Habp4 (hyaluronan binding protein 4) - Rat Genome Database

Send us a Message
Submit Data |  Help |  Video Tutorials |  News |  Publications |  Download |  REST API |  Citing RGD |  Contact   
Search RGD Grant Resources Citing RGD About Us Contact Us
Genes Variants Community Projects QTLs Strains Markers Genome Information Ontologies Cell Lines References Download Submit Data
OntoMate (Literature Search) JBrowse (Genome Browser) Synteny Browser (VCMap) Variant Visualizer Multi-Ontology Enrichment (MOET) Gene-Ortholog Location Finder (GOLF) InterViewer (Protein-Protein Interactions) PhenoMiner (Quatitative Phenotypes) Gene Annotator OLGA (Gene List Generator) AllianceMine GViewer (Genome Viewer)
Aging & Age-Related Disease Behavioral & Substance Use Disorder Cancer & Neoplastic Disease Cardiovascular Disease Coronavirus Disease Developmental Disease Diabetes Hematologic Disease Immune & Inflammatory Disease Infectious Disease Liver Disease Neurological Disease Obesity & Metabolic Syndrome Renal Disease Respiratory Disease Sensory Organ Disease
Find Models Genetic Models Autism Models Rat PhenoMiner (Quantitative Phenotypes) Chinchilla PhenoMiner Expected Ranges (Quantitative Phenotype) PhenoMiner Term Comparison Hybrid Rat Diversity Panel Phenotypes Phenotypes in Other Animal Models Animal Husbandry Strain Medical Records Phylogenetics Strain Availability Calendar Rats 101 Submissions Photo Archive
Pathways
Rat Community Forum Directory of Rat Laboratories Video Tutorials News RGD Publications RGD Presentations Archive Nomenclature Guidelines Resource Links Laboratory Resources Employment Resources
Advanced Search (OLGA)
Gene: Habp4 (hyaluronan binding protein 4) Rattus norvegicus
Analyze
Symbol: Habp4
Name: hyaluronan binding protein 4
RGD ID: 1306486
Description: Predicted to enable several functions, including SUMO binding activity; ribosome binding activity; and translation elongation factor binding activity. Involved in cellular response to mechanical stimulus. Located in nucleus and sarcomere. Orthologous to human HABP4 (hyaluronan binding protein 4); INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,4-dinitrotoluene; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: hyaluronic acid binding protein 4; IHABP-4; IHABP4; intracellular hyaluronan-binding protein 4; ki-1/57 intracellular antigen; LOC361196
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Black Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: GRCr8 - GRCr8 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr817940,672 - 963,358 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl17941,389 - 963,300 (-)EnsemblGRCr8
mRatBN7.217934,931 - 957,604 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl17935,654 - 957,565 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx17954,331 - 976,245 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0172,496,907 - 2,518,821 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.017951,753 - 973,667 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0171,679,561 - 1,702,245 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl171,679,627 - 1,701,623 (+)Ensemblrn6Rnor6.0
Rnor_5.0171,669,161 - 1,691,807 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4176,462,632 - 6,484,546 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera171,559,641 - 1,581,556 (+)NCBICelera
RGSC_v3.1176,461,911 - 6,484,529 (-)NCBI
Cytogenetic Map17p14NCBI
JBrowse:




Gene Ontology Annotations     Click to see Annotation Detail View

Cellular Component
Cajal body  (IEA,ISO,ISS)
cytoplasm  (IBA,IDA,IEA,ISO)
cytoplasmic stress granule  (IEA,ISO,ISS)
cytosol  (IEA,ISO)
Gemini of Cajal bodies  (IEA,ISO,ISS)
nuclear body  (IEA)
nuclear membrane  (IEA,ISO)
nuclear speck  (IEA,ISO,ISS)
nucleolus  (IEA,ISO,ISS)
nucleus  (IBA,IDA,IEA,ISO)
sarcomere  (IDA)
sarcoplasm  (IEA)
synapse  (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 GOA human gene data--August 2006 GOA data from the GO Consortium
3. MEF2C DNA-binding activity is inhibited through its interaction with the regulatory protein Ki-1/57. Kobarg CB, etal., FEBS Lett. 2005 May 9;579(12):2615-22. Epub 2005 Apr 8.
4. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:10887182   PMID:12477932   PMID:16879614   PMID:19523114   PMID:21771594   PMID:28695742  


