Crnkl1 (crooked neck pre-mRNA splicing factor 1) - Rat Genome Database
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Gene: Crnkl1 (crooked neck pre-mRNA splicing factor 1) Rattus norvegicus
Analyze
Symbol: Crnkl1
Name: crooked neck pre-mRNA splicing factor 1
RGD ID: 620507
Description: Predicted to have RNA binding activity. Involved in cellular response to brain-derived neurotrophic factor stimulus; cellular response to leukemia inhibitory factor; and cerebral cortex development. Predicted to localize to Prp19 complex; U2-type catalytic step 2 spliceosome; and post-mRNA release spliceosomal complex. Human ortholog(s) of this gene implicated in basal cell carcinoma. Orthologous to human CRNKL1 (crooked neck pre-mRNA splicing factor 1); PARTICIPATES IN spliceosome pathway; INTERACTS WITH 1,1,1-Trichloro-2-(o-chlorophenyl)-2-(p-chlorophenyl)ethane; 17alpha-ethynylestradiol; 2,4-dinitrotoluene.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: Crn; Crn, crooked neck-like 1; Crn, crooked neck-like 1 (Drosophila); crooked neck homolog; crooked neck pre-mRNA splicing factor-like 1; crooked neck pre-mRNA splicing factor-like 1 (Drosophila); crooked neck protein; crooked neck-like 1 protein-like; crooked neck-like protein 1; crooked neck-like protein 1-like; LOC100360434; LOC100910202; MGC93283
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Related Pseudogenes: Crnkl1-ps1  
Latest Assembly: Rnor_6.0 - RGSC Genome Assembly v6.0
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23133,338,593 - 133,354,329 (-)NCBI
Rnor_6.0 Ensembl618,349,167 - 18,351,536 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0618,349,226 - 18,351,540 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0628,249,112 - 28,251,426 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43134,538,940 - 134,554,660 (-)NCBIRGSC3.4rn4RGSC3.4
Celera6957,687 - 960,001 (+)NCBICelera
Cytogenetic Map6q12NCBI
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

Cellular Component

Molecular Function

Molecular Pathway Annotations     Click to see Annotation Detail View
References

Additional References at PubMed
PMID:11991638   PMID:12084575   PMID:12477932   PMID:15489334   PMID:22681889   PMID:28076346  


Genomics

Comparative Map Data
Crnkl1
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.23133,338,593 - 133,354,329 (-)NCBI
Rnor_6.0 Ensembl618,349,167 - 18,351,536 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.0618,349,226 - 18,351,540 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.0628,249,112 - 28,251,426 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.43134,538,940 - 134,554,660 (-)NCBIRGSC3.4rn4RGSC3.4
Celera6957,687 - 960,001 (+)NCBICelera
Cytogenetic Map6q12NCBI
CRNKL1
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl2020,034,368 - 20,056,046 (-)EnsemblGRCh38hg38GRCh38
GRCh382020,034,368 - 20,056,046 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh372020,015,012 - 20,036,690 (-)NCBIGRCh37GRCh37hg19GRCh37
GRCh372020,015,005 - 20,036,690 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 362019,963,012 - 19,984,690 (-)NCBINCBI36hg18NCBI36
Build 342019,963,011 - 19,984,690NCBI
Celera2020,089,029 - 20,110,711 (-)NCBI
Cytogenetic Map20p11.23NCBI
HuRef2019,976,670 - 19,998,362 (-)NCBIHuRef
CHM1_12020,015,382 - 20,037,072 (-)NCBICHM1_1
Crnkl1
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm392145,759,402 - 145,776,620 (-)NCBIGRCm39mm39
GRCm382145,917,482 - 145,934,700 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl2145,917,479 - 145,935,014 (-)EnsemblGRCm38mm10GRCm38
MGSCv372145,743,218 - 145,760,436 (-)NCBIGRCm37mm9NCBIm37
MGSCv362145,608,923 - 145,626,141 (-)NCBImm8
Celera2147,153,324 - 147,170,535 (-)NCBICelera
Cytogenetic Map2G1NCBI
Crnkl1
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495541528,158,351 - 28,172,055 (-)EnsemblChiLan1.0
ChiLan1.0NW_00495541528,158,351 - 28,171,335 (-)NCBIChiLan1.0ChiLan1.0
CRNKL1
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.12019,957,545 - 19,975,809 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl2019,959,356 - 19,979,094 (-)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v02019,992,092 - 20,010,809 (-)NCBIMhudiblu_PPA_v0panPan3
CRNKL1
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1 Ensembl243,294,616 - 3,310,702 (+)EnsemblCanFam3.1canFam3CanFam3.1
CanFam3.1243,294,607 - 3,310,846 (+)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
Crnkl1
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
SpeTri2.0NW_004936485328,077 - 351,323 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CRNKL1
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1728,077,707 - 28,111,545 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11728,079,541 - 28,111,871 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21731,810,243 - 31,816,810 (-)NCBISscrofa10.2Sscrofa10.2susScr3
CRNKL1
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1249,052,304 - 49,070,600 (-)NCBI
ChlSab1.1 Ensembl249,054,125 - 49,070,576 (-)Ensembl
Crnkl1
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462474120,565,686 - 20,581,708 (-)NCBI

