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Protein

APOBEC1 complementation factor

Gene

A1cf

Organism
Rattus norvegicus (Rat)
Status
Reviewed-Annotation score: Annotation score: 5 out of 5-Experimental evidence at protein leveli

Functioni

Essential component of the apolipoprotein B mRNA editing enzyme complex which is responsible for the postranscriptional editing of a CAA codon for Gln to a UAA codon for stop in APOB mRNA. Binds to APOB mRNA and is probably responsible for docking the catalytic subunit, APOBEC1, to the mRNA to allow it to deaminate its target cytosine. The complex also seems to protect the edited APOB mRNA from nonsense-mediated decay (By similarity).By similarity1 Publication

GO - Molecular functioni

  • mRNA binding Source: RGD
  • nucleotide binding Source: InterPro
  • single-stranded RNA binding Source: UniProtKB

GO - Biological processi

  • cytidine to uridine editing Source: HGNC
  • mRNA modification Source: InterPro
  • mRNA processing Source: UniProtKB-KW
  • protein stabilization Source: UniProtKB
Complete GO annotation...

Keywords - Biological processi

mRNA processing

Keywords - Ligandi

RNA-binding

Names & Taxonomyi

Protein namesi
Recommended name:
APOBEC1 complementation factor
Alternative name(s):
APOBEC1-stimulating protein
Gene namesi
Name:A1cf
Synonyms:Acf, AspBy similarity
OrganismiRattus norvegicus (Rat)
Taxonomic identifieri10116 [NCBI]
Taxonomic lineageiEukaryotaMetazoaChordataCraniataVertebrataEuteleostomiMammaliaEutheriaEuarchontogliresGliresRodentiaSciurognathiMuroideaMuridaeMurinaeRattus
Proteomesi
  • UP000002494 Componenti: Unplaced

Organism-specific databases

RGDi619834. A1cf.

Subcellular locationi

  • Nucleus 1 Publication
  • Endoplasmic reticulum 1 Publication
  • Cytoplasm 1 Publication

  • Note: Predominantly nuclear where it localizes to heterochromatin. Also cytoplasmic where it is found at the outer surface of the endoplasmic reticulum. Shuttles between the nucleus and cytoplasm. May be transported into the nucleus by the nuclear import protein TNPO2/TRN2 or by APOBEC1.

GO - Cellular componenti

  • apolipoprotein B mRNA editing enzyme complex Source: UniProtKB
  • cytoplasm Source: UniProtKB
  • endoplasmic reticulum Source: UniProtKB-SubCell
  • mRNA editing complex Source: RGD
  • nuclear heterochromatin Source: RGD
Complete GO annotation...

Keywords - Cellular componenti

Cytoplasm, Endoplasmic reticulum, Nucleus

PTM / Processingi

Molecule processing

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Chaini1 – 594594APOBEC1 complementation factorPRO_0000081485Add
BLAST

Amino acid modifications

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Modified residuei498 – 4981PhosphothreonineBy similarity

Keywords - PTMi

Phosphoprotein

Proteomic databases

PaxDbiQ923K9.
PRIDEiQ923K9.

PTM databases

iPTMnetiQ923K9.
PhosphoSiteiQ923K9.

Expressioni

Tissue specificityi

Isoforms 1 and 2 are widely expressed while isoforms 3 and 4 are restricted to liver and small intestine.1 Publication

Interactioni

Subunit structurei

Part of the apolipoprotein B mRNA editing complex with APOBEC1. Found in a complex with APOBEC1 and CELF2/CUGBP2. Interacts APOBEC1. Interacts with TNPO2; TNPO2 may be responsible for transport of A1CF into the nucleus. Interacts with SYNCRIP. Interacts with CELF2/CUGBP2 (By similarity).By similarity

Protein-protein interaction databases

MINTiMINT-4580759.
STRINGi10116.ENSRNOP00000062802.

Structurei

3D structure databases

ProteinModelPortaliQ923K9.
SMRiQ923K9. Positions 128-308.
ModBaseiSearch...
MobiDBiSearch...