Genomics

Comparative Map Data
Habp4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr817940,672 - 963,358 (-)NCBIGRCr8GRCr8GRCr8
GRCr8 Ensembl17941,389 - 963,300 (-)EnsemblGRCr8
mRatBN7.217934,931 - 957,604 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl17935,654 - 957,565 (-)EnsemblmRatBN7.2
UTH_Rnor_SHR_Utx17954,331 - 976,245 (-)NCBIUTH_Rnor_SHR_UtxUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0172,496,907 - 2,518,821 (-)NCBIUTH_Rnor_SHRSP_BbbUtx_1.0UTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.017951,753 - 973,667 (-)NCBIUTH_Rnor_WKY_Bbb_1.0UTH_Rnor_WKY_Bbb_1.0
Rnor_6.0171,679,561 - 1,702,245 (+)NCBIRnor_6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl171,679,627 - 1,701,623 (+)Ensemblrn6Rnor6.0
Rnor_5.0171,669,161 - 1,691,807 (+)NCBIRnor_5.0Rnor_5.0rn5
RGSC_v3.4176,462,632 - 6,484,546 (-)NCBIRGSC_v3.4RGSC_v3.4rn4
Celera171,559,641 - 1,581,556 (+)NCBICelera
RGSC_v3.1176,461,911 - 6,484,529 (-)NCBI
Cytogenetic Map17p14NCBI
HABP4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38996,450,102 - 96,491,336 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl996,450,160 - 96,491,336 (+)Ensemblhg38GRCh38
GRCh37999,212,451 - 99,253,618 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 36998,252,235 - 98,293,439 (+)NCBIBuild 36Build 36hg18NCBI36
Build 34996,292,041 - 96,332,342NCBI
Celera969,653,998 - 69,695,193 (+)NCBICelera
Cytogenetic Map9q22.32NCBI
HuRef968,823,310 - 68,864,515 (+)NCBIHuRef
CHM1_1999,359,257 - 99,400,445 (+)NCBICHM1_1
T2T-CHM13v2.09108,621,878 - 108,663,114 (+)NCBIT2T-CHM13v2.0
Habp4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391364,309,680 - 64,334,351 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1364,309,638 - 64,334,351 (+)EnsemblGRCm39 EnsemblGRCm39
GRCm381364,161,866 - 64,186,537 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1364,161,824 - 64,186,537 (+)Ensemblmm10GRCm38
MGSCv371364,263,174 - 64,287,845 (+)NCBIMGSCv37MGSCv37mm9NCBIm37
MGSCv361364,171,142 - 64,195,756 (+)NCBIMGSCv36mm8
Celera1365,825,382 - 65,849,877 (+)NCBICelera
Cytogenetic Map13B3NCBI
cM Map1333.26NCBI
Habp4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542223,450,251 - 23,475,984 (-)Ensembl
ChiLan1.0NW_00495542223,449,175 - 23,475,919 (-)NCBIChiLan1.0ChiLan1.0
HABP4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v21142,960,697 - 43,002,100 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1942,963,075 - 43,004,476 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0967,545,866 - 67,587,270 (+)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1995,640,088 - 95,708,956 (+)NCBIPanPan1.1PanPan1.1panPan2
PanPan1.1 Ensembl995,668,184 - 95,707,653 (+)EnsemblpanPan2panpan1.1
HABP4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1170,339,386 - 70,381,694 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl170,340,627 - 70,377,204 (-)EnsemblcanFam3CanFam3.1
Dog10K_Boxer_Tasha171,102,548 - 71,145,168 (-)NCBIDog10K_Boxer_TashaDog10K_Boxer_Tasha
ROS_Cfam_1.0170,638,461 - 70,681,245 (-)NCBIROS_Cfam_1.0ROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl170,638,461 - 70,681,444 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.1170,451,726 - 70,494,546 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.0170,214,850 - 70,257,618 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.0170,925,886 - 70,968,739 (-)NCBIUU_Cfam_GSD_1.0UU_Cfam_GSD_1.0
Habp4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_0244049446,186,158 - 6,207,913 (+)NCBIHiC_Itri_2
SpeTri2.0NW_004936487402,701 - 424,399 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
HABP4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1025,598,175 - 25,636,046 (-)EnsemblsusScr11Sscrofa11.1
Sscrofa11.11025,599,413 - 25,636,000 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21029,514,408 - 29,538,323 (+)NCBISscrofa10.2Sscrofa10.2susScr3
HABP4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.112106,645,715 - 106,685,444 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl12106,643,424 - 106,685,417 (-)EnsemblChlSab1.1 EnsemblchlSab2Vervet-AGM
Vero_WHO_p1.0NW_02366603895,044,457 - 95,084,354 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Habp4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462475318,047,970 - 18,078,150 (-)EnsemblHetGla_female_1.0 EnsemblhetGla2HetGla_female_1.0 Ensembl
HetGla 1.0NW_00462475318,048,042 - 18,077,322 (-)NCBIHetGla 1.0HetGla 1.0hetGla2
Habp4
(Rattus rattus - black rat)
Black Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Rrattus_CSIRO_v11475,368,272 - 75,390,324 (-)NCBIRrattus_CSIRO_v1