Position Markers
AU022874  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03140,127,552 - 140,128,369NCBIRnor6.0
Rnor_6.0618,349,710 - 18,349,915NCBIRnor6.0
Rnor_5.0628,249,596 - 28,249,801UniSTSRnor5.0
Rnor_5.03146,547,713 - 146,548,530UniSTSRnor5.0
RGSC_v3.4617,490,336 - 17,490,541UniSTSRGSC3.4
RGSC_v3.43134,540,543 - 134,541,360UniSTSRGSC3.4
Celera3132,205,323 - 132,206,140UniSTS
Celera6959,312 - 959,517UniSTS
Cytogenetic Map3q41UniSTS
RH143622  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0618,349,492 - 18,349,778NCBIRnor6.0
Rnor_6.03140,127,068 - 140,127,620NCBIRnor6.0
Rnor_5.0628,249,378 - 28,249,664UniSTSRnor5.0
Rnor_5.03146,547,229 - 146,547,781UniSTSRnor5.0
RGSC_v3.4617,490,118 - 17,490,404UniSTSRGSC3.4
RGSC_v3.43134,539,206 - 134,540,611UniSTSRGSC3.4
Celera3132,204,005 - 132,205,391UniSTS
Celera6959,449 - 959,735UniSTS
Cytogenetic Map3q41UniSTS
RH141585  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.03140,126,650 - 140,126,837NCBIRnor6.0
Rnor_5.03146,546,811 - 146,546,998UniSTSRnor5.0
RGSC_v3.43134,538,788 - 134,538,975UniSTSRGSC3.4
Celera3132,203,587 - 132,203,774UniSTS
RH 3.4 Map31168.59UniSTS
Cytogenetic Map3q41UniSTS
UniSTS:479086  
Rat AssemblyChrPosition (strand)SourceJBrowse
Rnor_6.0618,349,399 - 18,349,937NCBIRnor6.0
Rnor_5.0628,249,285 - 28,249,823UniSTSRnor5.0
RGSC_v3.4617,490,025 - 17,490,563UniSTSRGSC3.4
Celera6959,290 - 959,828UniSTS
Cytogenetic Map3q41UniSTS


