A1CF (APOBEC1 complementation factor) - Rat Genome Database

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Gene: A1CF (APOBEC1 complementation factor) Canis lupus familiaris
Analyze
Symbol: A1CF
Name: APOBEC1 complementation factor
RGD ID: 12113142
Description: ENCODES a protein that exhibits double-stranded RNA binding (ortholog); enzyme-substrate adaptor activity (ortholog); mRNA binding (ortholog); INVOLVED IN cytidine to uridine editing (ortholog); embryo implantation (ortholog); mRNA localization resulting in post-transcriptional regulation of gene expression (ortholog); ASSOCIATED WITH genetic disease (ortholog); gout (ortholog); hereditary breast ovarian cancer syndrome (ortholog); FOUND IN apolipoprotein B mRNA editing enzyme complex (ortholog); heterochromatin (ortholog); mRNA editing complex (ortholog)
Type: protein-coding
RefSeq Status: MODEL
RGD Orthologs
Human
Mouse
Rat
Chinchilla
Bonobo
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: CanFam3.1 - Dog CanFam3.1 Assembly
Position:
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12637,027,165 - 37,109,842 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2637,027,275 - 37,102,888 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2636,912,827 - 36,995,367 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02638,560,154 - 38,642,825 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2638,560,187 - 38,636,835 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12636,461,590 - 36,550,642 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02636,048,241 - 36,131,022 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02637,288,420 - 37,371,161 (+)NCBIUU_Cfam_GSD_1.0
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component

Molecular Function

References
Additional References at PubMed
PMID:30032202  


Genomics

Comparative Map Data
A1CF
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12637,027,165 - 37,109,842 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2637,027,275 - 37,102,888 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2636,912,827 - 36,995,367 (+)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02638,560,154 - 38,642,825 (+)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2638,560,187 - 38,636,835 (+)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12636,461,590 - 36,550,642 (+)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02636,048,241 - 36,131,022 (+)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02637,288,420 - 37,371,161 (+)NCBIUU_Cfam_GSD_1.0
A1CF
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh381050,799,409 - 50,885,627 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl1050,799,409 - 50,885,675 (-)EnsemblGRCh38hg38GRCh38
GRCh371052,559,169 - 52,645,387 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361052,236,331 - 52,315,441 (-)NCBINCBI36Build 36hg18NCBI36
Build 341052,236,330 - 52,315,441NCBI
Celera1045,829,119 - 45,908,228 (-)NCBICelera
Cytogenetic Map10q11.23NCBI
HuRef1046,537,685 - 46,623,956 (-)NCBIHuRef
CHM1_11052,841,000 - 52,927,266 (-)NCBICHM1_1
T2T-CHM13v2.01051,648,044 - 51,734,261 (-)NCBIT2T-CHM13v2.0
A1cf
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391931,846,156 - 31,929,765 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1931,846,164 - 31,926,395 (+)EnsemblGRCm39 Ensembl
GRCm381931,868,756 - 31,952,365 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1931,868,764 - 31,948,995 (+)EnsemblGRCm38mm10GRCm38
MGSCv371931,943,251 - 32,023,896 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361931,934,758 - 32,015,403 (+)NCBIMGSCv36mm8
Celera1932,656,858 - 32,737,433 (+)NCBICelera
Cytogenetic Map19C1NCBI
A1cf
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr81239,149,436 - 239,242,460 (+)NCBIGRCr8
mRatBN7.21229,736,037 - 229,823,499 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl1229,736,106 - 229,824,354 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1238,102,542 - 238,188,586 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01245,032,243 - 245,118,286 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.01237,866,865 - 237,946,606 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.01250,426,027 - 250,514,245 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl1250,426,158 - 250,514,866 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.01257,660,187 - 257,747,893 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41235,865,843 - 235,958,065 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.11236,029,865 - 236,122,088 (+)NCBI
Celera1226,856,680 - 226,943,695 (+)NCBICelera
Cytogenetic Map1q52NCBI
A1cf
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554255,992,538 - 6,077,770 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554255,992,538 - 6,077,769 (-)NCBIChiLan1.0ChiLan1.0
A1CF
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2863,106,674 - 63,197,715 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11063,111,996 - 63,203,037 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v01047,451,293 - 47,538,062 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.11049,588,168 - 49,675,543 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1049,588,168 - 49,675,543 (-)Ensemblpanpan1.1panPan2
A1cf
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721376,615,094 - 76,662,949 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049367352,130,943 - 2,177,815 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
A1CF
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1498,908,630 - 98,987,524 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11498,908,585 - 98,990,362 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214107,777,628 - 107,848,254 (+)NCBISscrofa10.2Sscrofa10.2susScr3
A1CF
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1980,286,872 - 80,367,587 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl980,314,081 - 80,370,348 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604840,941,786 - 41,019,626 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
A1cf
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462479112,757,319 - 12,868,422 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462479112,757,319 - 12,868,364 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in A1CF
1721 total Variants

