Ina (internexin neuronal intermediate filament protein, alpha) - Rat Genome Database

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Gene: Ina (internexin neuronal intermediate filament protein, alpha) Rattus norvegicus
Analyze
Symbol: Ina
Name: internexin neuronal intermediate filament protein, alpha
RGD ID: 2911
Description: Predicted to be a structural constituent of postsynaptic actin cytoskeleton and structural constituent of postsynaptic intermediate filament cytoskeleton. Involved in tissue regeneration. Localizes to glutamatergic synapse and postsynaptic intermediate filament cytoskeleton. Orthologous to human INA (internexin neuronal intermediate filament protein alpha); INTERACTS WITH 2,3,7,8-Tetrachlorodibenzofuran; 2,5-hexanedione; all-trans-retinoic acid.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: alpha-internexin; alpha-Inx; Inexa; internexin neuronal intermediate filament protein alpha; internexin, alpha; Intlaa; Nf66
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
mRatBN7.21245,896,775 - 245,908,330 (+)NCBI
Rnor_6.0 Ensembl1266,781,617 - 266,794,431 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01266,782,835 - 266,794,389 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01274,212,015 - 274,224,831 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41252,328,186 - 252,340,997 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11252,592,442 - 252,605,514 (+)NCBI
Celera1241,668,457 - 241,679,991 (+)NCBICelera
RH 3.4 Map11625.9RGD
Cytogenetic Map1q54NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


References

Additional References at PubMed
PMID:10221457   PMID:10350642   PMID:14561875   PMID:15121898   PMID:15673434   PMID:15686957   PMID:15880430   PMID:17005864   PMID:17634366   PMID:20124353   PMID:20131911   PMID:20439489  
PMID:22664934   PMID:22871113   PMID:22926577   PMID:24625528   PMID:25002582   PMID:25869803   PMID:29476059  