Variants

.
Variants in Habp4
28 total Variants
miRNA Target Status (No longer updated)

Predicted Target Of
Summary Value
Count of predictions:28
Count of miRNA genes:28
Interacting mature miRNAs:28
Transcripts:ENSRNOT00000025801
Prediction methods:Miranda, Rnahybrid
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
10401807Kidm52Kidney mass QTL 52kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)17131706603Rat
1354613Kidm14Kidney mass QTL 146.2kidney mass (VT:0002707)left kidney wet weight (CMO:0000083)17136045694Rat
1354581Bp247Blood pressure QTL 2474.5arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)17143999106Rat
1354662Rf49Renal function QTL 492.9blood creatinine amount (VT:0005328)plasma creatinine level (CMO:0000537)17143999106Rat
1354658Spl8Serum phospholipid level QTL 83.8blood VLDL phospholipid amount (VT:0010507)blood very low density lipoprotein phospholipid level (CMO:0001571)17143999106Rat
2324619Coatc4Coat color QTL 40.001coat/hair pigmentation trait (VT:0010463)pigmented dorsal coat/hair area to total dorsal coat/hair area ratio (CMO:0001811)17121499218Rat
1549900Iddm20Insulin dependent diabetes mellitus QTL 203.7pancreas integrity trait (VT:0010560)percentage of study population developing diabetes mellitus during a period of time (CMO:0001114)17122181410Rat
9590316Scort21Serum corticosterone level QTL 214.750.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)17122877318Rat
631207Niddm41Non-insulin dependent diabetes mellitus QTL 41blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)17138037084Rat

Markers in Region
BE115750  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.217935,706 - 936,737 (-)MAPPERmRatBN7.2
Rnor_6.0171,700,445 - 1,701,475NCBIRnor6.0
Rnor_5.0171,690,001 - 1,691,031UniSTSRnor5.0
RGSC_v3.4176,462,688 - 6,463,718UniSTSRGSC3.4
Celera171,580,470 - 1,581,500UniSTS
RH 3.4 Map1716.0UniSTS
Cytogenetic Map17p14UniSTS