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1598843Cm63Cardiac mass QTL 632.6heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)6123620518Rat
1578758Tcas9Tongue tumor susceptibility QTL 93.29tongue integrity trait (VT:0010553)number of squamous cell tumors of the tongue with diameter greater than 3 mm (CMO:0001950)6125048718Rat
738023Alc17Alcohol consumption QTL 173.10.003consumption behavior trait (VT:0002069)ethanol drink intake rate to body weight ratio (CMO:0001616)6135623029Rat
1354616Despr12Despair related QTL 120.0012locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)6135623029Rat
1549905Stresp10Stress response QTL 106.830.0066stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)6135623029Rat
2300176Bmd51Bone mineral density QTL 5111.70.0001femur mineral mass (VT:0010011)bone mineral density (CMO:0001226)6135623029Rat
2300190Bmd52Bone mineral density QTL 5211.20.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)6135623029Rat
1331743Uae28Urinary albumin excretion QTL 284.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)6141917988Rat
9589048Scfw3Subcutaneous fat weight QTL 34.570.001subcutaneous adipose mass (VT:1000472)abdominal subcutaneous fat pad weight (CMO:0002069)6142388212Rat
9589129Insul24Insulin level QTL 2419.060.001blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)6142388212Rat
7411603Foco13Food consumption QTL 135.50.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6142388212Rat
7411542Bw127Body weight QTL 1275.50.001body mass (VT:0001259)body weight gain (CMO:0000420)6142388212Rat
8552962Pigfal16Plasma insulin-like growth factor 1 level QTL 169.4blood insulin-like growth factor amount (VT:0010479)plasma insulin-like growth factor 1 level (CMO:0001299)6142388212Rat
2293709Bss23Bone structure and strength QTL 235.180.0001femur morphology trait (VT:0000559)femur cross-sectional area (CMO:0001661)6143665660Rat
2293650Bss31Bone structure and strength QTL 315.050.0001femur strength trait (VT:0010010)femur midshaft polar moment of inertia (CMO:0001669)6143665660Rat
2293656Bss28Bone structure and strength QTL 286.790.0001femur morphology trait (VT:0000559)femur midshaft cortical cross-sectional area (CMO:0001663)6143665660Rat
7411584Foco4Food consumption QTL 44.30.001eating behavior trait (VT:0001431)feed conversion ratio (CMO:0001312)6144015370Rat
738024Sach5Saccharine consumption QTL 53.90.00039consumption behavior trait (VT:0002069)saccharin intake volume to total fluid intake volume ratio (CMO:0001601)6144570292Rat
2301972Bp325Blood pressure QTL 3254.8arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)6175623393Rat
8693645Alc31Alcohol consumption QTL 313.70.038drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)613505323600274Rat
1359023Bp272Blood pressure QTL 2722.5arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)6112039328706721Rat
2292589Emca10Estrogen-induced mammary cancer QTL 100.048mammary gland integrity trait (VT:0010552)post-insult time to mammary tumor formation (CMO:0000345)6112039346120393Rat
1354664Slep2Serum leptin concentration QTL 24.49blood leptin amount (VT:0005667)serum leptin level (CMO:0000780)6112039375023446Rat
1576309Emca7Estrogen-induced mammary cancer QTL 74mammary gland integrity trait (VT:0010552)mammary tumor number (CMO:0000343)62537030111715717Rat
1578665Bss16Bone structure and strength QTL 164.4femur morphology trait (VT:0000559)bone trabecular cross-sectional area (CMO:0002311)6616172276002731Rat
1578668Bmd14Bone mineral density QTL 143.8femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)6616172276002731Rat
4145119Mcs25Mammary carcinoma susceptibility QTL 250.0001mammary gland integrity trait (VT:0010552)ratio of deaths to total study population during a period of time (CMO:0001023)67009971115379601Rat
1358190Ept1Estrogen-induced pituitary tumorigenesis QTL 14.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6808322221515439Rat
2292616Ept15Estrogen-induced pituitary tumorigenesis QTL 154.4pituitary gland mass (VT:0010496)pituitary gland wet weight (CMO:0000853)6808322221515439Rat
8693699Alc37Alcohol consumption QTL 372.60.224drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)6997427722477622Rat
8693690Alc35Alcohol consumption QTL 352.20.606drinking behavior trait (VT:0001422)calculated ethanol drink intake rate (CMO:0001615)6997427722477622Rat
634322Bw12Body weight QTL 120body mass (VT:0001259)body weight (CMO:0000012)71017386255173862Rat
2293706Bmd20Bone mineral density QTL 204.30.0002femur mineral mass (VT:0010011)total volumetric bone mineral density (CMO:0001728)61312295821165729Rat
1300128Rf16Renal function QTL 163.89renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295834367603Rat
1300164Rf15Renal function QTL 153.12renal blood flow trait (VT:2000006)absolute change in renal blood flow rate (CMO:0001168)61312295857516539Rat
10401812Kidm54Kidney mass QTL 54kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat
10401800Kidm49Kidney mass QTL 49kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)61681010761810107Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:154
Count of miRNA genes:112
Interacting mature miRNAs:123
Transcripts:ENSRNOT00000014632, ENSRNOT00000061588
Prediction methods:Microtar, Miranda, Rnahybrid, Targetscan
Result types:miRGate_prediction

