Ahctf1 (AT hook containing transcription factor 1) - Rat Genome Database

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Gene: Ahctf1 (AT hook containing transcription factor 1) Rattus norvegicus
Analyze
Symbol: Ahctf1
Name: AT hook containing transcription factor 1
RGD ID: 1561291
Description: Predicted to be involved in nuclear pore complex assembly and regulation of cytokinesis. Predicted to colocalize with chromatin; condensed chromosome kinetochore; and nuclear pore outer ring. Orthologous to human AHCTF1 (AT-hook containing transcription factor 1); INTERACTS WITH 17alpha-ethynylestradiol; 2,3,7,8-tetrachlorodibenzodioxine; bisphenol A.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: ELYS; LOC360886; RGD1561291; similar to transcription factor ELYS; transcription factor ELYS-like
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
mRatBN7.21391,481,932 - 91,536,391 (-)NCBI
Rnor_6.0 Ensembl1398,023,430 - 98,078,946 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01398,023,528 - 98,079,138 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013103,033,087 - 103,088,505 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41395,432,560 - 95,483,323 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1391,033,173 - 91,087,225 (-)NCBICelera
Cytogenetic Map13q26NCBI
JBrowse: View Region in Genome Browser (JBrowse)
Model


Disease Annotations     Click to see Annotation Detail View

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

References

Additional References at PubMed
PMID:11952839   PMID:15632090   PMID:17098863   PMID:19056867   PMID:30361391  


Genomics

Comparative Map Data
Ahctf1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21391,481,932 - 91,536,391 (-)NCBI
Rnor_6.0 Ensembl1398,023,430 - 98,078,946 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01398,023,528 - 98,079,138 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.013103,033,087 - 103,088,505 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41395,432,560 - 95,483,323 (-)NCBIRGSC3.4rn4RGSC3.4
Celera1391,033,173 - 91,087,225 (-)NCBICelera
Cytogenetic Map13q26NCBI
AHCTF1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1246,839,098 - 246,931,948 (-)EnsemblGRCh38hg38GRCh38
GRCh381246,839,098 - 246,931,948 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh371247,002,400 - 247,095,250 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 361245,069,023 - 245,148,302 (-)NCBINCBI36hg18NCBI36
Celera1220,298,863 - 220,391,306 (-)NCBI
Cytogenetic Map1q44NCBI
HuRef1217,396,102 - 217,488,405 (-)NCBIHuRef
CHM1_11248,274,635 - 248,367,575 (-)NCBICHM1_1
Ahctf1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm391179,572,469 - 179,631,580 (-)NCBIGRCm39mm39
GRCm39 Ensembl1179,572,459 - 179,631,245 (-)Ensembl
GRCm381179,744,904 - 179,804,015 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl1179,744,894 - 179,803,680 (-)EnsemblGRCm38mm10GRCm38
MGSCv371181,675,035 - 181,734,146 (-)NCBIGRCm37mm9NCBIm37
MGSCv361181,582,766 - 181,640,340 (-)NCBImm8
Celera1186,809,078 - 186,868,175 (-)NCBICelera
Cytogenetic Map1H4NCBI
cM Map183.62NCBI
Ahctf1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049554069,688,749 - 9,744,998 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049554069,687,237 - 9,754,426 (-)NCBIChiLan1.0ChiLan1.0
AHCTF1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11227,934,111 - 228,026,820 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1227,935,557 - 228,026,795 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01222,469,006 - 222,563,635 (-)NCBIMhudiblu_PPA_v0panPan3
AHCTF1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1737,550,045 - 37,627,428 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl737,543,496 - 37,627,131 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha737,033,475 - 37,110,578 (-)NCBI
ROS_Cfam_1.0737,383,897 - 37,461,128 (-)NCBI
UMICH_Zoey_3.1737,224,058 - 37,301,251 (-)NCBI
UNSW_CanFamBas_1.0737,231,362 - 37,308,602 (-)NCBI
UU_Cfam_GSD_1.0737,500,950 - 37,578,194 (-)NCBI
Ahctf1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934450,537,666 - 50,604,348 (-)NCBI
SpeTri2.0NW_0049365264,143,002 - 4,209,689 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
AHCTF1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1015,042,170 - 15,132,654 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11015,042,168 - 15,121,885 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21017,361,477 - 17,440,847 (+)NCBISscrofa10.2Sscrofa10.2susScr3
AHCTF1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.12583,889,934 - 83,978,965 (-)NCBI
ChlSab1.1 Ensembl2583,892,508 - 83,978,935 (-)Ensembl
Vero_WHO_p1.0NW_02366605586,190,965 - 86,287,548 (-)NCBI
Ahctf1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462477112,785,656 - 12,863,797 (+)NCBI