Genomics

Comparative Map Data
Ina
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21245,896,775 - 245,908,330 (+)NCBI
Rnor_6.0 Ensembl1266,781,617 - 266,794,431 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01266,782,835 - 266,794,389 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01274,212,015 - 274,224,831 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41252,328,186 - 252,340,997 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11252,592,442 - 252,605,514 (+)NCBI
Celera1241,668,457 - 241,679,991 (+)NCBICelera
RH 3.4 Map11625.9RGD
Cytogenetic Map1q54NCBI
INA
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl10103,277,138 - 103,290,346 (+)EnsemblGRCh38hg38GRCh38
GRCh3810103,277,138 - 103,290,346 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh3710105,036,895 - 105,050,103 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 3610105,026,910 - 105,040,093 (+)NCBINCBI36hg18NCBI36
Build 3410105,026,909 - 105,040,091NCBI
Celera1098,776,844 - 98,790,035 (+)NCBI
Cytogenetic Map10q24.33NCBI
HuRef1098,669,249 - 98,682,440 (+)NCBIHuRef
CHM1_110105,321,090 - 105,334,278 (+)NCBICHM1_1
Ina
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391947,003,120 - 47,013,766 (+)NCBIGRCm39mm39
GRCm39 Ensembl1947,003,137 - 47,013,766 (+)Ensembl
GRCm381947,014,681 - 47,025,327 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1947,014,698 - 47,025,327 (+)EnsemblGRCm38mm10GRCm38
MGSCv371947,089,188 - 47,098,848 (+)NCBIGRCm37mm9NCBIm37
MGSCv361947,068,013 - 47,077,971 (+)NCBImm8
Celera1947,782,907 - 47,792,585 (+)NCBICelera
Cytogenetic Map19C3NCBI
Ina
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0NW_0049554857,238,723 - 7,266,995 (-)NCBIChiLan1.0ChiLan1.0
INA
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.110103,340,438 - 103,353,888 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl10103,340,438 - 103,353,888 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01099,877,665 - 99,890,947 (+)NCBIMhudiblu_PPA_v0panPan3
INA
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12815,670,919 - 15,685,080 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2815,670,999 - 15,683,380 (+)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2815,843,032 - 15,857,216 (+)NCBI
ROS_Cfam_1.02816,146,691 - 16,160,880 (+)NCBI
UMICH_Zoey_3.12815,696,438 - 15,710,613 (+)NCBI
UNSW_CanFamBas_1.02815,728,136 - 15,742,330 (+)NCBI
UU_Cfam_GSD_1.02815,862,624 - 15,876,811 (+)NCBI
Ina
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440721331,144,424 - 31,157,296 (-)NCBI
SpeTri2.0NW_0049366002,747,649 - 2,760,517 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
INA
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl14114,227,993 - 114,240,560 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.114114,227,998 - 114,240,566 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.214124,168,530 - 124,181,111 (+)NCBISscrofa10.2Sscrofa10.2susScr3
INA
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1996,325,122 - 96,338,057 (+)NCBI
ChlSab1.1 Ensembl996,325,180 - 96,336,358 (+)Ensembl
Ina
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248312,529,710 - 2,541,630 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
70211Niddm24Non-insulin dependent diabetes mellitus QTL 243.79blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1236795785281795785Rat
631215Stl8Serum triglyceride level QTL 89.270.0001blood triglyceride amount (VT:0002644)serum triglyceride level (CMO:0000360)1245529606282763074Rat
2302040Pia35Pristane induced arthritis QTL 353.80.001blood immunoglobulin amount (VT:0002460)serum immunoglobulin G1 level (CMO:0002115)1236265430281265430Rat
2302378Insul11Insulin level QTL 113.25blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1156446196274977688Rat
724531Uae5Urinary albumin excretion QTL 54urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)1161321152273792054Rat
724533Rf51Renal function QTL 515.30.0002kidney plasma flow trait (VT:0005524)renal plasma flow (CMO:0001914)1238830534278228767Rat
724538Kidm1Kidney mass QTL 13.2kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1233663100273792054Rat
724552Glom2Glomerulus QTL 23.30.0001kidney glomerulus morphology trait (VT:0005325)count of superficial glomeruli directly contacting the kidney surface (CMO:0001001)1243272341282763074Rat
734767Niddm57Non-insulin dependent diabetes mellitus QTL 57body mass (VT:0001259)body weight (CMO:0000012)1244401175282365384Rat
734768Niddm59Non-insulin dependent diabetes mellitus QTL 59body mass (VT:0001259)body weight (CMO:0000012)1235850810280850810Rat
734769Niddm58Non-insulin dependent diabetes mellitus QTL 58body mass (VT:0001259)body weight (CMO:0000012)1244992467282365384Rat
631669Iddm9Insulin dependent diabetes mellitus QTL 92.80.039blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)1252955158280632620Rat
631690Scl5Serum cholesterol level QTL 52.1blood cholesterol amount (VT:0000180)serum total cholesterol level (CMO:0000363)1258132568282763074Rat
1354580Scort1Serum corticosterone level QTL 13.4blood corticosterone amount (VT:0005345)blood corticosterone level (CMO:0001172)1167394665278228889Rat
1581544Rf52Renal function QTL 520.05total urine protein amount (VT:0000032)urine protein excretion rate to body weight ratio (CMO:0001099)1252948438281795785Rat
731175Uae20Urinary albumin excretion QTL 203.50.0018urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1241482188281795785Rat
