Nap1l3 (nucleosome assembly protein 1-like 3) - Rat Genome Database

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Gene: Nap1l3 (nucleosome assembly protein 1-like 3) Rattus norvegicus
Analyze
Symbol: Nap1l3
Name: nucleosome assembly protein 1-like 3
RGD ID: 620990
Description: Predicted to enable chromatin binding activity and histone binding activity. Predicted to be involved in nucleosome assembly. Predicted to be active in chromatin and nucleus. Orthologous to human NAP1L3 (nucleosome assembly protein 1 like 3); INTERACTS WITH 17beta-estradiol; 2,3,7,8-tetrachlorodibenzodioxine; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: MGC124570
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Pig
Green Monkey
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X92,607,628 - 92,610,426 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX92,604,626 - 92,610,687 (-)EnsemblGRCr8
mRatBN7.2X88,347,595 - 88,350,393 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX88,347,598 - 88,350,393 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX90,020,382 - 90,023,197 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X93,495,070 - 93,497,895 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X91,032,608 - 91,035,406 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X95,059,334 - 95,062,132 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX95,059,337 - 95,062,132 (-)Ensemblrn6Rnor6.0
Rnor_5.0X94,947,138 - 94,949,936 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X112,244,521 - 112,247,319 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX89,512,530 - 89,515,352 (-)NCBICelera
RGSC_v3.1X112,318,049 - 112,320,664 (-)NCBI
Cytogenetic MapXq31NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
chromatin  (IBA)
nucleus  (IBA,IEA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Electronic Transfer of LocusLink and RefSeq Data NCBI rat LocusLink and RefSeq merged data July 26, 2002
4. GOA pipeline RGD automated data pipeline
5. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
6. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
7. Cloning, expression pattern and mapping to Xq of NAP1L3, a gene encoding a peptide homologous to human and yeast nucleosome assembly proteins. Watanabe TK, etal., Cytogenet Cell Genet 1996;74(4):281-5.
Additional References at PubMed
PMID:12477932   PMID:15489334  


Genomics

Comparative Map Data
Nap1l3
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8X92,607,628 - 92,610,426 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 EnsemblX92,604,626 - 92,610,687 (-)EnsemblGRCr8
mRatBN7.2X88,347,595 - 88,350,393 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 EnsemblX88,347,598 - 88,350,393 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_UtxX90,020,382 - 90,023,197 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0X93,495,070 - 93,497,895 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0X91,032,608 - 91,035,406 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0X95,059,334 - 95,062,132 (-)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 EnsemblX95,059,337 - 95,062,132 (-)Ensemblrn6Rnor6.0
Rnor_5.0X94,947,138 - 94,949,936 (-)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4X112,244,521 - 112,247,319 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
CeleraX89,512,530 - 89,515,352 (-)NCBICelera
RGSC_v3.1X112,318,049 - 112,320,664 (-)NCBI
Cytogenetic MapXq31NCBI
NAP1L3
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38X93,670,930 - 93,673,578 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 EnsemblX93,670,930 - 93,673,578 (-)Ensemblhg38GRCh38
GRCh37X92,925,929 - 92,928,577 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X92,812,585 - 92,815,264 (-)NCBIBuild 36Build 36hg18NCBI36
Build 34X92,732,076 - 92,734,753NCBI
CeleraX93,451,177 - 93,453,856 (-)NCBICelera
Cytogenetic MapXq21.32NCBI
HuRefX82,748,172 - 82,750,929 (-)NCBIHuRef
CHM1_1X92,818,596 - 92,821,352 (-)NCBICHM1_1
T2T-CHM13v2.0X92,116,100 - 92,118,747 (-)NCBIT2T-CHM13v2.0
Nap1l3
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X121,304,257 - 121,307,082 (-)NCBIGRCm39GRCm39mm39
GRCm39 EnsemblX121,304,262 - 121,307,098 (-)EnsemblGRCm39 EnsemblGRCm39
GRCm38X122,394,560 - 122,397,385 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX122,394,565 - 122,397,401 (-)Ensemblmm10GRCm38
MGSCv37X119,508,169 - 119,510,994 (-)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv36X118,511,504 - 118,514,329 (-)NCBIMGSCv36mm8
CeleraX108,897,262 - 108,900,087 (-)NCBICelera
Cytogenetic MapXE3NCBI
cM MapX49.81NCBI
NAP1L3
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2X93,282,013 - 93,284,646 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1X93,285,619 - 93,288,243 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0X82,895,237 - 82,897,938 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1X93,056,951 - 93,059,699 (-)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX93,057,803 - 93,059,323 (-)EnsemblpanPan2panpan1.1
NAP1L3
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X69,231,981 - 69,233,827 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX69,232,078 - 69,233,499 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_TashaX60,036,178 - 60,038,049 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0X70,602,437 - 70,604,308 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
UMICH_Zoey_3.1X68,231,645 - 68,233,516 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0X69,888,378 - 69,890,253 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0X69,481,410 - 69,483,266 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Nap1l3
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X69,949,159 - 69,951,706 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_004936649275,068 - 276,681 (+)EnsemblSpeTri2.0 Ensembl
SpeTri2.0NW_004936649274,677 - 277,545 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
NAP1L3
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX76,147,202 - 76,149,852 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.1X76,147,190 - 76,149,848 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X92,751,719 - 92,754,364 (+)NCBISscrofa10.2Sscrofa10.2susScr3
NAP1L3
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X82,210,242 - 82,212,997 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 EnsemblX82,211,097 - 82,212,620 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_0236660657,127,277 - 7,130,027 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0

