Mid1 (midline 1) - Rat Genome Database

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Gene: Mid1 (midline 1) Rattus norvegicus
Analyze
Symbol: Mid1
Name: midline 1
RGD ID: 2640
Description: Predicted to have several functions, including microtubule binding activity; protein homodimerization activity; and ubiquitin protein ligase binding activity. Predicted to be involved in negative regulation of microtubule depolymerization; positive regulation of stress-activated MAPK cascade; and protein localization to microtubule. Predicted to colocalize with cytoplasmic microtubule. Human ortholog(s) of this gene implicated in Opitz GBBB syndrome type I. Orthologous to human MID1 (midline 1); PARTICIPATES IN ubiquitin/proteasome degradation pathway; INTERACTS WITH 2,3,7,8-tetrachlorodibenzodioxine; 2,3,7,8-Tetrachlorodibenzofuran; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: PROVISIONAL
Also known as: E3 ubiquitin-protein ligase Midline-1; finger on X and Y (in rat only on X); Fxy; midline 1 (Opitz/BBB syndrome); midline-1; Midline1; RING finger protein Midline-1; RING-type E3 ubiquitin transferase Midline-1; tripartite motif-containing protein 18
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
mRatBN7.2X24,116,674 - 24,491,205 (-)NCBI
Rnor_6.0 EnsemblX25,458,771 - 25,628,272 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X25,458,782 - 25,839,941 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X25,869,975 - 26,249,296 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X44,751,950 - 44,879,999 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X44,805,418 - 44,933,468 (-)NCBI
CeleraX24,547,301 - 24,674,105 (-)NCBICelera
Cytogenetic MapXq13NCBI
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

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11806752   PMID:15070402   PMID:17438131   PMID:18005432   PMID:18949047   PMID:22493164   PMID:22829933   PMID:25416956  


Genomics

Comparative Map Data
Mid1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.2X24,116,674 - 24,491,205 (-)NCBI
Rnor_6.0 EnsemblX25,458,771 - 25,628,272 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0X25,458,782 - 25,839,941 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0X25,869,975 - 26,249,296 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4X44,751,950 - 44,879,999 (-)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.1X44,805,418 - 44,933,468 (-)NCBI
CeleraX24,547,301 - 24,674,105 (-)NCBICelera
Cytogenetic MapXq13NCBI
MID1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 EnsemblX10,445,310 - 10,833,654 (-)EnsemblGRCh38hg38GRCh38
GRCh38X10,445,310 - 10,833,683 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh37X10,413,350 - 10,851,802 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36X10,373,596 - 10,761,730 (-)NCBINCBI36hg18NCBI36
Build 34X10,225,901 - 10,398,195NCBI
CeleraX14,584,610 - 14,973,762 (-)NCBI
Cytogenetic MapXp22.2NCBI
HuRefX8,245,662 - 8,632,012 (-)NCBIHuRef
CHM1_1X10,443,740 - 10,882,213 (-)NCBICHM1_1
Mid1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39X168,468,178 - 168,773,794 (+)NCBIGRCm39mm39
GRCm39 EnsemblX168,468,195 - 168,788,732 (+)Ensembl
GRCm38X169,685,199 - 169,990,798 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 EnsemblX169,685,199 - 170,005,736 (+)EnsemblGRCm38mm10GRCm38
MGSCv37X166,123,179 - 166,428,730 (+)NCBIGRCm37mm9NCBIm37
MGSCv36X165,029,352 - 165,344,845 (+)NCBImm8
CeleraX152,849,611 - 153,131,383 (+)NCBICelera
Cytogenetic MapXF5NCBI
cM MapX79.19NCBI
Mid1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555442,484,854 - 2,719,112 (+)EnsemblChiLan1.0
ChiLan1.0NW_0049555442,379,766 - 2,718,282 (+)NCBIChiLan1.0ChiLan1.0
MID1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.1X10,328,476 - 10,715,914 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 EnsemblX10,328,476 - 10,459,284 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v0X3,075,834 - 3,463,845 (-)NCBIMhudiblu_PPA_v0panPan3
MID1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1X7,087,890 - 7,438,553 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 EnsemblX7,089,831 - 7,194,267 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_TashaX7,042,862 - 7,395,336 (-)NCBI
ROS_Cfam_1.0X7,033,632 - 7,390,212 (-)NCBI
UMICH_Zoey_3.1X7,023,168 - 7,375,574 (-)NCBI
UNSW_CanFamBas_1.0X7,058,915 - 7,411,617 (-)NCBI
UU_Cfam_GSD_1.0X7,049,392 - 7,406,171 (-)NCBI
Mid1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2X414,418 - 767,610 (-)NCBI
SpeTri2.0NW_004936470414,420 - 576,717 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
MID1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 EnsemblX7,237,942 - 7,620,011 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1X7,235,386 - 7,906,049 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2X7,630,961 - 7,771,708 (-)NCBISscrofa10.2Sscrofa10.2susScr3
MID1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1X8,897,424 - 9,289,187 (-)NCBI
ChlSab1.1 EnsemblX8,895,602 - 9,076,871 (-)Ensembl
Mid1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046248823,504,660 - 3,876,526 (+)NCBI