738032Hcas5Hepatocarcinoma susceptibility QTL 53.12liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1191825895279986079Rat
631536Lnnr2Liver neoplastic nodule remodeling QTL 22.90.0005liver integrity trait (VT:0010547)liver remodeling tumorous lesion number to liver total tumorous lesion number ratio (CMO:0001705)1255728828282763074Rat
1598821Rf55Renal function QTL 556.3renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1238824734279986079Rat
1598839Rf56Renal function QTL 56renal blood flow trait (VT:2000006)ratio of change in renal blood flow to change in renal perfusion pressure (CMO:0001239)1266793821279986079Rat
2300175Bmd40Bone mineral density QTL 4015.40.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)1221901238266901238Rat
2293655Bss36Bone structure and strength QTL 3610.660.0001femur strength trait (VT:0010010)femur ultimate force (CMO:0001675)1221901238266901238Rat
2293674Bss39Bone structure and strength QTL 397.10.0001femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)1221901238266901238Rat
2293694Bss38Bone structure and strength QTL 387.050.0001femur strength trait (VT:0010010)femur stiffness (CMO:0001674)1221901238266901238Rat
631836Stl31Serum triglyceride level QTL 314.640.00000487blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)1259295704282763074Rat
631837Niddm35Non-insulin dependent diabetes mellitus QTL 350.01blood insulin amount (VT:0001560)serum insulin level (CMO:0000358)1258709726281795785Rat
631843Bw116Body weight QTL 1164.10.016abdominal adipose amount (VT:1000220)abdominal fat pad weight (CMO:0000088)1244401175282365384Rat
634313Niddm43Non-insulin dependent diabetes mellitus QTL 43blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1217054291281795785Rat
1357399Bw45Body weight QTL 453.05body mass (VT:0001259)body mass index (BMI) (CMO:0000105)1225689973270689973Rat
1357404Bw42Body weight QTL 424.490.0001body mass (VT:0001259)body weight (CMO:0000012)1225689973270689973Rat
1600388Niddm67Non-insulin dependent diabetes mellitus QTL 675.840.000004blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1213476630278978026Rat
1600392Bw123Body weight QTL 1230.001body mass (VT:0001259)body weight (CMO:0000012)1244087148282763074Rat
1600395Niddm69Non-insulin dependent diabetes mellitus QTL 694.140.0002blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)1213476630278978026Rat
1600396Niddm68Non-insulin dependent diabetes mellitus QTL 684.970.0003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1213476630278978026Rat
1600397Edcs4Endometrial carcinoma susceptibility QTL 42.2uterus morphology trait (VT:0001120)percentage of study population developing endometrioid carcinoma during a period of time (CMO:0001759)1226706329271706329Rat
1578759Uae30Urinary albumin excretion QTL 303.30.003urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1161321256273791893Rat
1578763Kidm29Kidney mass QTL 293.30.0001kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)1196395041282763074Rat
1578778Pur4Proteinuria QTL 43.30.003total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1161321256273791893Rat
1300108Rf8Renal function QTL 83.75renal blood flow trait (VT:2000006)absolute change in renal vascular resistance (CMO:0001900)1249206242281795785Rat
1354610Bw34Body weight QTL 344.1body mass (VT:0001259)body weight (CMO:0000012)1161784169278228889Rat
1354624Cm35Cardiac mass QTL355.7heart left ventricle mass (VT:0007031)calculated heart weight (CMO:0000073)1192639698278228889Rat
1354646Kidm18Kidney mass QTL 185.7kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1161784169278228889Rat
1354652Kidm20Kidney mass QTL 204.3kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)1192639698278228889Rat
1354661Bw33Body weight QTL 335.2body mass (VT:0001259)body weight (CMO:0000012)1161784169278228889Rat
1549910Bw54Body weight QTL 540.05body mass (VT:0001259)body weight (CMO:0000012)1236795785281795785Rat
2316896Gluco57Glucose level QTL 577.2blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1249607907266793958Rat
1549837Hcar15Hepatocarcinoma resistance QTL 150.05liver integrity trait (VT:0010547)liver tumorous lesion number (CMO:0001068)1163796316282763074Rat
1358890Bp259Blood pressure QTL 2593.06arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1230420627282645769Rat
1358898Bp255Blood pressure QTL 2553.6arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1208517798266948272Rat
61327Eae7Experimental allergic encephalomyelitis QTL 75.6body mass (VT:0001259)change in body weight (CMO:0002045)1236265430281265430Rat
61400Niddm1Non-insulin dependent diabetes mellitus QTL 111blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)1238830408266793958Rat
7394701Uae46Urinary albumin excretion QTL 463.60.0056urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1221901238266901238Rat
7387289Uae45Urinary albumin excretion QTL 452.860.0021urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1244148899282763074Rat
10053715Scort24Serum corticosterone level QTL 242.130.0088blood corticosterone amount (VT:0005345)plasma corticosterone level (CMO:0001173)1242302911282763074Rat
10059587Bw173Body weight QTL 1733.230.025body mass (VT:0001259)body weight (CMO:0000012)1222492538267492538Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:195
Count of miRNA genes:135
Interacting mature miRNAs:163
Transcripts:ENSRNOT00000027417
Prediction methods:Miranda, 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.


