Litafd (LITAF domain containing) - Rat Genome Database

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Gene: Litafd (LITAF domain containing) Rattus norvegicus
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Symbol: Litafd
Name: LITAF domain containing
RGD ID: 1564086
Description: Predicted to enable metal ion binding activity. Predicted to be located in lysosomal membrane. Orthologous to human LITAFD (LITAF domain containing); INTERACTS WITH (1->4)-beta-D-glucan (ortholog); perfluorooctane-1-sulfonic acid (ortholog).
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: AC129395.1; lipopolysaccharide-induced tumor necrosis factor-alpha factor homolog; LOC497862; RGD1564086; RGD1564086
RGD Orthologs
Human
Mouse
Bonobo
Dog
Squirrel
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8107,438,372 - 7,442,349 (-)NCBIGRCr8
mRatBN7.2106,931,719 - 6,935,869 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl106,931,707 - 6,934,913 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1011,638,917 - 11,642,787 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01011,135,381 - 11,139,250 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0106,786,490 - 6,790,377 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0107,026,271 - 7,029,705 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl107,026,301 - 7,029,136 (-)NCBIRnor6.0rn6Rnor6.0
Rnor_5.0105,828,532 - 5,832,032 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4106,970,991 - 6,974,096 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera105,927,188 - 5,930,621 (-)NCBICelera
Cytogenetic Map10q12NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


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. 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.

Genomics

Comparative Map Data
Litafd
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8107,438,372 - 7,442,349 (-)NCBIGRCr8
mRatBN7.2106,931,719 - 6,935,869 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl106,931,707 - 6,934,913 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx1011,638,917 - 11,642,787 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.01011,135,381 - 11,139,250 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0106,786,490 - 6,790,377 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0107,026,271 - 7,029,705 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl107,026,301 - 7,029,136 (-)NCBIRnor6.0rn6Rnor6.0
Rnor_5.0105,828,532 - 5,832,032 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4106,970,991 - 6,974,096 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
Celera105,927,188 - 5,930,621 (-)NCBICelera
Cytogenetic Map10q12NCBI
LITAFD
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38168,882,351 - 8,885,350 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl168,882,351 - 8,885,351 (+)EnsemblGRCh38hg38GRCh38
GRCh37168,976,208 - 8,979,207 (+)NCBIGRCh37GRCh37hg19GRCh37
Cytogenetic Map16p13.2NCBI
CHM1_1168,976,208 - 8,979,173 (+)NCBICHM1_1
T2T-CHM13v2.0168,915,087 - 8,918,086 (+)NCBIT2T-CHM13v2.0
Litafd
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39168,489,542 - 8,501,769 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl168,498,634 - 8,501,775 (+)EnsemblGRCm39 Ensembl
GRCm38168,679,919 - 8,683,905 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl168,680,770 - 8,683,911 (+)EnsemblGRCm38mm10GRCm38
MGSCv37168,680,863 - 8,683,998 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36168,596,091 - 8,599,228 (+)NCBIMGSCv36mm8
Celera169,326,485 - 9,329,623 (+)NCBICelera
Cytogenetic Map16A1NCBI
cM Map164.27NCBI
LITAFD
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2189,421,994 - 9,424,952 (+)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan11613,199,322 - 13,206,887 (+)NCBINHGRI_mPanPan1
LITAFD
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1633,319,376 - 33,323,370 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha634,710,284 - 34,714,279 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.0633,518,089 - 33,522,082 (-)NCBIROS_Cfam_1.0
UMICH_Zoey_3.1633,320,725 - 33,324,714 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0633,190,619 - 33,194,596 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0633,612,344 - 33,616,337 (-)NCBIUU_Cfam_GSD_1.0
Litafd
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024409344109,835,937 - 109,842,268 (+)NCBIHiC_Itri_2
SpeTri2.0NW_0049365307,682,745 - 7,687,674 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0

