Apba3 (amyloid beta precursor protein binding family A member 3) - Rat Genome Database
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Gene: Apba3 (amyloid beta precursor protein binding family A member 3) Rattus norvegicus
Analyze
Symbol: Apba3
Name: amyloid beta precursor protein binding family A member 3
RGD ID: 620846
Description: Exhibits amyloid-beta binding activity. Predicted to be involved in several processes, including chemical synaptic transmission; in utero embryonic development; and negative regulation of catalytic activity. Predicted to localize to perinuclear region of cytoplasm. Orthologous to human APBA3 (amyloid beta precursor protein binding family A member 3); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; ammonium chloride.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: adapter protein X11gamma; amyloid beta (A4) precursor protein-binding family A member 3 (X11-like 2); amyloid beta (A4) precursor protein-binding, family A, member 3; amyloid beta (A4) precursor protein-binding, family A, member 3 (X11-like 2); amyloid beta A4 precursor protein-binding family A member 3; amyloid-beta A4 precursor protein-binding family A member 3; mint-3; Mint3; neuron-specific X11L2 protein; neuronal Munc18-1-interacting protein 3
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.278,446,212 - 8,451,310 (-)NCBI
Rnor_6.0 Ensembl711,314,424 - 11,319,516 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0711,314,468 - 11,319,540 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0711,481,876 - 11,486,939 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.479,930,024 - 9,934,446 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.179,930,023 - 9,934,446 (-)NCBI
Celera76,634,549 - 6,638,968 (-)NCBICelera
Cytogenetic Map7q11NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View
amenorrhea  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:1302262   PMID:9860131   PMID:12477932   PMID:17167098   PMID:19726677   PMID:24867948   PMID:25931508  


Genomics

Comparative Map Data
Apba3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.278,446,212 - 8,451,310 (-)NCBI
Rnor_6.0 Ensembl711,314,424 - 11,319,516 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0711,314,468 - 11,319,540 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0711,481,876 - 11,486,939 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.479,930,024 - 9,934,446 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.179,930,023 - 9,934,446 (-)NCBI
Celera76,634,549 - 6,638,968 (-)NCBICelera
Cytogenetic Map7q11NCBI
APBA3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl193,750,772 - 3,761,692 (-)EnsemblGRCh38hg38GRCh38
GRCh38193,750,772 - 3,761,696 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37193,750,770 - 3,761,690 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36193,701,771 - 3,712,673 (-)NCBINCBI36hg18NCBI36
Build 34193,701,770 - 3,712,673NCBI
Celera193,688,414 - 3,699,318 (-)NCBI
Cytogenetic Map19p13.3NCBI
HuRef193,515,484 - 3,526,388 (-)NCBIHuRef
CHM1_1193,750,394 - 3,761,300 (-)NCBICHM1_1
Apba3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391081,102,799 - 81,109,081 (+)NCBIGRCm39mm39
GRCm39 Ensembl1081,102,794 - 81,109,080 (+)Ensembl
GRCm381081,266,935 - 81,273,247 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1081,266,960 - 81,273,246 (+)EnsemblGRCm38mm10GRCm38
MGSCv371080,730,917 - 80,735,992 (+)NCBIGRCm37mm9NCBIm37
MGSCv361080,671,369 - 80,676,357 (+)NCBImm8
Celera1082,288,520 - 82,293,595 (+)NCBICelera
Cytogenetic Map10C1NCBI
Apba3
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554955,647,356 - 5,653,360 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554955,647,274 - 5,654,634 (-)NCBIChiLan1.0ChiLan1.0
APBA3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1193,722,896 - 3,734,153 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl193,722,896 - 3,734,153 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0192,774,535 - 2,785,404 (-)NCBIMhudiblu_PPA_v0panPan3
APBA3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl2055,713,773 - 55,721,655 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.12055,712,908 - 55,720,532 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Apba3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049365882,124,286 - 2,130,085 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
APBA3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl274,930,087 - 74,946,888 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1274,930,077 - 74,945,372 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2275,521,563 - 75,535,984 (+)NCBISscrofa10.2Sscrofa10.2susScr3
APBA3
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.163,505,907 - 3,517,464 (-)NCBI
ChlSab1.1 Ensembl63,506,044 - 3,517,462 (-)Ensembl
Apba3
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248286,398,541 - 6,405,904 (-)NCBI

Position Markers
RH128401  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0711,314,527 - 11,314,807NCBIRnor6.0
Rnor_5.0711,481,935 - 11,482,215UniSTSRnor5.0
RGSC_v3.479,930,073 - 9,930,353UniSTSRGSC3.4
Celera76,634,598 - 6,634,878UniSTS
Cytogenetic Map7q11UniSTS
RH131893  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0711,314,337 - 11,314,487NCBIRnor6.0
Rnor_5.0711,481,745 - 11,481,895UniSTSRnor5.0
RGSC_v3.479,929,883 - 9,930,033UniSTSRGSC3.4
Celera76,634,408 - 6,634,558UniSTS
Cytogenetic Map7q11UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2298550Neuinf6Neuroinflammation QTL 63.3nervous system integrity trait (VT:0010566)spinal cord RT1-B protein level (CMO:0002132)7134147172Rat
724560Plsm3Polydactyly-luxate syndrome (PLS) morphotypes QTL 30.0003tibia length (VT:0004357)tibia length (CMO:0000450)7137009673Rat
631503Bp102Blood pressure QTL 1021.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)7595196950951969Rat
634336Anxrr17Anxiety related response QTL 173.66locomotor behavior trait (VT:0001392)number of entries into a discrete space in an experimental apparatus (CMO:0000960)72920071124838025Rat
1300176Hrtrt10Heart rate QTL 103.19heart pumping trait (VT:2000009)heart rate (CMO:0000002)7265313832258115Rat
2317047Wbc4White blood cell count QTL 40.01leukocyte quantity (VT:0000217)white blood cell count (CMO:0000027)7138119654Rat
61410Bw19Body weight QTL 196.20.001body mass (VT:0001259)body weight (CMO:0000012)7591147750911477Rat
7411566Bw136Body weight QTL 13610.40.001body mass (VT:0001259)body weight gain (CMO:0000420)7134828535Rat
9590142Scort5Serum corticosterone level QTL 524.40.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)7134828535Rat
10755438Coatc9Coat color QTL 90coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)7975804554758045Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:101
Count of miRNA genes:81
Interacting mature miRNAs:84
Transcripts:ENSRNOT00000027784
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
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.


