Necab3 (N-terminal EF-hand calcium binding protein 3) - Rat Genome Database

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Gene: Necab3 (N-terminal EF-hand calcium binding protein 3) Rattus norvegicus
Analyze
No known orthologs.
Symbol: Necab3 (Ensembl: E2f1)
Name: N-terminal EF-hand calcium binding protein 3 (Ensembl:E2F transcription factor 1)
RGD ID: 1310124
Description: ENCODES a protein that exhibits calcium ion binding (inferred); metal ion binding (inferred); INVOLVED IN regulation of amyloid precursor protein biosynthetic process (inferred); FOUND IN cytoplasm (inferred); endoplasmic reticulum (inferred); endoplasmic reticulum membrane (inferred); INTERACTS WITH 2,2',4,4'-Tetrabromodiphenyl ether; 6-propyl-2-thiouracil; acrylamide
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: amyloid beta (A4) precursor protein-binding, family A, member 1 binding protein; amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein; Apba2bp; LOC311562; N-terminal EF-hand calcium-binding protein 3
RGD Orthologs
Alliance Orthologs
More Info homologs ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr83163,509,682 - 163,524,598 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl3163,509,683 - 163,524,155 (-)EnsemblGRCr8
mRatBN7.23143,049,477 - 143,064,372 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl3143,049,478 - 143,075,361 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx3146,916,075 - 146,930,552 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.03155,534,239 - 155,548,716 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.03153,273,607 - 153,288,084 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.03150,047,826 - 150,062,806 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl3150,047,826 - 150,073,721 (-)Ensemblrn6Rnor6.0
Rnor_5.03156,420,460 - 156,435,023 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.43145,017,420 - 145,031,905 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera3141,783,955 - 141,798,427 (-)NCBICelera
RGSC_v3.13144,923,608 - 144,927,575 (-)NCBI
Cytogenetic Map3q41NCBI
JBrowse:




Gene-Chemical Interaction Annotations     Click to see Annotation Detail View
Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Rat ISS GO annotations from GOA human gene data--August 2006 GOA data from the GO Consortium
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. GOA pipeline RGD automated data pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10833507   PMID:12780348   PMID:14697346  


Genomics

Variants

.
Variants in Necab3
190 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:115
Count of miRNA genes:83
Interacting mature miRNAs:101
Transcripts:ENSRNOT00000022115
Prediction methods: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.


QTLs in Region (GRCr8)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
2301411Bp320Blood pressure QTL 3200.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3141555229186555229Rat
12879876Bw182Body weight QTL 1820.003body mass (VT:0001259)body weight (CMO:0000012)3141555229186555229Rat
1582233Insul10Insulin level QTL 105.40.0015blood insulin amount (VT:0001560)serum insulin level times blood glucose level (CMO:0002040)3133259579178259579Rat
12879872Cm97Cardiac mass QTL 970.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)3141555229186555229Rat
1578653Vnigr3Vascular neointimal growth QTL 33.1artery morphology trait (VT:0002191)artery neointimal hyperplastic lesion area (CMO:0001414)3151075912189428310Rat
12879873Cm96Cardiac mass QTL 960.001heart mass (VT:0007028)heart wet weight to body weight ratio (CMO:0002408)3141555229186555229Rat
2302373Gluco39Glucose level QTL 395.01blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)3129154923182114333Rat
12879874Cm98Cardiac mass QTL 980.005heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)3141555229186555229Rat
1298068Bp167Blood pressure QTL 1670.004arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3161492708189428310Rat
12879875Kidm64Kidney mass QTL 640.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)3141555229186555229Rat
70216Cm14Cardiac mass QTL 142.1heart mass (VT:0007028)heart wet weight (CMO:0000069)351581665184004958Rat
2292591Esta4Estrogen-induced thymic atrophy QTL 4thymus mass (VT:0004954)thymus wet weight (CMO:0000855)367641776167835660Rat
61335Bp20Blood pressure QTL 203arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3161799493176036425Rat
1331726Bp208Blood pressure QTL 2083.129arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)3161799270187311134Rat
1578754Stresp16Stress response QTL 1640.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)3133134628178134628Rat
1582213Insul6Insulin level QTL 63.70.0009blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
1300173Rf11Renal function QTL 113.38renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)3141508991166376254Rat
9589106Insul23Insulin level QTL 2313.860.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)3152055202189428310Rat
10755461Coatc16Coat color QTL 16coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)3142898802187898802Rat
8662816Vetf4Vascular elastic tissue fragility QTL 44renal artery integrity trait (VT:0010642)number of ruptures of the internal elastic lamina of the renal arteries (CMO:0002563)379649560177741895Rat
1559282Emca5Estrogen-induced mammary cancer QTL 53.9mammary gland integrity trait (VT:0010552)percentage of study population developing mammary tumors during a period of time (CMO:0000948)3145335553189428310Rat
2303620Vencon4Ventilatory control QTL 43.9respiration trait (VT:0001943)tidal volume (CMO:0000222)3125116475170116475Rat
1582256Insul9Insulin level QTL 94.40.0016blood insulin amount (VT:0001560)absolute change in serum insulin level (CMO:0002038)3155759447189428310Rat
1576306Schws3Schwannoma susceptibility QTL 30.001nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)3139299381184299381Rat
1300159Kidm4Kidney mass QTL 43.83kidney mass (VT:0002707)right kidney wet weight to body weight ratio (CMO:0001953)3141508991177728348Rat
5686842Rf59Renal function QTL 59urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)3122395989167395989Rat
631673Iddm13Insulin dependent diabetes mellitus QTL 131.30.663blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)3137114333182114333Rat
1582248Insul7Insulin level QTL 73.90.0041blood insulin amount (VT:0001560)calculated serum insulin level (CMO:0000359)3155759447189428310Rat
2301971Cm71Cardiac mass QTL 714.63heart left ventricle mass (VT:0007031)heart left ventricle weight (CMO:0000776)3131036586176036586Rat
2301970Bw81Body weight QTL 815.19body mass (VT:0001259)body weight (CMO:0000012)3131036586176036586Rat
1581546Pur13Proteinuria QTL 132.930.0335urine total protein amount (VT:0000032)urine protein excretion rate (CMO:0000759)398651826167012663Rat
1578666Vnigr1Vascular neointimal growth QTL 14.6artery morphology trait (VT:0002191)artery lumen area (CMO:0001409)3151075912189428310Rat
1578656Vnigr2Vascular neointimal growth QTL 24.2artery morphology trait (VT:0002191)lesioned artery residual lumen area (CMO:0001417)3151075912189428310Rat
12879871Am7Aortic mass QTL 70.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)3141555229186555229Rat
631541Bp81Blood pressure QTL 814arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)3144575244189428310Rat
2293087Iddm27Insulin dependent diabetes mellitus QTL 272.68blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)3160357340167835660Rat


