Ferd3l (Fer3-like bHLH transcription factor) - 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 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: Ferd3l (Fer3-like bHLH transcription factor) Rattus norvegicus
Analyze
Symbol: Ferd3l
Name: Fer3-like bHLH transcription factor
RGD ID: 1311812
Description: Predicted to enable DNA-binding transcription repressor activity, RNA polymerase II-specific and RNA polymerase II transcription regulatory region sequence-specific DNA binding activity. Predicted to be involved in developmental process and negative regulation of transcription by RNA polymerase II. Predicted to act upstream of or within several processes, including floor plate development; regulation of dopaminergic neuron differentiation; and regulation of neurogenesis. Predicted to be located in nucleus. Orthologous to human FERD3L (Fer3 like bHLH transcription factor); INTERACTS WITH 6-propyl-2-thiouracil; acrylamide; amitrole.
Type: protein-coding
RefSeq Status: PROVISIONAL
Previously known as: Fer3-like; Fer3-like (Drosophila); LOC366598
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Orthologs
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8656,372,778 - 56,373,667 (+)NCBIGRCr8
mRatBN7.2650,645,379 - 50,646,268 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl650,645,379 - 50,646,268 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx650,926,154 - 50,927,042 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0651,241,096 - 51,241,984 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0650,697,311 - 50,698,199 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0653,371,706 - 53,372,596 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl653,371,706 - 53,372,584 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0662,993,988 - 62,994,878 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4652,576,336 - 52,577,225 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1652,579,517 - 52,580,018 (+)NCBI
Celera649,811,740 - 49,812,629 (+)NCBICelera
Cytogenetic Map6q16NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

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

Cellular Component
nucleus  (ISO)

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. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
3. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:12217327   PMID:20460368  


Genomics

Comparative Map Data
Ferd3l
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8656,372,778 - 56,373,667 (+)NCBIGRCr8
mRatBN7.2650,645,379 - 50,646,268 (+)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl650,645,379 - 50,646,268 (+)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx650,926,154 - 50,927,042 (+)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0651,241,096 - 51,241,984 (+)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0650,697,311 - 50,698,199 (+)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0653,371,706 - 53,372,596 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl653,371,706 - 53,372,584 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0662,993,988 - 62,994,878 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4652,576,336 - 52,577,225 (+)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1652,579,517 - 52,580,018 (+)NCBI
Celera649,811,740 - 49,812,629 (+)NCBICelera
Cytogenetic Map6q16NCBI
FERD3L
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38719,144,782 - 19,145,421 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl719,144,782 - 19,145,421 (-)EnsemblGRCh38hg38GRCh38
GRCh37719,184,405 - 19,185,044 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36719,150,930 - 19,151,569 (-)NCBINCBI36Build 36hg18NCBI36
Build 34718,957,644 - 18,958,284NCBI
Celera719,164,004 - 19,164,643 (-)NCBICelera
Cytogenetic Map7p21.1NCBI
HuRef719,068,815 - 19,069,457 (-)NCBIHuRef
CHM1_1719,185,176 - 19,185,815 (-)NCBICHM1_1
T2T-CHM13v2.0719,274,718 - 19,275,357 (-)NCBIT2T-CHM13v2.0
CRA_TCAGchr7v2719,235,856 - 19,236,495 (-)NCBI
Ferd3l
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391233,978,424 - 33,979,309 (+)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl1233,978,424 - 33,979,309 (+)EnsemblGRCm39 Ensembl
GRCm381233,928,425 - 33,929,310 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1233,928,425 - 33,929,310 (+)EnsemblGRCm38mm10GRCm38
MGSCv371234,613,290 - 34,614,175 (+)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv361234,513,672 - 34,514,557 (+)NCBIMGSCv36mm8
Celera1235,361,893 - 35,362,778 (+)NCBICelera
Cytogenetic Map12A3NCBI
cM Map1214.79NCBI
Ferd3l
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541022,034,413 - 22,034,907 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541022,034,413 - 22,034,978 (-)NCBIChiLan1.0ChiLan1.0
FERD3L
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2623,968,459 - 23,973,668 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1772,293,183 - 72,298,392 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0719,792,423 - 19,794,919 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1719,116,087 - 19,116,742 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl719,116,192 - 19,116,689 (-)Ensemblpanpan1.1panPan2
FERD3L
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11433,413,829 - 33,415,408 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1433,414,275 - 33,414,778 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1432,944,848 - 32,945,403 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01433,337,648 - 33,338,202 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1433,337,699 - 33,338,202 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11433,446,448 - 33,447,005 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01433,147,591 - 33,148,148 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01433,464,072 - 33,464,626 (-)NCBIUU_Cfam_GSD_1.0
Ferd3l
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440511877,679,522 - 77,683,570 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049365465,358,097 - 5,358,603 (-)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049365465,358,006 - 5,358,652 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
FERD3L
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl988,321,883 - 88,322,377 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1988,316,353 - 88,323,221 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2997,358,322 - 97,360,631 (-)NCBISscrofa10.2Sscrofa10.2susScr3
FERD3L
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12139,008,956 - 39,013,302 (+)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl2139,011,258 - 39,011,758 (+)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_02366604265,529,145 - 65,531,055 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Ferd3l
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_00462473911,318,333 - 11,318,851 (+)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_00462473911,315,336 - 11,319,030 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Ferd3l
7 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:160
Count of miRNA genes:114
Interacting mature miRNAs:127
Transcripts:ENSRNOT00000014731
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
9590290Uminl2Urine mineral level QTL 23.960.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)63878398983783989Rat
8693632Alc27Alcohol consumption QTL 272.20.791drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)63432335751121479Rat
634318Bw118Body weight QTL 1183.55abdominal fat pad mass (VT:1000711)abdominal fat pad weight (CMO:0000088)63330954957730294Rat
634307Bp141Blood pressure QTL 1414arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)63523041780230417Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)61653614061536140Rat
634330Pia16Pristane induced arthritis QTL 163.9joint integrity trait (VT:0010548)arthritic paw count (CMO:0001460)645790088104200226Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61436878859368788Rat
1331779Rf38Renal function QTL 382.876kidney blood vessel physiology trait (VT:0100012)absolute change in renal vascular resistance (CMO:0001900)63207442872227641Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)6507449754641141Rat
1354632Scl29Serum cholesterol level QTL 293.74blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)63509870971636405Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)610894415110548006Rat
2293839Kiddil2Kidney dilation QTL 24.8kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)615107216107351382Rat
9590140Scort4Serum corticosterone level QTL 414.490.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
9590306Scort18Serum corticosterone level QTL 182.880.001blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)63878398983783989Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)61173566972593685Rat
2293841Kiddil4Kidney dilation QTL 44.4kidney pelvis morphology trait (VT:0004194)hydronephrosis severity score (CMO:0001208)62086642281133036Rat
1641898Colcr4Colorectal carcinoma resistance QTL43.710.0007intestine integrity trait (VT:0010554)well differentiated malignant colorectal tumor surface area measurement (CMO:0002077)62033877762613667Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61173566972593685Rat
6893340Cm77Cardiac mass QTL 770.260.57heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)63330954981132889Rat
70199Coreg1Compensatory renal growth QTL 111.8kidney mass (VT:0002707)compensatory renal growth score (CMO:0001894)63569161857730540Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6172227641Rat
1300143Rf14Renal function QTL 142.92renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)63443413777102317Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)61653614071636405Rat