Position Markers
RH138593  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.21391,488,995 - 91,489,200 (+)MAPPER
Rnor_6.01398,030,588 - 98,030,792NCBIRnor6.0
Rnor_5.013103,040,147 - 103,040,351UniSTSRnor5.0
RGSC_v3.41395,439,809 - 95,440,013UniSTSRGSC3.4
Celera1391,040,232 - 91,040,436UniSTS
RH 3.4 Map13605.6UniSTS
Cytogenetic Map13q26UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)131107975663Rat
1354666Bp244Blood pressure QTL 2444.9arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)131107975663Rat
1581570Eae17Experimental allergic encephalomyelitis QTL 174.1nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)1312193394108478121Rat
7207885Glom27Glomerulus QTL 273.9kidney glomerulus integrity trait (VT:0010546)kidney crescentic glomeruli count to kidney normal glomeruli count ratio (CMO:0002139)1324502279108770533Rat
1354621Rf47Renal function QTL 473.7kidney renin amount (VT:0010559)kidney renin level (CMO:0002166)1335301263107975663Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)absolute change in mean arterial blood pressure (CMO:0000533)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)133614753399968921Rat
70181BpQTLcluster11Blood pressure QTL cluster 116.922arterial blood pressure trait (VT:2000000)diastolic blood pressure (CMO:0000005)133614753399968921Rat
1641901Alcrsp6Alcohol response QTL 6response to alcohol trait (VT:0010489)duration of loss of righting reflex (CMO:0002289)1357903612102903612Rat
1354655Bp241Blood pressure QTL 2413.9arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)1362975663107975663Rat
12879475Bp400Blood pressure QTL 400arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)1366971778111971778Rat
2293687Bss26Bone structure and strength QTL 264.60.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)1371230858114033958Rat
2293702Bss34Bone structure and strength QTL 344.610.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)1371230858114033958Rat
7387280Uae43Urinary albumin excretion QTL 435.690.4174urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)1372583716114033958Rat
10755455Coatc13Coat color QTL 130coat/hair pigmentation trait (VT:0010463)pigmented ventral coat/hair area to total ventral coat/hair area ratio (CMO:0001812)777694986114033958Rat
8655959Pur32Proteinuria QTL 328.4total urine protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)1379567081103613733Rat
2293341Glom15Glomerulus QTL 159.1kidney glomerulus integrity trait (VT:0010546)kidney sclerotic glomeruli count to total glomeruli count ratio (CMO:0001269)1380403559108770687Rat
4889606Gluco63Glucose level QTL 632.860.003blood glucose amount (VT:0000188)blood glucose level area under curve (AUC) (CMO:0000350)1386833393114033958Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:13
Count of miRNA genes:12
Interacting mature miRNAs:13
Transcripts:ENSRNOT00000035875
Prediction methods:Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

The detailed report is available here: Full Report CSV TAB Printer

miRNA Target Status data imported from miRGate (http://mirgate.bioinfo.cnio.es/).
For more information about miRGate, see PMID:25858286 or access the full paper here.