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
hemolymphoid system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
sensory system
visual system
7 1 17 47 57 118 84 11 46 27 32 17 17

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001098724 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591780 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017591781 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105072 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105073 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039105074 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283840 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283841 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283842 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283843 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283844 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283845 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283846 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063283847 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide CB801563 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH474050 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CK598536 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO397705 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000003 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Ensembl Acc Id: ENSRNOT00000022115   ⟹   ENSRNOP00000022115
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3163,509,683 - 163,524,155 (-)Ensembl
mRatBN7.2 Ensembl3143,049,478 - 143,063,951 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000022428   ⟹   ENSRNOP00000022428
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl3143,049,478 - 143,075,361 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000086933   ⟹   ENSRNOP00000070039
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl3163,509,683 - 163,524,155 (-)Ensembl
mRatBN7.2 Ensembl3143,049,478 - 143,063,951 (-)Ensembl
RefSeq Acc Id: NM_001098724   ⟹   NP_001092194
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83163,509,683 - 163,524,155 (-)NCBI
mRatBN7.23143,049,478 - 143,063,951 (-)NCBI
Rnor_6.03150,047,826 - 150,062,311 (-)NCBI
Rnor_5.03156,420,460 - 156,435,023 (-)NCBI
RGSC_v3.43145,017,420 - 145,031,905 (-)RGD
Celera3141,783,955 - 141,798,427 (-)RGD
Sequence:
RefSeq Acc Id: XM_039105072   ⟹   XP_038961000
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83163,509,682 - 163,524,598 (-)NCBI
mRatBN7.23143,049,477 - 143,064,372 (-)NCBI
RefSeq Acc Id: XM_039105073   ⟹   XP_038961001
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83163,509,682 - 163,524,598 (-)NCBI
mRatBN7.23143,049,477 - 143,064,372 (-)NCBI
RefSeq Acc Id: XM_039105074   ⟹   XP_038961002
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83163,509,682 - 163,524,598 (-)NCBI
mRatBN7.23143,049,477 - 143,064,372 (-)NCBI
RefSeq Acc Id: XM_063283840   ⟹   XP_063139910
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83163,509,682 - 163,524,598 (-)NCBI
RefSeq Acc Id: XM_063283841   ⟹   XP_063139911
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83163,509,682 - 163,524,598 (-)NCBI
RefSeq Acc Id: XM_063283842   ⟹   XP_063139912
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83163,509,682 - 163,514,282 (-)NCBI
RefSeq Acc Id: XM_063283843   ⟹   XP_063139913
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83163,509,682 - 163,513,708 (-)NCBI
RefSeq Acc Id: XM_063283844   ⟹   XP_063139914
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83163,509,682 - 163,514,282 (-)NCBI
RefSeq Acc Id: XM_063283845   ⟹   XP_063139915
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83163,509,682 - 163,514,282 (-)NCBI
RefSeq Acc Id: XM_063283846   ⟹   XP_063139916
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83163,509,682 - 163,514,282 (-)NCBI
RefSeq Acc Id: XM_063283847   ⟹   XP_063139917
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr83163,509,682 - 163,514,282 (-)NCBI
RefSeq Acc Id: NP_001092194   ⟸   NM_001098724
- UniProtKB: D3ZKY0 (UniProtKB/TrEMBL),   A6KHZ2 (UniProtKB/TrEMBL),   A6KHZ1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_038961002   ⟸   XM_039105074
- Peptide Label: isoform X4
- UniProtKB: A6KHZ1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038961001   ⟸   XM_039105073
- Peptide Label: isoform X2
- UniProtKB: A6KHZ1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038961000   ⟸   XM_039105072
- Peptide Label: isoform X1
- UniProtKB: A6KHZ1 (UniProtKB/TrEMBL)
Ensembl Acc Id: ENSRNOP00000022115   ⟸   ENSRNOT00000022115
Ensembl Acc Id: ENSRNOP00000070039   ⟸   ENSRNOT00000086933
Ensembl Acc Id: ENSRNOP00000022428   ⟸   ENSRNOT00000022428
RefSeq Acc Id: XP_063139911   ⟸   XM_063283841
- Peptide Label: isoform X5
- UniProtKB: A6KHZ1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139910   ⟸   XM_063283840
- Peptide Label: isoform X3
- UniProtKB: A6KHZ1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139917   ⟸   XM_063283847
- Peptide Label: isoform X11
- UniProtKB: A6KHZ4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139916   ⟸   XM_063283846
- Peptide Label: isoform X10
- UniProtKB: A6KHZ4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139915   ⟸   XM_063283845
- Peptide Label: isoform X9
- UniProtKB: A6KHZ4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139914   ⟸   XM_063283844
- Peptide Label: isoform X8
- UniProtKB: A6KHZ4 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063139912   ⟸   XM_063283842
- Peptide Label: isoform X6
RefSeq Acc Id: XP_063139913   ⟸   XM_063283843
- Peptide Label: isoform X7
Protein Domains
ABM   EF-hand

