Dpf1 (double PHD fingers 1) - Rat Genome Database
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Gene: Dpf1 (double PHD fingers 1) Rattus norvegicus
Analyze
Symbol: Dpf1
Name: double PHD fingers 1
RGD ID: 61868
Description: Predicted to have sequence-specific double-stranded DNA binding activity. Involved in nervous system development. Predicted to localize to nBAF complex. Orthologous to human DPF1 (double PHD fingers 1); PARTICIPATES IN SWI/SNF family mediated chromatin remodeling pathway; INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil; acetamide.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: BAF45B; BRG1-associated factor 45B; D4, zinc and double PHD fingers family 1; Neud4; neuro-d4; neuronal d4 domain family member; zinc finger protein neuro-d4
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2184,602,212 - 84,615,954 (+)NCBI
Rnor_6.0 Ensembl187,248,489 - 87,258,070 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0187,248,448 - 87,258,070 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0188,426,945 - 88,437,120 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4184,444,143 - 84,452,889 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1184,522,204 - 84,531,762 (+)NCBI
Celera178,992,981 - 79,002,564 (+)NCBICelera
Cytogenetic Map1q21NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component
cellular_component  (ND)
chromatin  (IBA)
cytoplasm  (IEA)
nBAF complex  (IBA,IEA,ISO,ISS)

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:12477932   PMID:17640523   PMID:23785148  


Genomics

Comparative Map Data
Dpf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2184,602,212 - 84,615,954 (+)NCBI
Rnor_6.0 Ensembl187,248,489 - 87,258,070 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0187,248,448 - 87,258,070 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0188,426,945 - 88,437,120 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4184,444,143 - 84,452,889 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1184,522,204 - 84,531,762 (+)NCBI
Celera178,992,981 - 79,002,564 (+)NCBICelera
Cytogenetic Map1q21NCBI
DPF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1938,211,006 - 38,229,714 (-)EnsemblGRCh38hg38GRCh38
GRCh381938,211,006 - 38,229,695 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371938,701,646 - 38,720,335 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361943,394,187 - 43,406,628 (-)NCBINCBI36hg18NCBI36
Celera1935,503,879 - 35,522,555 (-)NCBI
Cytogenetic Map19q13.2NCBI
HuRef1935,150,952 - 35,163,719 (-)NCBIHuRef
CHM1_11938,701,987 - 38,720,686 (-)NCBICHM1_1
Dpf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39729,003,366 - 29,017,017 (+)NCBIGRCm39mm39
GRCm39 Ensembl729,003,376 - 29,017,668 (+)Ensembl
GRCm38729,303,952 - 29,317,592 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl729,303,951 - 29,318,243 (+)EnsemblGRCm38mm10GRCm38
MGSCv37730,089,024 - 30,102,605 (+)NCBIGRCm37mm9NCBIm37
MGSCv36729,012,765 - 29,026,346 (+)NCBImm8
Celera723,874,277 - 23,887,947 (+)NCBICelera
Cytogenetic Map7B1NCBI
Dpf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554681,195,146 - 1,211,311 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049554681,195,152 - 1,209,774 (+)NCBIChiLan1.0ChiLan1.0
DPF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11943,875,879 - 43,888,611 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1943,875,879 - 43,889,021 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01935,301,009 - 35,320,126 (-)NCBIMhudiblu_PPA_v0panPan3
DPF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl1114,757,864 - 114,765,602 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.11114,753,368 - 114,763,965 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Dpf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_0049368011,004,841 - 1,013,784 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
DPF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl647,142,688 - 47,155,347 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1647,142,006 - 47,155,340 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2642,620,257 - 42,627,472 (+)NCBISscrofa10.2Sscrofa10.2susScr3
DPF1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1632,855,371 - 32,873,889 (-)NCBI
ChlSab1.1 Ensembl632,856,436 - 32,868,067 (-)Ensembl
Dpf1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462479411,700,139 - 11,714,979 (-)NCBI