Position Markers
DXRat85  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X24,126,708 - 24,127,019 (+)MAPPER
Rnor_6.0X25,468,817 - 25,469,127NCBIRnor6.0
Rnor_5.0X25,880,010 - 25,880,320UniSTSRnor5.0
RGSC_v3.4X44,758,364 - 44,758,676RGDRGSC3.4
RGSC_v3.4X44,758,366 - 44,758,676UniSTSRGSC3.4
RGSC_v3.1X44,811,819 - 44,812,280RGD
CeleraX24,553,717 - 24,554,027UniSTS
SHRSP x BN MapX6.8999RGD
SHRSP x BN MapX6.8999UniSTS
Cytogenetic MapXq21UniSTS
DXGot43  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X24,184,822 - 24,185,068 (+)MAPPER
Rnor_6.0X25,527,228 - 25,527,473NCBIRnor6.0
Rnor_5.0X25,938,421 - 25,938,666UniSTSRnor5.0
RGSC_v3.4X44,816,472 - 44,816,718RGDRGSC3.4
RGSC_v3.4X44,816,473 - 44,816,718UniSTSRGSC3.4
RGSC_v3.1X44,869,941 - 44,870,187RGD
Cytogenetic MapXq21UniSTS
DXUia1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X24,152,281 - 24,152,398 (+)MAPPER
Rnor_6.0X25,494,390 - 25,494,506NCBIRnor6.0
Rnor_5.0X25,905,583 - 25,905,699UniSTSRnor5.0
RGSC_v3.4X44,783,938 - 44,784,055RGDRGSC3.4
RGSC_v3.4X44,783,939 - 44,784,055UniSTSRGSC3.4
RGSC_v3.1X44,837,407 - 44,837,524RGD
CeleraX24,579,290 - 24,579,406UniSTS
Cytogenetic MapXq21UniSTS
PMC311143P1  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2X24,160,061 - 24,160,163 (+)MAPPER
Rnor_6.0X25,502,169 - 25,502,270NCBIRnor6.0
Rnor_5.0X25,913,362 - 25,913,463UniSTSRnor5.0
RGSC_v3.4X44,791,718 - 44,791,819UniSTSRGSC3.4
CeleraX24,587,069 - 24,587,170UniSTS
Cytogenetic MapXq21UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
731181Uae27Urinary albumin excretion QTL 272.70.0059urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)X144092703Rat
70165Bp64Blood pressure QTL 645.2arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)X166260933443848Rat
1298071Edpm12Estrogen-dependent pituitary mass QTL 123.2pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)X428214049282140Rat
631666Iddm5Insulin dependent diabetes mellitus QTL 5blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X595407850954078Rat
61430Cia18Collagen induced arthritis QTL 183.1joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)X15688119127888215Rat
71116Niddm16Non-insulin dependent diabetes mellitus QTL 167.81blood glucose amount (VT:0000188)plasma glucose level (CMO:0000042)X1815335263153352Rat
1598873Memor2Memory QTL 22.5exploratory behavior trait (VT:0010471)average horizontal distance in proximity to the target during voluntary locomotion in an experimental apparatus (CMO:0002674)X2159262344320739Rat
2290375Gluco34Glucose level QTL 342.75blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)X2159262344468300Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:106
Count of miRNA genes:91
Interacting mature miRNAs:100
Transcripts:ENSRNOT00000004873
Prediction methods:Microtar, Miranda, Pita, 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.