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 74 5
Low 3 6 15 4 3 4 14 32 2
Below cutoff 28 19 14 15 14 8 9 17 4 8 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000027417   ⟹   ENSRNOP00000027417
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1266,781,617 - 266,794,431 (+)Ensembl
RefSeq Acc Id: NM_019128   ⟹   NP_062001
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21245,896,775 - 245,908,330 (+)NCBI
Rnor_6.01266,782,835 - 266,794,389 (+)NCBI
Rnor_5.01274,212,015 - 274,224,831 (+)NCBI
RGSC_v3.41252,328,186 - 252,340,997 (+)RGD
Celera1241,668,457 - 241,679,991 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_062001 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAA41444 (Get FASTA)   NCBI Sequence Viewer  
  CAA36264 (Get FASTA)   NCBI Sequence Viewer  
  EDL94366 (Get FASTA)   NCBI Sequence Viewer  
  P23565 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_062001   ⟸   NM_019128
- UniProtKB: G3V8Q2 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000027417   ⟸   ENSRNOT00000027417
Protein Domains
IF rod

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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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)
Visual CSV TAB Printer
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 274213439 274213440 C T snv SBH/Ygl (MCW), ZF (KyushuU), KFRS3B/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), RCS/Kyo (KyushuU), HTX/Kyo (KyushuU), BUF/MNa (KyushuU), IS/Kyo (KyushuU), Crl:SD (UDEL), LE/OrlBarth (UDEL), SDLEF7/Barth (UDEL), MNS/Gib (KNAW), LE/Stm (Illumina) (KNAW), FHL/EurMcwi (KNAW), FHH/EurMcwi (KNAW), BUF/N (KNAW), SBN/Ygl (KNAW), SBH/Ygl (KNAW), WAG/Rij (KNAW), MHS/Gib (KNAW), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBN/Ygl (MCW), LH/MavRrrc (KNAW), LN/MavRrrc (KNAW)
1 274213482 274213483 C G snv ZF (KyushuU), Crl:SD (UDEL), SDLEF7/Barth (UDEL), FHL/EurMcwi (MCW), IS-Tlk/Kyo (KyushuU), SBN/Ygl (MCW), IS/Kyo (KyushuU)
1 274213548 274213549 C T snv LE/OrlBarth (UDEL), KFRS3B/Kyo (KyushuU), SBN/Ygl (MCW), FHL/EurMcwi (MCW), SDLEF7/Barth (UDEL), RCS/Kyo (KyushuU), Crl:SD (UDEL), IS-Tlk/Kyo (KyushuU), IS/Kyo (KyushuU), ZF (KyushuU), SBH/Ygl (MCW), LEC/Tj (KyushuU), HTX/Kyo (KyushuU)
1 274213566 274213567 A G snv SDLEF7/Barth (UDEL), IS/Kyo (KyushuU), HTX/Kyo (KyushuU), RCS/Kyo (KyushuU), IS-Tlk/Kyo (KyushuU), LEC/Tj (KyushuU), KFRS3B/Kyo (KyushuU), ZF (KyushuU)
1 274213612 274213613 C A snv IS/Kyo (KyushuU), KFRS3B/Kyo (KyushuU), LEC/Tj (KyushuU), IS-Tlk/Kyo (KyushuU), FHL/EurMcwi (MCW), SBN/Ygl (MCW), SDLEF7/Barth (UDEL), Crl:SD (UDEL), ZF (KyushuU), HTX/Kyo (KyushuU), RCS/Kyo (KyushuU)
1 274213634 274213635 G C snv LE/Stm (KyushuU), FHH/EurMcwi (MCW), SBH/Ygl (MCW)
1 274213748 274213749 C A snv IS/Kyo (KyushuU)