Position Markers
BF397080  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0187,252,290 - 87,252,435NCBIRnor6.0
Rnor_5.0188,431,340 - 88,431,485UniSTSRnor5.0
RGSC_v3.4184,447,874 - 84,448,021UniSTSRGSC3.4
Celera178,996,782 - 78,996,929UniSTS
RH 3.4 Map1844.1UniSTS
Cytogenetic Map1q21UniSTS
Dpf1  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0187,256,979 - 87,258,017NCBIRnor6.0
Rnor_5.0188,436,029 - 88,437,067UniSTSRnor5.0
Celera179,001,473 - 79,002,511UniSTS
Cytogenetic Map1q21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
631688Hcas2Hepatocarcinoma susceptibility QTL 230.0001liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)15655769122614963Rat
631495Bp96Blood pressure QTL 964.52arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)123406428108057505Rat
1358359Sradr1Stress Responsive Adrenal Weight QTL 14.74adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)125951907130917265Rat
70225Bp58Blood pressure QTL 583.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)134993530173445086Rat
1300172Bp172Blood pressure QTL 1723.56arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)13537750894364229Rat
10059597Bp377Blood pressure QTL 3773.420.025arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)135377692217372257Rat
2313051Bss57Bone structure and strength QTL 573.70.0001tibia strength trait (VT:1000284)bone polar moment of inertia (CMO:0001558)143579208126240667Rat
2313059Bss55Bone structure and strength QTL 553.20.0001tibia size trait (VT:0100001)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313072Bss53Bone structure and strength QTL 534.30.0001tibia length (VT:0004357)tibia length (CMO:0000450)143579208126240667Rat
2313078Bss54Bone structure and strength QTL 543.50.0001tibia area (VT:1000281)tibia midshaft cross-sectional area (CMO:0001717)143579208126240667Rat
2313094Bss58Bone structure and strength QTL 583.70.0001tibia strength trait (VT:1000284)tibia total energy absorbed before break (CMO:0001736)143579208126240667Rat
2313098Bmd70Bone mineral density QTL 703.60.0001tibia mineral mass (VT:1000283)cortical volumetric bone mineral density (CMO:0001730)143579208126240667Rat
2313099Bss56Bone structure and strength QTL 562.40.0001tibia size trait (VT:0100001)tibia midshaft endosteal cross-sectional area (CMO:0001716)143579208126240667Rat
2313402Anxrr24Anxiety related response QTL 24aggression-related behavior trait (VT:0015014)tameness/aggressiveness composite score (CMO:0002136)149147799156446783Rat
1578649Bmd8Bone mineral density QTL 84.9femur mineral mass (VT:0010011)trabecular volumetric bone mineral density (CMO:0001729)14957857794578577Rat
1578654Bss10Bone structure and strength QTL 104femur morphology trait (VT:0000559)femoral neck cortical cross-sectional area (CMO:0001702)149578577169852184Rat
634314Niddm44Non-insulin dependent diabetes mellitus QTL 44blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)149578693217054291Rat
6903308Scl36Serum cholesterol QTL 3620.0125blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)15052271494225616Rat
61342Bp27Blood pressure QTL 273.40.0006arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)157761301104391981Rat
2300164Bmd44Bone mineral density QTL 445.40.0001lumbar vertebra mineral mass (VT:0010511)volumetric bone mineral density (CMO:0001553)158209327103209327Rat
2298545Neuinf8Neuroinflammation QTL 84.6nervous system integrity trait (VT:0010566)spinal cord beta-2 microglobulin mRNA level (CMO:0002125)158354072161711996Rat
7421628Bp361Blood pressure QTL 3610.001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)164588516125875986Rat
1300121Hrtrt1Heart rate QTL 13.7heart pumping trait (VT:2000009)heart rate (CMO:0000002)166113339122614963Rat
631512Scl6Serum cholesterol level QTL 69.6blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)16722768394201552Rat
1549903Bp267Blood pressure QTL 267arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)179134941113593716Rat
7411712Strs4Sensitivity to stroke QTL 48.7cerebrum integrity trait (VT:0010549)percentage of study population developing cerebrovascular lesions during a period of time (CMO:0000932)179689548124689548Rat
61433Cia2Collagen induced arthritis QTL 25joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)17968976594909507Rat
1578780Cm52Cardiac mass QTL 523.30.0001heart mass (VT:0007028)heart wet weight (CMO:0000069)182788437239853971Rat
10054135Gmadr2Adrenal mass QTL 21.970.0129adrenal gland mass (VT:0010420)both adrenal glands wet weight (CMO:0000164)183502376128502376Rat
2313083Bmd74Bone mineral density QTL 7440.0001tibia mineral mass (VT:1000283)total volumetric bone mineral density (CMO:0001728)183656882126240667Rat
61344Bp29Blood pressure QTL 297.5arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)185779320130779320Rat
1582234Gluco18Glucose level QTL 183.40.0003blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)185917265130917265Rat
4889494Scort2Serum corticosterone level QTL 24.2blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)186776571131776571Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:290
Count of miRNA genes:105
Interacting mature miRNAs:115
Transcripts:ENSRNOT00000028091, ENSRNOT00000046435
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.