Family & Domainsi

Domains and Repeats

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Domaini56 – 13479RRM 1PROSITE-ProRule annotationAdd
BLAST
Domaini136 – 21883RRM 2PROSITE-ProRule annotationAdd
BLAST
Domaini231 – 30373RRM 3PROSITE-ProRule annotationAdd
BLAST

Region

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Regioni359 – 40850Required for nuclear localizationBy similarityAdd
BLAST

Domaini

The RRM domains are necessary but not sufficient for binding to APOB mRNA. Additional residues in the pre-RRM and C-terminal regions are required for RNA-binding and for complementing APOBEC1 activity (By similarity).By similarity

Sequence similaritiesi

Contains 3 RRM (RNA recognition motif) domains.PROSITE-ProRule annotation

Keywords - Domaini

Repeat

Phylogenomic databases

eggNOGiKOG0117. Eukaryota.
ENOG410XTJ5. LUCA.
HOGENOMiHOG000186083.
HOVERGENiHBG051917.
InParanoidiQ923K9.
PhylomeDBiQ923K9.

Family and domain databases

Gene3Di3.30.160.20. 1 hit.
3.30.70.330. 2 hits.
InterProiIPR033111. A1CF.
IPR014720. dsRBD_dom.
IPR006535. HnRNP_R/Q_splicing_fac.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PANTHERiPTHR24012:SF313. PTHR24012:SF313. 3 hits.
PfamiPF00076. RRM_1. 3 hits.
[Graphical view]
SMARTiSM00360. RRM. 3 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 3 hits.
TIGRFAMsiTIGR01648. hnRNP-R-Q. 1 hit.
PROSITEiPS50102. RRM. 3 hits.
[Graphical view]

Sequences (4)i

Sequence statusi: Complete.

This entry describes 4 isoformsi produced by alternative splicing. AlignAdd to basket

Isoform 11 Publication (identifier: Q923K9-1) [UniParc]FASTAAdd to basket

Also known as: ACF651 Publication

This isoform has been chosen as the 'canonical' sequence. All positional information in this entry refers to it. This is also the sequence that appears in the downloadable versions of the entry.

« Hide

        10         20         30         40         50
MESNHKSGDG LSGTQKEAAL RALVQRTGYS LVQENGQRKY GGPPPGWDTT
60 70 80 90 100
PPERGCEIFI GKLPRDLFED ELIPLCEKIG KIYEMRMMMD FNGNNRGYAF
110 120 130 140 150
VTFSNKQEAK NAIKQLNNYE IRNGRLLGVC ASVDNCRLFV GGIPKTKKRE
160 170 180 190 200
EILSEMKKVT EGVVDVIVYP SAADKTKNRG FAFVEYESHR AAAMARRRLL
210 220 230 240 250
PGRIQLWGHP IAVDWAEPEV EVDEDTMSSV KILYVRNLML STSEEMIEKE
260 270 280 290 300
FNSIKPGAVE RVKKIRDYAF VHFSNREDAV EAMKALNGKV LDGSPIEVTL
310 320 330 340 350
AKPVDKDSYV RYTRGTGGRN TMLQEYTYPL SHVYDPTTTY LGAPVFYTPQ
360 370 380 390 400
AYAAIPSLHF PATKGHLSNR ALIRTPSVRE IYMNVPVGAA GVRGLGGRGY
410 420 430 440 450
LAYTGLGRGY QVKGDKRQDK LYDLLPGMEL TPMNTISLKP QGVKLAPQIL
460 470 480 490 500
EEICQKNNWG QPVYQLHSAI GQDQRQLFLY KVTIPALASQ NPAIHPFTPP
510 520 530 540 550
KLSAYVDEAK RYAAEHTLQT LGIPTEGGDA GTTAPTATSA TVFPGYAVPS
560 570 580 590
ATAPVSTAQL KQAVTLGQDL AAYTTYEVYP TFAVTTRGDG YGTF
Length:594
Mass (Da):65,620
Last modified:December 1, 2001 - v1
Checksum:iF04D93EE25D5EF6C
GO
Isoform 21 Publication (identifier: Q923K9-2) [UniParc]FASTAAdd to basket

Also known as: ACF641 Publication

The sequence of this isoform differs from the canonical sequence as follows:
     380-387: Missing.