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 renal system reproductive system respiratory system appendage
High
Medium 3 35 52 41 9 41 8 11 63 35 35 10 8
Low 8 5 10 11 6 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027784   ⟹   ENSRNOP00000027784
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl711,314,424 - 11,319,516 (-)Ensembl
RefSeq Acc Id: NM_031781   ⟹   NP_113969
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.278,446,222 - 8,450,644 (-)NCBI
Rnor_6.0711,314,478 - 11,318,900 (-)NCBI
Rnor_5.0711,481,876 - 11,486,939 (-)NCBI
RGSC_v3.479,930,024 - 9,934,446 (-)RGD
Celera76,634,549 - 6,638,968 (-)RGD
Sequence:
RefSeq Acc Id: XM_006241018   ⟹   XP_006241080
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.278,446,212 - 8,451,310 (-)NCBI
Rnor_6.0711,314,468 - 11,319,540 (-)NCBI
Rnor_5.0711,481,876 - 11,486,939 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006241019   ⟹   XP_006241081
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.278,446,212 - 8,451,258 (-)NCBI
Rnor_6.0711,314,468 - 11,319,403 (-)NCBI
Rnor_5.0711,481,876 - 11,486,939 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006241020   ⟹   XP_006241082
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.278,446,212 - 8,451,310 (-)NCBI
Rnor_6.0711,314,468 - 11,319,538 (-)NCBI
Rnor_5.0711,481,876 - 11,486,939 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039079956   ⟹   XP_038935884
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.278,446,212 - 8,451,255 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_113969   ⟸   NM_031781
- UniProtKB: O70248 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006241080   ⟸   XM_006241018
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_006241082   ⟸   XM_006241020
- Peptide Label: isoform X2
- UniProtKB: O70248 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006241081   ⟸   XM_006241019
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: ENSRNOP00000027784   ⟸   ENSRNOT00000027784
RefSeq Acc Id: XP_038935884   ⟸   XM_039079956
- Peptide Label: isoform X2
Protein Domains
PDZ   PID

Transcriptome

eQTL   View at Phenogen
WGCNA   View at Phenogen
Tissue/Strain Expression   View at Phenogen

Promoters
RGD ID:13694979
Promoter ID:EPDNEW_R5504
Type:initiation region
Name:Apba3_1
Description:amyloid beta precursor protein binding family A member 3
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0711,319,477 - 11,319,537EPDNEW

Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
Visual CSV TAB Printer
Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
Visual CSV TAB Printer
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
Visual CSV TAB Printer
Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 11483306 11483307 C T snv BUF/N (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
7 11315898 11315899 C T snv Buf/N (MCW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620846 AgrOrtholog
Ensembl Genes ENSRNOG00000020466 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000027784 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000027784 UniProtKB/Swiss-Prot
Gene3D-CATH 2.30.29.30 UniProtKB/Swiss-Prot
  2.30.42.10 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:9102177 IMAGE-MGC_LOAD
InterPro Apba3 UniProtKB/Swiss-Prot
  PDZ UniProtKB/Swiss-Prot
  PDZ_sf UniProtKB/Swiss-Prot
  PH-like_dom_sf UniProtKB/Swiss-Prot
  PTB/PI_dom UniProtKB/Swiss-Prot
KEGG Report rno:83611 UniProtKB/Swiss-Prot
MGC_CLONE MGC:187359 IMAGE-MGC_LOAD
NCBI Gene 83611 ENTREZGENE
PANTHER PTHR12345:SF9 UniProtKB/Swiss-Prot
Pfam PDZ UniProtKB/Swiss-Prot
  PID UniProtKB/Swiss-Prot
PhenoGen Apba3 PhenoGen
PROSITE PDZ UniProtKB/Swiss-Prot
  PID UniProtKB/Swiss-Prot
SMART PDZ UniProtKB/Swiss-Prot
  PTB UniProtKB/Swiss-Prot
Superfamily-SCOP SSF50156 UniProtKB/Swiss-Prot
UniProt APBA3_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary B1WBQ3 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-01-27 Apba3  amyloid beta precursor protein binding family A member 3  Apba3  amyloid beta (A4) precursor protein-binding, family A, member 3  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2004-12-14 Apba3  amyloid beta (A4) precursor protein-binding, family A, member 3    amyloid beta (A4) precursor protein-binding, family A, member 3 (X11-like 2)  Name updated 1299863 APPROVED
2002-08-07 Apba3  amyloid beta (A4) precursor protein-binding, family A, member 3 (X11-like 2)      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed ubiquitously in contrast to brain-specific expression of family members Mint1 and Mint2 1302262