Expression


RNA-SEQ Expression
High: > 1000 TPM value   Medium: Between 11 and 1000 TPM
Low: Between 0.5 and 10 TPM   Below Cutoff: < 0.5 TPM

alimentary part of gastrointestinal system circulatory system endocrine system exocrine system hemolymphoid system hepatobiliary system integumental system musculoskeletal system nervous system renal system reproductive system respiratory system appendage
High
Medium 72 4 28
Low 3 28 36 28 1 28 2 2 17 13 11
Below cutoff 15 17 9 18 9 8 9 13 8

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001105729 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006228678 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_006228685 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088375 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088377 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088383 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088390 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088394 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088397 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088402 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088407 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088416 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088421 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088425 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088431 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039088436 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC159415 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473979 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CO396551 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JACYVU010000033 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  X66022 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000028091   ⟹   ENSRNOP00000028091
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl187,248,489 - 87,258,070 (+)Ensembl
RefSeq Acc Id: NM_001105729   ⟹   NP_001099199
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,606,367 - 84,615,950 (+)NCBI
Rnor_6.0187,248,489 - 87,258,070 (+)NCBI
Rnor_5.0188,426,945 - 88,437,120 (+)NCBI
RGSC_v3.4184,444,143 - 84,452,889 (+)RGD
Celera178,992,981 - 79,002,564 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006228677   ⟹   XP_006228739
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0187,248,448 - 87,258,070 (+)NCBI
Rnor_5.0188,426,945 - 88,437,120 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006228678   ⟹   XP_006228740
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,606,307 - 84,615,954 (+)NCBI
Rnor_6.0187,248,465 - 87,258,070 (+)NCBI
Rnor_5.0188,426,945 - 88,437,120 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006228679   ⟹   XP_006228741
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0187,248,469 - 87,258,070 (+)NCBI
Rnor_5.0188,426,945 - 88,437,120 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006228681   ⟹   XP_006228743
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0187,248,468 - 87,258,070 (+)NCBI
Rnor_5.0188,426,945 - 88,437,120 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006228684   ⟹   XP_006228746
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0187,248,463 - 87,258,070 (+)NCBI
Rnor_5.0188,426,945 - 88,437,120 (+)NCBI
Sequence:
RefSeq Acc Id: XM_006228685   ⟹   XP_006228747
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,606,395 - 84,615,954 (+)NCBI
Rnor_6.0187,248,512 - 87,258,070 (+)NCBI
Rnor_5.0188,426,945 - 88,437,120 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589599   ⟹   XP_017445088
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0187,248,747 - 87,258,070 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589600   ⟹   XP_017445089
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0187,248,749 - 87,258,070 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589601   ⟹   XP_017445090
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0187,248,746 - 87,258,070 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589603   ⟹   XP_017445092