Show »
Length:586
Mass (Da):64,674
Checksum:iA183261CF5C85FF7
GO
Isoform 31 Publication (identifier: Q923K9-3) [UniParc]FASTAAdd to basket

Also known as: ACF451 Publication

The sequence of this isoform differs from the canonical sequence as follows:
     380-405: EIYMNVPVGAAGVRGLGGRGYLAYTG → GCSRTPSIYLCFLTAVHAGVHHIHVQ
     406-594: Missing.

Show »
Length:405
Mass (Da):45,454
Checksum:iB9824131BD18CCD4
GO
Isoform 41 Publication (identifier: Q923K9-4) [UniParc]FASTAAdd to basket

Also known as: ACF431 Publication

The sequence of this isoform differs from the canonical sequence as follows:
     380-383: EIYM → GNIS
     384-594: Missing.

Show »
Length:383
Mass (Da):42,996
Checksum:iE3ECF5E16C2714F2
GO

Experimental Info

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Sequence conflicti348 – 3481T → A in AAO15465 (PubMed:14570923).Curated
Sequence conflicti348 – 3481T → A in AAO15466 (PubMed:14570923).Curated
Sequence conflicti405 – 4051G → P in AAO15467 (PubMed:14570923).Curated

Alternative sequence

Feature keyPosition(s)LengthDescriptionGraphical viewFeature identifierActions
Alternative sequencei380 – 40526EIYMN…LAYTG → GCSRTPSIYLCFLTAVHAGV HHIHVQ in isoform 3. 1 PublicationVSP_051933Add
BLAST
Alternative sequencei380 – 3878Missing in isoform 2. 1 PublicationVSP_051934
Alternative sequencei380 – 3834EIYM → GNIS in isoform 4. 1 PublicationVSP_051935
Alternative sequencei384 – 594211Missing in isoform 4. 1 PublicationVSP_051936Add
BLAST
Alternative sequencei406 – 594189Missing in isoform 3. 1 PublicationVSP_051937Add
BLAST

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF290984 mRNA. Translation: AAK83095.1.
AF442133 mRNA. Translation: AAO15465.1.
AF442134 mRNA. Translation: AAO15466.1.
AF442135 Genomic DNA. Translation: AAO15467.1.
AF442135 Genomic DNA. Translation: AAO15468.1.
AY028945 mRNA. Translation: AAK50145.1.
RefSeqiNP_596891.1. NM_133400.1. [Q923K9-2]
UniGeneiRn.162520.

Genome annotation databases

GeneIDi170912.
KEGGirno:170912.
UCSCiRGD:619834. rat. [Q923K9-1]

Keywords - Coding sequence diversityi

Alternative splicing

Cross-referencesi

Sequence databases

Select the link destinations:
EMBLi
GenBanki
DDBJi
Links Updated
AF290984 mRNA. Translation: AAK83095.1.
AF442133 mRNA. Translation: AAO15465.1.
AF442134 mRNA. Translation: AAO15466.1.
AF442135 Genomic DNA. Translation: AAO15467.1.
AF442135 Genomic DNA. Translation: AAO15468.1.
AY028945 mRNA. Translation: AAK50145.1.
RefSeqiNP_596891.1. NM_133400.1. [Q923K9-2]
UniGeneiRn.162520.

3D structure databases

ProteinModelPortaliQ923K9.
SMRiQ923K9. Positions 128-308.
ModBaseiSearch...
MobiDBiSearch...

Protein-protein interaction databases

MINTiMINT-4580759.
STRINGi10116.ENSRNOP00000062802.

PTM databases

iPTMnetiQ923K9.
PhosphoSiteiQ923K9.

Proteomic databases

PaxDbiQ923K9.
PRIDEiQ923K9.

Protocols and materials databases

Structural Biology KnowledgebaseSearch...

Genome annotation databases

GeneIDi170912.
KEGGirno:170912.
UCSCiRGD:619834. rat. [Q923K9-1]

Organism-specific databases

CTDi29974.
RGDi619834. A1cf.

Phylogenomic databases

eggNOGiKOG0117. Eukaryota.
ENOG410XTJ5. LUCA.
HOGENOMiHOG000186083.
HOVERGENiHBG051917.
InParanoidiQ923K9.
PhylomeDBiQ923K9.