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 4 3 2 2 2 2 36 24 29 5 2
Low 3 39 53 38 19 38 6 9 38 11 8 6 6
Below cutoff 1 1 1 4

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000004873   ⟹   ENSRNOP00000004873
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX25,462,401 - 25,590,048 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086414   ⟹   ENSRNOP00000072598
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 EnsemblX25,458,771 - 25,628,272 (-)Ensembl
RefSeq Acc Id: NM_022927   ⟹   NP_075216
RefSeq Status: PROVISIONAL
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X24,120,293 - 24,248,353 (-)NCBI
Rnor_6.0X25,462,401 - 25,590,048 (-)NCBI
Rnor_5.0X25,869,975 - 26,249,296 (-)NCBI
RGSC_v3.4X44,751,950 - 44,879,999 (-)RGD
CeleraX24,547,301 - 24,674,105 (-)RGD
Sequence:
RefSeq Acc Id: XM_006256825   ⟹   XP_006256887
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X24,116,674 - 24,286,857 (-)NCBI
Rnor_6.0X25,458,782 - 25,629,434 (-)NCBI
Rnor_5.0X25,869,975 - 26,249,296 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602142   ⟹   XP_017457631
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X24,116,674 - 24,491,205 (-)NCBI
Rnor_6.0X25,458,782 - 25,839,941 (-)NCBI
Sequence:
RefSeq Acc Id: XM_017602143   ⟹   XP_017457632
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X24,116,674 - 24,345,018 (-)NCBI
Rnor_6.0X25,458,782 - 25,688,440 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039099997   ⟹   XP_038955925
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X24,116,674 - 24,345,464 (-)NCBI
RefSeq Acc Id: XM_039099998   ⟹   XP_038955926
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2X24,116,674 - 24,286,857 (-)NCBI
Reference Sequences
RefSeq Acc Id: NP_075216   ⟸   NM_022927
- UniProtKB: P82458 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_006256887   ⟸   XM_006256825
- Peptide Label: isoform X1
- UniProtKB: P82458 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017457631   ⟸   XM_017602142
- Peptide Label: isoform X1
- UniProtKB: P82458 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: XP_017457632   ⟸   XM_017602143
- Peptide Label: isoform X1
- UniProtKB: P82458 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000004873   ⟸   ENSRNOT00000004873
RefSeq Acc Id: ENSRNOP00000072598   ⟸   ENSRNOT00000086414
RefSeq Acc Id: XP_038955925   ⟸   XM_039099997
- Peptide Label: isoform X1
RefSeq Acc Id: XP_038955926   ⟸   XM_039099998
- Peptide Label: isoform X2
Protein Domains
B30.2/SPRY   COS   Fibronectin type-III

Transcriptome

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

Promoters
RGD ID:13701779
Promoter ID:EPDNEW_R12303
Type:single initiation site
Name:Mid1_2
Description:midline 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12304  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X25,590,000 - 25,590,060EPDNEW
RGD ID:13701787
Promoter ID:EPDNEW_R12304
Type:initiation region
Name:Mid1_1
Description:midline 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Alternative Promoters:null; see alsoEPDNEW_R12303  
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0X25,628,244 - 25,628,304EPDNEW