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0187,248,748 - 87,258,070 (+)NCBI
Sequence:
RefSeq Acc Id: XM_017589604   ⟹   XP_017445093
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0187,248,745 - 87,258,070 (+)NCBI
Sequence:
RefSeq Acc Id: XM_039088375   ⟹   XP_038944303
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,602,212 - 84,615,954 (+)NCBI
RefSeq Acc Id: XM_039088377   ⟹   XP_038944305
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,602,212 - 84,615,954 (+)NCBI
RefSeq Acc Id: XM_039088383   ⟹   XP_038944311
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,605,643 - 84,615,954 (+)NCBI
RefSeq Acc Id: XM_039088390   ⟹   XP_038944318
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,605,645 - 84,615,954 (+)NCBI
RefSeq Acc Id: XM_039088394   ⟹   XP_038944322
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,602,212 - 84,615,954 (+)NCBI
RefSeq Acc Id: XM_039088397   ⟹   XP_038944325
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,602,212 - 84,615,954 (+)NCBI
RefSeq Acc Id: XM_039088402   ⟹   XP_038944330
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,602,212 - 84,615,954 (+)NCBI
RefSeq Acc Id: XM_039088407   ⟹   XP_038944335
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,602,213 - 84,615,954 (+)NCBI
RefSeq Acc Id: XM_039088416   ⟹   XP_038944344
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,606,677 - 84,615,954 (+)NCBI
RefSeq Acc Id: XM_039088421   ⟹   XP_038944349
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,602,212 - 84,615,954 (+)NCBI
RefSeq Acc Id: XM_039088425   ⟹   XP_038944353
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,602,212 - 84,615,954 (+)NCBI
RefSeq Acc Id: XM_039088431   ⟹   XP_038944359
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,606,658 - 84,615,954 (+)NCBI
RefSeq Acc Id: XM_039088436   ⟹   XP_038944364
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2184,607,361 - 84,615,954 (+)NCBI
Reference Sequences
RefSeq Acc Id: NP_001099199   ⟸   NM_001105729
- UniProtKB: B0K016 (UniProtKB/TrEMBL),   A0A0H2UHS4 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006228746   ⟸   XM_006228684
- Peptide Label: isoform X8
- Sequence:
RefSeq Acc Id: XP_006228739   ⟸   XM_006228677
- Peptide Label: isoform X10
- Sequence:
RefSeq Acc Id: XP_006228740   ⟸   XM_006228678
- Peptide Label: isoform X9
- Sequence:
RefSeq Acc Id: XP_006228741   ⟸   XM_006228679
- Peptide Label: isoform X5
- Sequence:
RefSeq Acc Id: XP_006228743   ⟸   XM_006228681
- Peptide Label: isoform X11
- Sequence:
RefSeq Acc Id: XP_006228747   ⟸   XM_006228685
- Peptide Label: isoform X14
- Sequence:
RefSeq Acc Id: XP_017445093   ⟸   XM_017589604
- Peptide Label: isoform X7
- Sequence:
RefSeq Acc Id: XP_017445090   ⟸   XM_017589601
- Peptide Label: isoform X3
- Sequence:
RefSeq Acc Id: XP_017445088   ⟸   XM_017589599
- Peptide Label: isoform X1
- Sequence:
RefSeq Acc Id: XP_017445092   ⟸   XM_017589603
- Peptide Label: isoform X6
- Sequence:
RefSeq Acc Id: XP_017445089   ⟸   XM_017589600
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000028091   ⟸   ENSRNOT00000028091
RefSeq Acc Id: XP_038944303   ⟸   XM_039088375
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038944305   ⟸   XM_039088377
- Peptide Label: isoform X2
RefSeq Acc Id: XP_038944322   ⟸   XM_039088394
- Peptide Label: isoform X5
RefSeq Acc Id: XP_038944330   ⟸   XM_039088402
- Peptide Label: isoform X7
RefSeq Acc Id: XP_038944325   ⟸   XM_039088397
- Peptide Label: isoform X6
RefSeq Acc Id: XP_038944349   ⟸   XM_039088421
- Peptide Label: isoform X11
RefSeq Acc Id: XP_038944353   ⟸   XM_039088425
- Peptide Label: isoform X12
RefSeq Acc Id: XP_038944335   ⟸   XM_039088407
- Peptide Label: isoform X8
RefSeq Acc Id: XP_038944311   ⟸   XM_039088383
- Peptide Label: isoform X3
RefSeq Acc Id: XP_038944318   ⟸   XM_039088390
- Peptide Label: isoform X4
RefSeq Acc Id: XP_038944359   ⟸   XM_039088431
- Peptide Label: isoform X13
RefSeq Acc Id: XP_038944344   ⟸   XM_039088416
- Peptide Label: isoform X10
RefSeq Acc Id: XP_038944364   ⟸   XM_039088436
- Peptide Label: isoform X13
Protein Domains
C2H2-type   PHD-type