Miscellaneous databases

NextBioi621377.
PROiQ923K9.

Family and domain databases

Gene3Di3.30.160.20. 1 hit.
3.30.70.330. 2 hits.
InterProiIPR033111. A1CF.
IPR014720. dsRBD_dom.
IPR006535. HnRNP_R/Q_splicing_fac.
IPR012677. Nucleotide-bd_a/b_plait.
IPR000504. RRM_dom.
[Graphical view]
PANTHERiPTHR24012:SF313. PTHR24012:SF313. 3 hits.
PfamiPF00076. RRM_1. 3 hits.
[Graphical view]
SMARTiSM00360. RRM. 3 hits.
[Graphical view]
SUPFAMiSSF54928. SSF54928. 3 hits.
TIGRFAMsiTIGR01648. hnRNP-R-Q. 1 hit.
PROSITEiPS50102. RRM. 3 hits.
[Graphical view]
ProtoNetiSearch...

Publicationsi

  1. "The editosome for cytidine to uridine mRNA editing has a native complexity of 27S: identification of intracellular domains containing active and inactive editing factors."
    Sowden M.P., Ballatori N., de Mesy Jensen K.L., Hamilton Reed L., Smith H.C.
    J. Cell Sci. 115:1027-1039(2002) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 2), SUBCELLULAR LOCATION.
    Strain: Sprague-DawleyImported.
    Tissue: Liver1 Publication.
  2. "Identification of novel alternative splice variants of APOBEC-1 complementation factor with different capacities to support apolipoprotein B mRNA editing."
    Sowden M.P., Lehmann D.M., Lin X., Smith C.O., Smith H.C.
    J. Biol. Chem. 279:197-206(2004) [PubMed] [Europe PMC] [Abstract]
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORMS 3 AND 4), NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 295-594 (ISOFORM 3), NUCLEOTIDE SEQUENCE [GENOMIC DNA] OF 295-409 (ISOFORM 1), TISSUE SPECIFICITY.
    Strain: Sprague-DawleyImported.
    Tissue: Liver1 Publication.
  3. "An isoform of rat APOBEC-1 complementation factor p66/ACF."
    Sowden M.P., Smith H.C.
    Submitted (MAR-2001) to the EMBL/GenBank/DDBJ databases
    Cited for: NUCLEOTIDE SEQUENCE [MRNA] (ISOFORM 1).
    Strain: Sprague-Dawley.
  4. "Purification and molecular cloning of a novel essential component of the apolipoprotein B mRNA editing enzyme-complex."
    Lellek H., Kirsten R., Diehl I., Apostel F., Buck F., Greeve J.
    J. Biol. Chem. 275:19848-19856(2000) [PubMed] [Europe PMC] [Abstract]
    Cited for: PARTIAL PROTEIN SEQUENCE, FUNCTION.
    Tissue: Liver1 Publication.

Entry informationi

Entry nameiA1CF_RAT
AccessioniPrimary (citable) accession number: Q923K9
Secondary accession number(s): Q8CH55
, Q8CH56, Q8CH57, Q8CH58, Q924K3
Entry historyi
Integrated into UniProtKB/Swiss-Prot: December 20, 2005
Last sequence update: December 1, 2001
Last modified: May 11, 2016
This is version 109 of the entry and version 1 of the sequence. [Complete history]
Entry statusiReviewed (UniProtKB/Swiss-Prot)
Annotation programChordata Protein Annotation Program

Miscellaneousi

Keywords - Technical termi

Complete proteome, Direct protein sequencing, Reference proteome

Documents

  1. SIMILARITY comments
    Index of protein domains and families

Similar proteinsi

Links to similar proteins from the UniProt Reference Clusters (UniRef) at 100%, 90% and 50% sequence identity:
100%UniRef100 combines identical sequences and sub-fragments with 11 or more residues from any organism into one UniRef entry.
90%UniRef90 is built by clustering UniRef100 sequences that have at least 90% sequence identity to, and 80% overlap with, the longest sequence (a.k.a seed sequence).
50%UniRef50 is built by clustering UniRef90 seed sequences that have at least 50% sequence identity to, and 80% overlap with, the longest sequence in the cluster.