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 67 164 91 90 59 92 59 6 356 192 11 143 81 92 31 17 17

Sequence


Ensembl Acc Id: ENSRNOT00000025801   ⟹   ENSRNOP00000025801
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8 Ensembl17941,389 - 963,300 (-)Ensembl
mRatBN7.2 Ensembl17935,654 - 957,565 (-)Ensembl
Rnor_6.0 Ensembl171,679,627 - 1,701,623 (+)Ensembl
RefSeq Acc Id: NM_001079940   ⟹   NP_001073409
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr817941,386 - 963,300 (-)NCBI
mRatBN7.217935,651 - 957,565 (-)NCBI
Rnor_6.0171,679,617 - 1,701,531 (+)NCBI
Rnor_5.0171,669,161 - 1,691,807 (+)NCBI
RGSC_v3.4176,462,632 - 6,484,546 (-)RGD
Celera171,559,641 - 1,581,556 (+)RGD
Sequence:
RefSeq Acc Id: XM_006253494   ⟹   XP_006253556
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr817940,672 - 963,358 (-)NCBI
mRatBN7.217934,931 - 957,604 (-)NCBI
Rnor_6.0171,679,561 - 1,702,245 (+)NCBI
Rnor_5.0171,669,161 - 1,691,807 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_001073409 (Get FASTA)   NCBI Sequence Viewer  
  XP_006253556 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein A1L1K8 (Get FASTA)   NCBI Sequence Viewer  
  AAI29112 (Get FASTA)   NCBI Sequence Viewer  
  EDL84429 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000025801
  ENSRNOP00000025801.4
RefSeq Acc Id: NP_001073409   ⟸   NM_001079940
- UniProtKB: A1L1K8 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006253556   ⟸   XM_006253494
- Peptide Label: isoform X1
- Sequence:
Ensembl Acc Id: ENSRNOP00000025801   ⟸   ENSRNOT00000025801

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-A1L1K8-F1-model_v2 AlphaFold A1L1K8 1-411 view protein structure

Transcriptome

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

Promoters
RGD ID:13700261
Promoter ID:EPDNEW_R10785
Type:multiple initiation site
Name:Habp4_1
Description:hyaluronan binding protein 4
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_6.0171,679,603 - 1,679,663EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1306486 AgrOrtholog
BioCyc Gene G2FUF-10538 BioCyc
Ensembl Genes ENSRNOG00000019027 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000025801 ENTREZGENE
  ENSRNOT00000025801.7 UniProtKB/Swiss-Prot
IMAGE_CLONE IMAGE:7111244 IMAGE-MGC_LOAD
InterPro HABP4/SERBP1 UniProtKB/Swiss-Prot
  HABP4_PAIRBP1-bd UniProtKB/Swiss-Prot
  IHABP4_N UniProtKB/Swiss-Prot
KEGG Report rno:361196 UniProtKB/Swiss-Prot
MGC_CLONE MGC:156749 IMAGE-MGC_LOAD
NCBI Gene 361196 ENTREZGENE
PANTHER INTRACELLULAR HYALURONAN-BINDING PROTEIN 4 UniProtKB/Swiss-Prot
  PTHR12299 UniProtKB/Swiss-Prot
Pfam HABP4_PAI-RBP1 UniProtKB/Swiss-Prot
  IHABP4_N UniProtKB/Swiss-Prot
PhenoGen Habp4 PhenoGen
RatGTEx ENSRNOG00000019027 RatGTEx
SMART HABP4_PAI-RBP1 UniProtKB/Swiss-Prot
UniProt A1L1K8 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-10-17 Habp4  hyaluronan binding protein 4  Habp4  hyaluronic acid binding protein 4   Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Habp4  hyaluronic acid binding protein 4   Habp4_predicted  hyaluronic acid binding protein 4 (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Habp4_predicted  hyaluronic acid binding protein 4 (predicted)      Symbol and Name status set to approved 70820 APPROVED