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

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


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 3 12 27 16 17 16 61 21 33 11
Low 3 53 64 43 21 43 8 14 84 42 44 11 8
Below cutoff 21 23 23 23 8 8 3 7 5 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000061588   ⟹   ENSRNOP00000073513
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl618,349,167 - 18,351,536 (-)Ensembl
RefSeq Acc Id: NM_053797   ⟹   NP_446249
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.23133,338,593 - 133,354,329 (-)NCBI
Rnor_6.0618,349,226 - 18,351,540 (-)NCBI
Rnor_5.0628,249,112 - 28,251,426 (-)NCBI
RGSC_v3.43134,538,940 - 134,554,660 (-)RGD
Celera6957,687 - 960,001 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_446249 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAH85718 (Get FASTA)   NCBI Sequence Viewer  
  P63155 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_446249   ⟸   NM_053797
- UniProtKB: P63155 (UniProtKB/Swiss-Prot)
- Sequence:
RefSeq Acc Id: ENSRNOP00000073513   ⟸   ENSRNOT00000061588
Protein Domains
TPR_REGION

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)
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)
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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)
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
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)
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
WN/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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620507 AgrOrtholog
Ensembl Genes ENSRNOG00000010587 UniProtKB/Swiss-Prot
  ENSRNOG00000040045 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000014632 UniProtKB/Swiss-Prot
  ENSRNOP00000073513 ENTREZGENE, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000014632 UniProtKB/Swiss-Prot
  ENSRNOT00000061588 ENTREZGENE, UniProtKB/TrEMBL
Gene3D-CATH 1.25.40.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7190212 IMAGE-MGC_LOAD
InterPro HAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPR-contain_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  TPR-like_helical_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:100910202 UniProtKB/Swiss-Prot
  rno:102548514 UniProtKB/Swiss-Prot
MGC_CLONE MGC:93283 IMAGE-MGC_LOAD
NCBI Gene 100910202 ENTREZGENE
Pfam HAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Crnkl1 PhenoGen
PROSITE TPR_REGION UniProtKB/TrEMBL
SMART HAT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF48452 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A0G2K5Q2_RAT UniProtKB/TrEMBL
  CRNL1_RAT UniProtKB/Swiss-Prot, ENTREZGENE
UniProt Secondary Q9CQC1 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2015-07-29 Crnkl1  crooked neck pre-mRNA splicing factor 1  LOC100360434  crooked neck-like 1 protein-like  Data Merged 737654 PROVISIONAL
2013-12-11 Crnkl1  crooked neck pre-mRNA splicing factor 1  Crnkl1  crooked neck pre-mRNA splicing factor-like 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2013-11-27 Crnkl1  crooked neck pre-mRNA splicing factor-like 1 (Drosophila)  LOC100910202  crooked neck-like protein 1-like  Data Merged 737654 APPROVED
2012-07-05 LOC100910202  crooked neck-like protein 1-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2010-05-06 LOC100360434  crooked neck-like 1 protein-like      Symbol and Name status set to provisional 70820 PROVISIONAL
2008-10-15 Crnkl1  crooked neck pre-mRNA splicing factor-like 1 (Drosophila)  Crnkl1  Crn, crooked neck-like 1 (Drosophila)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2006-03-30 Crnkl1  Crn, crooked neck-like 1 (Drosophila)    crooked neck protein  Name updated 1299863 APPROVED
2004-09-10 Crnkl1  crooked neck protein  Crn    Symbol and Name updated 1299863 APPROVED
2002-08-07 Crn  crooked neck protein      Symbol and Name status set to provisional 70820 PROVISIONAL