Markers in Region
Nato3-pending  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2650,645,436 - 50,645,889 (+)MAPPERmRatBN7.2
Rnor_6.0653,371,764 - 53,372,216NCBIRnor6.0
Rnor_5.0662,994,046 - 62,994,498UniSTSRnor5.0
RGSC_v3.4652,576,394 - 52,576,846UniSTSRGSC3.4
Celera649,811,798 - 49,812,250UniSTS
Cytogenetic Map6q16UniSTS


Expression

RNA-SEQ Expression

appendage
circulatory system
ectoderm
endocrine system
endoderm
exocrine system
hepatobiliary system
mesenchyme
mesoderm
nervous system
renal system
reproductive system
1 4 42 4 4 4 4 10 4 42 1 11

Sequence


Ensembl Acc Id: ENSRNOT00000014731   ⟹   ENSRNOP00000014731
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl650,645,379 - 50,646,268 (+)Ensembl
Rnor_6.0 Ensembl653,371,706 - 53,372,584 (+)Ensembl
RefSeq Acc Id: NM_001108980   ⟹   NP_001102450
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8656,372,778 - 56,373,667 (+)NCBI
mRatBN7.2650,645,379 - 50,646,268 (+)NCBI
Rnor_6.0653,371,706 - 53,372,596 (+)NCBI
Rnor_5.0662,993,988 - 62,994,878 (+)NCBI
RGSC_v3.4652,576,336 - 52,577,225 (+)RGD
Celera649,811,740 - 49,812,629 (+)RGD
Sequence:
Protein Sequences
Protein RefSeqs NP_001102450 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDM03296 (Get FASTA)   NCBI Sequence Viewer  
Ensembl Protein ENSRNOP00000014731.2
RefSeq Acc Id: NP_001102450   ⟸   NM_001108980
- UniProtKB: D4A114 (UniProtKB/TrEMBL),   A6HB91 (UniProtKB/TrEMBL)
- Sequence:
Ensembl Acc Id: ENSRNOP00000014731   ⟸   ENSRNOT00000014731
Protein Domains
bHLH

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4A114-F1-model_v2 AlphaFold D4A114 1-166 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:1311812 AgrOrtholog
BioCyc Gene G2FUF-37824 BioCyc
Ensembl Genes ENSRNOG00000011091 Ensembl, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014731.5 UniProtKB/TrEMBL
Gene3D-CATH 4.10.280.10 UniProtKB/TrEMBL
InterPro E-box_TF_Regulators UniProtKB/TrEMBL
  HLH_DNA-bd UniProtKB/TrEMBL
  HLH_DNA-bd_sf UniProtKB/TrEMBL
KEGG Report rno:366598 UniProtKB/TrEMBL
NCBI Gene 366598 ENTREZGENE
PANTHER BASIC HELIX-LOOP-HELIX TRANSCRIPTION FACTOR, TWIST UniProtKB/TrEMBL
  FER3-LIKE PROTEIN UniProtKB/TrEMBL
Pfam HLH UniProtKB/TrEMBL
PhenoGen Ferd3l PhenoGen
PROSITE HLH UniProtKB/TrEMBL
RatGTEx ENSRNOG00000011091 RatGTEx
SMART HLH UniProtKB/TrEMBL
Superfamily-SCOP HLH_basic UniProtKB/TrEMBL
UniProt A6HB91 ENTREZGENE, UniProtKB/TrEMBL
  D4A114 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-11-11 Ferd3l  Fer3-like bHLH transcription factor  Ferd3l  Fer3-like (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-04-30 Ferd3l  Fer3-like (Drosophila)   Ferd3l_predicted  Fer3-like (Drosophila) (predicted)  'predicted' is removed 2292626 APPROVED
2005-01-12 Ferd3l_predicted  Fer3-like (Drosophila) (predicted)      Symbol and Name status set to approved 70820 APPROVED