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 2 29 55 39 19 39 8 8 74 34 41 11 8
Low 1 14 2 2 2 3 1
Below cutoff

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000035875   ⟹   ENSRNOP00000037261
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1398,023,528 - 98,078,946 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000078034   ⟹   ENSRNOP00000071711
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1398,023,430 - 98,078,555 (-)Ensembl
RefSeq Acc Id: NM_001271270   ⟹   NP_001258199
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21391,481,936 - 91,536,391 (-)NCBI
Rnor_6.01398,023,528 - 98,078,946 (-)NCBI
Rnor_5.013103,033,087 - 103,088,505 (-)NCBI
Celera1391,033,173 - 91,087,225 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006250386   ⟹   XP_006250448
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21391,481,932 - 91,536,060 (-)NCBI
Rnor_6.01398,023,528 - 98,078,617 (-)NCBI
Rnor_5.013103,033,087 - 103,088,505 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008769858   ⟹   XP_008768080
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01398,023,528 - 98,079,138 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039090921   ⟹   XP_038946849
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21391,498,935 - 91,536,061 (-)NCBI
RefSeq Acc Id: XR_005492256
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21391,483,495 - 91,536,060 (-)NCBI
RefSeq Acc Id: XR_005492257
RefSeq Status:
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21391,490,581 - 91,536,061 (-)NCBI
Protein Sequences
Protein RefSeqs NP_001258199 (Get FASTA)   NCBI Sequence Viewer  
  XP_006250448 (Get FASTA)   NCBI Sequence Viewer  
  XP_038946849 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein EDL94815 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_001258199   ⟸   NM_001271270
- UniProtKB: D3ZZZ0 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006250448   ⟸   XM_006250386
- Peptide Label: isoform X1
- UniProtKB: A0A0G2K160 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008768080   ⟸   XM_008769858
- Peptide Label: isoform X2
- Sequence:
RefSeq Acc Id: ENSRNOP00000037261   ⟸   ENSRNOT00000035875
RefSeq Acc Id: ENSRNOP00000071711   ⟸   ENSRNOT00000078034
RefSeq Acc Id: XP_038946849   ⟸   XM_039090921
- Peptide Label: isoform X2
Protein Domains
ELYS   ELYS-bb

Transcriptome

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

Promoters
RGD ID:13699054
Promoter ID:EPDNEW_R9579
Type:initiation region
Name:Ahctf1_1
Description:AT hook containing transcription factor 1
SO ACC ID:SO:0000170
Source:EPDNEW (Eukaryotic Promoter Database, http://epd.vital-it.ch/)
Experiment Methods:Single-end sequencing.
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.01398,078,946 - 98,079,006EPDNEW

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)
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
M520/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
MHS/Gib (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
MNS/Gib (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
MR/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
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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1561291 AgrOrtholog
Ensembl Genes ENSRNOG00000023541 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000037261 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000071711 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000035875 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOT00000078034 UniProtKB/TrEMBL
InterPro ELYS-bb UniProtKB/TrEMBL
  ELYS_dom UniProtKB/TrEMBL
KEGG Report rno:360886 UniProtKB/TrEMBL
NCBI Gene 360886 ENTREZGENE
Pfam ELYS UniProtKB/TrEMBL
  ELYS-bb UniProtKB/TrEMBL
PhenoGen Ahctf1 PhenoGen
UniProt A0A0G2K160 ENTREZGENE, UniProtKB/TrEMBL
  D3ZZZ0 ENTREZGENE, UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2013-05-24 Ahctf1  AT hook containing transcription factor 1  LOC100365024  transcription factor ELYS-like  Data Merged 1643240 APPROVED
2010-05-05 LOC100365024  transcription factor ELYS-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-04-30 Ahctf1  AT hook containing transcription factor 1   Ahctf1_predicted  AT hook containing transcription factor 1 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Ahctf1_predicted  AT hook containing transcription factor 1 (predicted)  RGD1561291_predicted  similar to transcription factor ELYS (predicted)  Symbol and Name updated 1299863 APPROVED
2006-03-07 RGD1561291_predicted  similar to transcription factor ELYS (predicted)  LOC360886  similar to transcription factor ELYS  Symbol and Name status set to approved 1299863 APPROVED
2006-02-09 LOC360886  similar to transcription factor ELYS      Symbol and Name status set to provisional 70820 PROVISIONAL