 2014500723-A/180600: Polycomb-Associated Non-Coding RNAs.
JD172529 - Sequence 153553 from Patent EP1572962.
MA608689 - JP 2018138019-A/180615: Polycomb-Associated Non-Coding RNAs.
MA608685 - JP 2018138019-A/180611: Polycomb-Associated Non-Coding RNAs.
MA608684 - JP 2018138019-A/180610: Polycomb-Associated Non-Coding RNAs.
MA608682 - JP 2018138019-A/180608: Polycomb-Associated Non-Coding RNAs.
MA608681 - JP 2018138019-A/180607: Polycomb-Associated Non-Coding RNAs.
MA608680 - JP 2018138019-A/180606: Polycomb-Associated Non-Coding RNAs.
MA608679 - JP 2018138019-A/180605: Polycomb-Associated Non-Coding RNAs.
MA608676 - JP 2018138019-A/180602: Polycomb-Associated Non-Coding RNAs.
MA608675 - JP 2018138019-A/180601: Polycomb-Associated Non-Coding RNAs.
MA608674 - JP 2018138019-A/180600: Polycomb-Associated Non-Coding RNAs.
MA443739 - JP 2018138019-A/15665: Polycomb-Associated Non-Coding RNAs.
MA574439 - JP 2018138019-A/146365: Polycomb-Associated Non-Coding RNAs.

-  Biochemical and Signaling Pathways
  Reactome (by CSHL, EBI, and GO)

Protein P61221 (Reactome details) participates in the following event(s):

R-HSA-5223305 ABCE1 binds RNASEL, inhibiting it
R-HSA-909733 Interferon alpha/beta signaling
R-HSA-913531 Interferon Signaling
R-HSA-1280215 Cytokine Signaling in Immune system
R-HSA-168256 Immune System

-  Other Names for This Gene
  Alternate Gene Symbols: ABCE1_HUMAN, ENST00000296577.1, ENST00000296577.2, ENST00000296577.3, ENST00000296577.4, ENST00000296577.5, ENST00000296577.6, ENST00000296577.7, ENST00000296577.8, NM_002940, O88793, OK/SW-cl.40, P61221, Q13181, Q13864, Q6NR76, Q96AL0, Q96B10, Q99K66, RLI, RNASEL1, RNASELI, RNS4I, uc317lvc.1, uc317lvc.2
UCSC ID: ENST00000296577.9_4
RefSeq Accession: NM_002940.3
Protein: P61221 (aka ABCE1_HUMAN or ABE1_HUMAN)

-  Gene Model Information
  Click here for a detailed description of the fields of the table above.

-  Methods, Credits, and Use Restrictions
  Click here for details on how this gene model was made and data restrictions if any.