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 reproductive system respiratory system adipose tissue
High
Medium 6 6 6
Low 5
Below cutoff 5 16 6 6 5 12 8 10 6

Sequence

Nucleotide Sequences
RefSeq Transcripts XM_022410422 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038437670 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038437671 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038512542 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038512543 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038576032 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038576033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038640243 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_038640244 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_534776 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_855933 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide AAEX04000026 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAHUQ010000288 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAQRD010000065 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAAUVH010000375 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  REHQ01000026 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

RefSeq Acc Id: ENSCAFT00000024715   ⟹   ENSCAFP00000022926
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.1 Ensembl2637,027,275 - 37,102,888 (+)Ensembl
RefSeq Acc Id: ENSCAFT00845050874   ⟹   ENSCAFP00845039883
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.0 Ensembl2638,560,187 - 38,636,835 (+)Ensembl
RefSeq Acc Id: XM_038437670   ⟹   XP_038293598
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.02638,560,154 - 38,642,825 (+)NCBI
RefSeq Acc Id: XM_038437671   ⟹   XP_038293599
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
ROS_Cfam_1.02638,560,154 - 38,642,825 (+)NCBI
RefSeq Acc Id: XM_038512542   ⟹   XP_038368470
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.12636,461,590 - 36,550,642 (+)NCBI
RefSeq Acc Id: XM_038512543   ⟹   XP_038368471
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UMICH_Zoey_3.12636,461,590 - 36,550,642 (+)NCBI
RefSeq Acc Id: XM_038576032   ⟹   XP_038431960
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.02637,288,420 - 37,371,161 (+)NCBI
RefSeq Acc Id: XM_038576033   ⟹   XP_038431961
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UU_Cfam_GSD_1.02637,288,420 - 37,371,161 (+)NCBI
RefSeq Acc Id: XM_038640243   ⟹   XP_038496171
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.02636,048,241 - 36,131,022 (+)NCBI
RefSeq Acc Id: XM_038640244   ⟹   XP_038496172
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
UNSW_CanFamBas_1.02636,048,241 - 36,123,976 (+)NCBI
RefSeq Acc Id: XM_534776   ⟹   XP_534776
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.12637,027,169 - 37,109,842 (+)NCBI
Dog10K_Boxer_Tasha2636,912,827 - 36,995,367 (+)NCBI
Sequence:
RefSeq Acc Id: XM_855933   ⟹   XP_861026
Type: CODING
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.12637,027,192 - 37,109,842 (+)NCBI
Dog10K_Boxer_Tasha2636,912,827 - 36,995,367 (+)NCBI
Sequence:
RefSeq Acc Id: XP_534776   ⟸   XM_534776
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LRJ1 (UniProtKB/TrEMBL),   A0A8C0TIC8 (UniProtKB/TrEMBL),   A0A8I3PZK3 (UniProtKB/TrEMBL),   A0A8C0R8F3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_861026   ⟸   XM_855933
- Peptide Label: isoform X2
- UniProtKB: A0A8C0R8F3 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSCAFP00000022926   ⟸   ENSCAFT00000024715
RefSeq Acc Id: XP_038368470   ⟸   XM_038512542
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038368471   ⟸   XM_038512543
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038496171   ⟸   XM_038640243
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038496172   ⟸   XM_038640244
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038293598   ⟸   XM_038437670
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LRJ1 (UniProtKB/TrEMBL),   A0A8C0TIC8 (UniProtKB/TrEMBL),   A0A8I3PZK3 (UniProtKB/TrEMBL),   A0A8C0R8F3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038293599   ⟸   XM_038437671
- Peptide Label: isoform X2
- UniProtKB: A0A8C0R8F3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038431960   ⟸   XM_038576032
- Peptide Label: isoform X1
- UniProtKB: A0A8C0LRJ1 (UniProtKB/TrEMBL),   A0A8C0R8F3 (UniProtKB/TrEMBL),   A0A8C0TIC8 (UniProtKB/TrEMBL),   A0A8I3PZK3 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038431961   ⟸   XM_038576033
- Peptide Label: isoform X2
- UniProtKB: A0A8C0R8F3 (UniProtKB/TrEMBL)
RefSeq Acc Id: ENSCAFP00845039883   ⟸   ENSCAFT00845050874
Protein Domains
RRM