Variants

.
Variants in Litafd
47 total Variants

QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
634329Pia15Pristane induced arthritis QTL 153.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10124158324Rat
2293680Bss40Bone structure and strength QTL 405.660.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)10135225947Rat
634327Hc4Hypercalciuria QTL 42.4urine calcium amount (VT:0002985)urine calcium excretion rate (CMO:0000763)10138328221Rat
7411611Foco17Food consumption QTL 1718.70.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)10142315980Rat
70223Bp57Blood pressure QTL 575arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)10180676123Rat
10401803Kidm50Kidney mass QTL 50kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1041834445418344Rat
631554Bp133Blood pressure QTL 1330.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1074336463851208Rat
1576304Schws7Schwannoma susceptibility QTL 70.0115nervous system integrity trait (VT:0010566)percentage of study population developing trigeminal nerve neurilemmomas during a period of time (CMO:0002017)10476552719816042Rat
631828Alc5Alcohol consumption QTL 52.4consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402717245662Rat
737820Alc9Alcohol consumption QTL 92.2consumption behavior trait (VT:0002069)ethanol drink intake rate (CMO:0001407)10514402719233348Rat
2313064Bmd71Bone mineral density QTL 710.90.0001tibia mineral mass (VT:1000283)compact volumetric bone mineral density (CMO:0001730)10538701450387014Rat
2313066Bss63Bone structure and strength QTL 631.40.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)10538701450387014Rat
2313081Bss64Bone structure and strength QTL 641.30.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)10538701450387014Rat
2313095Bss62Bone structure and strength QTL 621.50.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2313104Bss61Bone structure and strength QTL 610.90.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)10538701450387014Rat
2298544Neuinf9Neuroinflammation QTL 94.6nervous system integrity trait (VT:0010566)spinal cord complement component 1, q subcomponent, B chain mRNA level (CMO:0002126)10580199062146030Rat
631660Hcar1Hepatocarcinoma resistance QTL 13.40.0001liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)10615418215990232Rat
8662860Vetf10Vascular elastic tissue fragility QTL 10artery integrity trait (VT:0010639)number of ruptures of the internal elastic lamina of the abdominal aorta and iliac arteries (CMO:0002562)10615418273453136Rat
61427Cia16Collagen induced arthritis QTL 163.2joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)10635789696121100Rat
1578761Stresp21Stress response QTL 213.3thymus mass (VT:0004954)thymus wet weight (CMO:0000855)10637574651375746Rat


Expression


Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000091942   ⟹   ENSRNOP00000070396
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl106,931,707 - 6,933,645 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000109189   ⟹   ENSRNOP00000085205
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl106,931,707 - 6,934,913 (-)Ensembl
RefSeq Acc Id: NM_001395427   ⟹   NP_001382356
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8107,438,382 - 7,442,349 (-)NCBI
mRatBN7.2106,931,719 - 6,935,685 (-)NCBI
RefSeq Acc Id: NM_001395428   ⟹   NP_001382357
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8107,438,382 - 7,442,349 (-)NCBI
mRatBN7.2106,931,719 - 6,935,685 (-)NCBI
RefSeq Acc Id: XM_039087048   ⟹   XP_038942976
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8107,438,372 - 7,441,451 (-)NCBI
mRatBN7.2106,932,254 - 6,935,869 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001382356 (Get FASTA)   NCBI Sequence Viewer  
  NP_001382357 (Get FASTA)   NCBI Sequence Viewer  
  XP_038942976 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000070396.2
  ENSRNOP00000085205.1
Reference Protein Sequences
RefSeq Acc Id: XP_038942976   ⟸   XM_039087048
- Peptide Label: isoform X1
RefSeq Acc Id: ENSRNOP00000085205   ⟸   ENSRNOT00000109189
RefSeq Acc Id: ENSRNOP00000070396   ⟸   ENSRNOT00000091942
RefSeq Acc Id: NP_001382357   ⟸   NM_001395428
- Peptide Label: isoform 2
RefSeq Acc Id: NP_001382356   ⟸   NM_001395427
- Peptide Label: isoform 1
Protein Domains
LITAF

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A0A0G2JXT5-F1-model_v2 AlphaFold A0A0G2JXT5 1-149 view protein structure

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:1564086 AgrOrtholog
BioCyc Gene G2FUF-26098 BioCyc
Ensembl Genes ENSRNOG00000055413 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000091942.2 UniProtKB/TrEMBL
  ENSRNOT00000109189.1 UniProtKB/TrEMBL
InterPro LITAF UniProtKB/TrEMBL
  LITAF_fam UniProtKB/TrEMBL
NCBI Gene 497862 ENTREZGENE
PANTHER LITAF DOMAIN-CONTAINING PROTEIN UniProtKB/TrEMBL
  PTHR23292 UniProtKB/TrEMBL
Pfam zf-LITAF-like UniProtKB/TrEMBL
PhenoGen Litafd PhenoGen
PROSITE LITAF UniProtKB/TrEMBL
RatGTEx ENSRNOG00000055413 RatGTEx
SMART LITAF UniProtKB/TrEMBL
UniProt A0A0G2JXT5_RAT UniProtKB/TrEMBL
  A0A8I6GCK9_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2022-06-02 Litafd  LITAF domain containing  AC129395.1    Data merged from RGD:15009439 737654 PROVISIONAL
2021-02-23 Litafd  LITAF domain containing  RGD1564086  RGD1564086  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2019-11-08 AC129395.1        Symbol and Name status set to provisional 45752 PROVISIONAL
2008-04-30 RGD1564086  RGD1564086   RGD1564086_predicted  RGD1564086 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-07 RGD1564086_predicted  RGD1564086 (predicted)  LOC497862  LOC497862  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC497862  LOC497862      Symbol and Name status set to provisional 70820 PROVISIONAL