Transcriptome

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


Strain Variation

Strain Sequence Variants (Rnor 6.0)
ACI/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
ACI/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
ACI/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
BBDP/Wor (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
BN/SsN (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Buf/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
COP/CrCrl (MCW & UW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
University of Wisconsin (Dr. James Shull)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Charles River Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob) and UW Madison (Dr. James Shull)
F344/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
F344/NRrrc (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
FHH/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHH/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
FHL/EurMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
FHL/EurMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
GH/OmrMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
GK/Ox (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LE/Stm (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/Crl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LEW/NCrlBR (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LH/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LL/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
LN/MavRrrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
M520/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
MHS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MNS/Gib (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
MR/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
SBH/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBH/Ygl sequenced by MCW
SBH/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SBN/Ygl (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: SBN/Ygl sequenced by MCW
SBN/Ygl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHR/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SHRSP/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SR/JrHsd (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Harlan Laboratories
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SR/JrHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/Jr (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
SS/JrHsdMcwi (MCW)
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Sequenced By: Medical College of Wisconsin (Dr. Howard Jacob)
Platform: Illumina HiSeq 2000
Secondary Analysis: BWA v0.7.7 and GATK v3.2-2
Breeder: Medical College of Wisconsin
Description: Provided by the Medical College of Wisconsin (Dr. Howard Jacob)
SS/JrHsdMcwi (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WAG/Rij (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/Gcrc (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
WKY/NCrl (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WKY/NHsd (RGD)
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Platform: Illumina HiSeq 2000
Secondary Analysis: BWA mem 0.7.15, GATK v.3.6-0
Description: Sequences from Atanur et al and Hermsen et al realigned to the Rnor 6.0 assembly and reanalyzed by RGD
WN/N (MCW)
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Sequenced By: Royal Netherland Academy of Arts and Sciences (Dr. Edwin Cuppen)
Max Delbruck Center for Molecular Medicine (Dr. Norbert Huebner)
Platform: SOLiD 4 and 5500
Secondary Analysis: liftOver (Batch Coordinate Conversion)--genome.ucsc.edu
Breeder: National Institutes of Health
Description: Founder strain for the heterogeneous stock (HS) rat population; SNPs from the RGSC 3.4 assembly were "lifted over" from RGSC 3.4 to Rnor 5.0 and from Rnor 5.0 to Rnor 6.0; Provided by Medical College of Wisconsin
Damaging Variants


Assembly: Rnor_5.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 88432576 88432577 G T snv GK/Ox (KNAW)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 87253526 87253527 G T snv GK/Ox (RGD)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:61868 AgrOrtholog
Ensembl Genes ENSRNOG00000020687 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000028091 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000028091 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 3.30.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:8368092 IMAGE-MGC_LOAD
InterPro DPF1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Requiem/DPF_N_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C2H2_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_C2H2_type UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_FYVE_PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_PHD-finger UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:50545 UniProtKB/TrEMBL
MGC_CLONE MGC:188698 IMAGE-MGC_LOAD
NCBI Gene 50545 ENTREZGENE
PANTHER PTHR10615:SF12 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Requiem_N UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Dpf1 PhenoGen
PROSITE ZF_PHD_1 UniProtKB/Swiss-Prot
  ZF_PHD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZINC_FINGER_C2H2_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART PHD UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  ZnF_C2H2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF57667 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  SSF57903 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0H2UHS4 ENTREZGENE, UniProtKB/TrEMBL
  B0K016 ENTREZGENE, UniProtKB/TrEMBL
  DPF1_RAT UniProtKB/Swiss-Prot, ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2016-02-17 Dpf1  double PHD fingers 1  Dpf1  D4, zinc and double PHD fingers family 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-03-11 Dpf1  D4, zinc and double PHD fingers family 1  Neud4  neuronal d4 domain family member  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Neud4  neuronal d4 domain family member      Name updated 70584 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_domains contains a nuclear localization signal, a Kruppel-type zinc-finger and a cysteine/histidine-rich motif 61670
gene_expression transcripts are expressed in neuronal cell bodies 61670