Variants

.
Variants in Nap1l3
10 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:529
Count of miRNA genes:269
Interacting mature miRNAs:316
Transcripts:ENSRNOT00000049956
Prediction methods:Microtar, Miranda, Pita
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
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X80434318125434318Rat
738035Stresp1Stress response QTL 14.960.000011stress-related behavior trait (VT:0010451)defensive burying - copingX45182909117740458Rat

Markers in Region
RH132228  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X88,347,678 - 88,347,866 (+)MAPPERmRatBN7.2
Rnor_6.0X95,059,418 - 95,059,605NCBIRnor6.0
Rnor_5.0X94,947,222 - 94,947,409UniSTSRnor5.0
RGSC_v3.4X112,244,605 - 112,244,792UniSTSRGSC3.4
CeleraX89,512,614 - 89,512,801UniSTS
Cytogenetic MapXq32UniSTS
NAP1L3  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X88,348,625 - 88,348,791 (+)MAPPERmRatBN7.2
Rnor_6.0X95,060,365 - 95,060,530NCBIRnor6.0
Rnor_5.0X94,948,169 - 94,948,334UniSTSRnor5.0
RGSC_v3.4X112,245,552 - 112,245,717UniSTSRGSC3.4
CeleraX89,513,561 - 89,513,726UniSTS
Cytogenetic MapXq32UniSTS


Expression

RNA-SEQ Expression

alimentary part of gastrointestinal system
appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hemolymphoid system
hepatobiliary system
integumental system
mesenchyme
mesoderm
musculoskeletal system
nervous system
renal system
reproductive system
respiratory system
sensory system
visual system
16 12 67 162 91 90 59 37 59 6 301 137 11 141 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000049956   ⟹   ENSRNOP00000048930
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX92,604,716 - 92,610,525 (-)Ensembl
mRatBN7.2 EnsemblX88,347,598 - 88,350,393 (-)Ensembl
Rnor_6.0 EnsemblX95,059,337 - 95,062,132 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000124505   ⟹   ENSRNOP00000103159
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX92,604,626 - 92,610,687 (-)Ensembl
Ensembl Acc Id: ENSRNOT00000162821   ⟹   ENSRNOP00000103744
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 EnsemblX92,605,451 - 92,610,591 (-)Ensembl
RefSeq Acc Id: NM_133402   ⟹   NP_596893
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8X92,607,628 - 92,610,426 (-)NCBI
mRatBN7.2X88,347,595 - 88,350,393 (-)NCBI
Rnor_6.0X95,059,334 - 95,062,132 (-)NCBI
Rnor_5.0X94,947,138 - 94,949,936 (-)NCBI
RGSC_v3.4X112,244,521 - 112,247,319 (-)RGD
CeleraX89,512,530 - 89,515,352 (-)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_596893 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAI01933 (Get FASTA)   NCBI Sequence Viewer  
  BAB62331 (Get FASTA)   NCBI Sequence Viewer  
  EDM07058 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000048930
  ENSRNOP00000048930.3
GenBank Protein Q924R9 (Get FASTA)   NCBI Sequence Viewer  
RefSeq Acc Id: NP_596893   ⟸   NM_133402
- UniProtKB: Q924R9 (UniProtKB/Swiss-Prot),   A6IVC2 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000048930   ⟸   ENSRNOT00000049956
Ensembl Acc Id: ENSRNOP00000103744   ⟸   ENSRNOT00000162821
Ensembl Acc Id: ENSRNOP00000103159   ⟸   ENSRNOT00000124505

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q924R9-F1-model_v2 AlphaFold Q924R9 1-536 view protein structure

Transcriptome

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

Promoters
RGD ID:13701921
Promoter ID:EPDNEW_R12445
Type:single initiation site
Name:Nap1l3_1
Description:nucleosome assembly protein 1-like 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_6.0X95,062,151 - 95,062,211EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620990 AgrOrtholog
BioCyc Gene G2FUF-1756 BioCyc
Ensembl Genes ENSRNOG00000029087 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000049956 ENTREZGENE
  ENSRNOT00000049956.4 UniProtKB/Swiss-Prot
Gene3D-CATH 1.20.5.1500 UniProtKB/Swiss-Prot
  Nucleosome assembly protein UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7938895 IMAGE-MGC_LOAD
InterPro NAP-like_sf UniProtKB/Swiss-Prot
  NAP_family UniProtKB/Swiss-Prot
KEGG Report rno:170914 UniProtKB/Swiss-Prot
MGC_CLONE MGC:124570 IMAGE-MGC_LOAD
NCBI Gene 170914 ENTREZGENE
PANTHER PTHR11875 UniProtKB/Swiss-Prot
Pfam NAP UniProtKB/Swiss-Prot
PhenoGen Nap1l3 PhenoGen
RatGTEx ENSRNOG00000029087 RatGTEx
Superfamily-SCOP SSF143113 UniProtKB/Swiss-Prot
UniProt A6IVC2 ENTREZGENE, UniProtKB/TrEMBL
  NP1L3_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2004-09-10 Nap1l3  nucleosome assembly protein 1-like 3      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Nap1l3  nucleosome assembly protein 1-like 3      Symbol and Name status set to provisional 70820 PROVISIONAL