Promoters
RGD ID:13688056
Promoter ID:EPDNEW_C6125
Type:initiation region
Name:A1CF_1
Description:APOBEC1 complementation factor
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Dog AssemblyChrPosition (strand)Source
CanFam3.12637,027,270 - 37,027,330EPDNEW

Additional Information

Database Acc Id Source(s)
Ensembl Genes ENSCAFG00000015581 Ensembl, UniProtKB/TrEMBL
  ENSCAFG00030022282 UniProtKB/TrEMBL
  ENSCAFG00040023244 UniProtKB/TrEMBL
  ENSCAFG00845028778 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSCAFT00000024715.5 UniProtKB/TrEMBL
  ENSCAFT00030040938.1 UniProtKB/TrEMBL
  ENSCAFT00040043186.1 UniProtKB/TrEMBL
  ENSCAFT00040043225.1 UniProtKB/TrEMBL
  ENSCAFT00845050874 ENTREZGENE
  ENSCAFT00845050874.1 UniProtKB/TrEMBL
Gene3D-CATH 3.30.160.20 UniProtKB/TrEMBL
  3.30.70.330 UniProtKB/TrEMBL
InterPro A1CF_DSRM UniProtKB/TrEMBL
  ACF_RRM1 UniProtKB/TrEMBL
  HnRNP_R/Q_splicing_fac UniProtKB/TrEMBL
  Nucleotide-bd_a/b_plait_sf UniProtKB/TrEMBL
  RBD_domain_sf UniProtKB/TrEMBL
  RRM_dom UniProtKB/TrEMBL
KEGG Report cfa:477581 UniProtKB/TrEMBL
NCBI Gene A1CF ENTREZGENE
PANTHER HETEROGENEOUS NUCLEAR RIBONUCLEOPROTEIN UniProtKB/TrEMBL
  PTHR21245:SF8 UniProtKB/TrEMBL
Pfam DND1_DSRM UniProtKB/TrEMBL
  RRM_1 UniProtKB/TrEMBL
PROSITE RRM UniProtKB/TrEMBL
SMART RRM UniProtKB/TrEMBL
Superfamily-SCOP dsRNA-binding domain-like UniProtKB/TrEMBL
  SSF54928 UniProtKB/TrEMBL
UniProt A0A8C0LRJ1 ENTREZGENE
  A0A8C0P368_CANLF UniProtKB/TrEMBL
  A0A8C0R8F3 ENTREZGENE
  A0A8C0TIC8 ENTREZGENE, UniProtKB/TrEMBL
  A0A8I3PZK3 ENTREZGENE, UniProtKB/TrEMBL
VGNC ID VGNC:37399 ENTREZGENE