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)
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
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: RGSC_v3.4

Chromosome Start Pos End Pos Reference Nucleotide Variant Nucleotide Variant Type Strain
X 44868226 44868227 T G snv LE/Stm (KNAW)


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:2640 AgrOrtholog
Ensembl Genes ENSRNOG00000003613 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Protein ENSRNOP00000004873 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOP00000072598 ENTREZGENE, UniProtKB/Swiss-Prot
Ensembl Transcript ENSRNOT00000004873 ENTREZGENE, UniProtKB/Swiss-Prot
  ENSRNOT00000086414 UniProtKB/Swiss-Prot
Gene3D-CATH 2.60.120.920 UniProtKB/Swiss-Prot
  2.60.40.10 UniProtKB/Swiss-Prot
  3.30.40.10 UniProtKB/Swiss-Prot
InterPro B30.2/SPRY UniProtKB/Swiss-Prot
  B30.2/SPRY_sf UniProtKB/Swiss-Prot
  Bbox_C UniProtKB/Swiss-Prot
  Butyrophylin_SPRY UniProtKB/Swiss-Prot
  ConA-like_dom_sf UniProtKB/Swiss-Prot
  COS_domain UniProtKB/Swiss-Prot
  FN3_dom UniProtKB/Swiss-Prot
  FN3_sf UniProtKB/Swiss-Prot
  Ig-like_fold UniProtKB/Swiss-Prot
  MID1 UniProtKB/Swiss-Prot
  Midline-1_COS UniProtKB/Swiss-Prot
  PRY UniProtKB/Swiss-Prot
  SPRY_dom UniProtKB/Swiss-Prot
  Znf-RING_LisH UniProtKB/Swiss-Prot
  Znf_B-box UniProtKB/Swiss-Prot
  Znf_RING UniProtKB/Swiss-Prot
  Znf_RING/FYVE/PHD UniProtKB/Swiss-Prot
  Znf_RING_CS UniProtKB/Swiss-Prot
KEGG Report rno:54252 UniProtKB/Swiss-Prot
NCBI Gene 54252 ENTREZGENE
PANTHER PTHR24099:SF23 UniProtKB/Swiss-Prot
Pfam COS UniProtKB/Swiss-Prot
  fn3 UniProtKB/Swiss-Prot
  PRY UniProtKB/Swiss-Prot
  SPRY UniProtKB/Swiss-Prot
  zf-B_box UniProtKB/Swiss-Prot
  zf-RING_UBOX UniProtKB/Swiss-Prot
PhenoGen Mid1 PhenoGen
PRINTS BUTYPHLNCDUF UniProtKB/Swiss-Prot
PROSITE B302_SPRY UniProtKB/Swiss-Prot
  COS UniProtKB/Swiss-Prot
  FN3 UniProtKB/Swiss-Prot
  ZF_BBOX UniProtKB/Swiss-Prot
  ZF_RING_1 UniProtKB/Swiss-Prot
  ZF_RING_2 UniProtKB/Swiss-Prot
SMART BBC UniProtKB/Swiss-Prot
  BBOX UniProtKB/Swiss-Prot
  FN3 UniProtKB/Swiss-Prot
  RING UniProtKB/Swiss-Prot
  SPRY UniProtKB/Swiss-Prot
Superfamily-SCOP SSF49265 UniProtKB/Swiss-Prot
  SSF49899 UniProtKB/Swiss-Prot
UniProt P82458 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2014-06-25 Mid1  midline 1  Mid1  midline 1 (Opitz/BBB syndrome)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-02-27 Mid1  midline 1 (Opitz/BBB syndrome)  Mid1  midline 1  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2002-06-10 Mid1  midline 1      Name updated 70584 APPROVED
2001-06-12 Mid1  Midline1      Symbol and Name updated to reflect Human and Mouse nomenclature 62408 APPROVED
2001-06-12 Fxy  Finger on X and Y (in rat only on X)      Symbol and Name withdrawn 62408 WITHDRAWN