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1310124 AgrOrtholog
BioCyc Gene G2FUF-47172 BioCyc
Ensembl Genes ENSRNOG00000016708 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000022115 ENTREZGENE
  ENSRNOT00000022115.9 UniProtKB/TrEMBL
  ENSRNOT00000086933.3 UniProtKB/TrEMBL
Gene3D-CATH 3.30.70.100 UniProtKB/TrEMBL
  EF-hand UniProtKB/TrEMBL
InterPro Antibiotic_mOase UniProtKB/TrEMBL
  Dimeric_a/b-barrel UniProtKB/TrEMBL
  EF-hand-like_dom UniProtKB/TrEMBL
  EF_Hand_1_Ca_BS UniProtKB/TrEMBL
  EF_hand_Ca-bd UniProtKB/TrEMBL
  NECAB1/2/3 UniProtKB/TrEMBL
KEGG Report rno:311562 UniProtKB/TrEMBL
NCBI Gene 311562 ENTREZGENE
PANTHER N-TERMINAL EF-HAND CALCIUM-BINDING PROTEIN 3 UniProtKB/TrEMBL
  PTHR12178 UniProtKB/TrEMBL
Pfam ABM UniProtKB/TrEMBL
  EF_hand_3 UniProtKB/TrEMBL
PhenoGen Necab3 PhenoGen
PROSITE ABM UniProtKB/TrEMBL
  EF_HAND_1 UniProtKB/TrEMBL
  EF_HAND_2 UniProtKB/TrEMBL
RatGTEx ENSRNOG00000016708 RatGTEx
SMART EFh UniProtKB/TrEMBL
Superfamily-SCOP Dimer_A_B_barrel UniProtKB/TrEMBL
  SSF47473 UniProtKB/TrEMBL
UniProt A0A0G2JWW3_RAT UniProtKB/TrEMBL
  A6KHZ1 ENTREZGENE, UniProtKB/TrEMBL
  A6KHZ2 ENTREZGENE, UniProtKB/TrEMBL
  A6KHZ4 ENTREZGENE, UniProtKB/TrEMBL
  D3ZKY0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-25 Necab3  N-terminal EF-hand calcium binding protein 3  Apba2bp_predicted  amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein (predicted)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2007-09-25   amyloid beta (A4) precursor protein-binding, family A, member 2 binding protein (predicted)  Apba2bp_predicted  amyloid beta (A4) precursor protein-binding, family A, member 1 binding protein (predicted)  Name updated 1299863 APPROVED
2005-01-12 Apba2bp_predicted  amyloid beta (A4) precursor protein-binding, family A, member 1 binding protein (predicted)      Symbol and Name status set to approved 70820 APPROVED