Assembly: Rnor_6.0

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 266783041 266783042 C T snv LN/MavRrrc (RGD), LE/Stm (RGD), MHS/Gib (RGD), SBN/Ygl (RGD), SBN/Ygl (MCW), SBH/Ygl (MCW), LH/MavRrrc (RGD), FHH/EurMcwi (MCW), FHL/EurMcwi (MCW), SBH/Ygl (RGD), MNS/Gib (RGD)
1 266783084 266783085 C G snv MHS/Gib (RGD), FHL/EurMcwi (MCW), SBN/Ygl (MCW), MNS/Gib (RGD), SBN/Ygl (RGD)
1 266783150 266783151 C T snv LN/MavRrrc (RGD), LH/MavRrrc (RGD), LE/Stm (RGD), SBN/Ygl (MCW), FHL/EurMcwi (MCW), SBH/Ygl (MCW), SBN/Ygl (RGD), SBH/Ygl (RGD), MHS/Gib (RGD)
1 266783168 266783169 A G snv MHS/Gib (RGD), SBN/Ygl (RGD), SBN/Ygl (MCW)
1 266783214 266783215 C A snv SBN/Ygl (MCW), MR/N (MCW), FHL/EurMcwi (MCW), MHS/Gib (RGD), SBN/Ygl (RGD)
1 266783236 266783237 G C snv LH/MavRrrc (RGD), LE/Stm (RGD), LN/MavRrrc (RGD), SBH/Ygl (MCW), SBH/Ygl (RGD)


Assembly: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
1 252329610 252329611 C T snv LCR/2Mco (UMich), FHH/EurMcwi (MDC), LCR/1Mco (UMich), FHH/EurMcwi (MCW), HCR/2Mco (UMich), HCR/1Mco (UMich), FHL/EurMcwi (MCW)
1 252329653 252329654 C G snv FHL/EurMcwi (MCW)
1 252329719 252329720 C T snv FHL/EurMcwi (MCW), HCR/1Mco (UMich), LCR/2Mco (UMich), HCR/2Mco (UMich)
1 252329783 252329784 C A snv MR/N (KNAW), FHL/EurMcwi (MCW)
1 252329805 252329806 G C snv LCR/2Mco (UMich), FHH/EurMcwi (MDC), LCR/1Mco (UMich)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2911 AgrOrtholog
Ensembl Genes ENSRNOG00000020248 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000027417 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000027417 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.20.5.1160 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Alpha-Inx UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_conserved UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_rod_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_rod_dom_coil1B UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Intermed_filament_DNA-bd UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:24503 UniProtKB/TrEMBL
NCBI Gene 24503 ENTREZGENE
PANTHER PTHR45652:SF18 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Filament UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Filament_head UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Ina PhenoGen
PROSITE IF_ROD_1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  IF_ROD_2 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
SMART Filament UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
TIGR TC233138
UniProt AINX_RAT UniProtKB/Swiss-Prot
  G3V8Q2 ENTREZGENE, UniProtKB/TrEMBL
  P23565 ENTREZGENE


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-02-14 Ina  internexin neuronal intermediate filament protein, alpha  Inexa  internexin, alpha  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Inexa  internexin, alpha      Symbol and Name status set to approved 70586 APPROVED

RGD Curation Notes
Note Type Note Reference
gene_expression found predominantly in adult CNS 625364
gene_expression mRNA level decreases as development progresses 628341
gene_expression mRNA noticed in uninjured facial neurons 628341
gene_function self-assembling class-iv neuronal intermediate filament 69861
gene_function self-assembling class-iv neuronal intermediate filament 625364
gene_process first neurofilament which is expressed during development 628341
gene_process may mediate neuronal regeneration 628341
gene_process involved in morphogenesis of neurons 69861
gene_process involved in morphogenesis of neurons 625364
gene_product 64-66 kDa protein 628341
gene_regulation expression is dependent on the rate of muscle reinnervation 628341