Crispld2 (cysteine-rich secretory protein LCCL domain containing 2) - Rat Genome Database

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Gene: Crispld2 (cysteine-rich secretory protein LCCL domain containing 2) Rattus norvegicus
Analyze
Symbol: Crispld2
Name: cysteine-rich secretory protein LCCL domain containing 2
RGD ID: 620860
Description: Predicted to have heparin binding activity. Involved in lung development. Predicted to localize to extracellular matrix; extracellular space; and transport vesicle. Orthologous to human CRISPLD2 (cysteine rich secretory protein LCCL domain containing 2); INTERACTS WITH 1,2,4-trimethylbenzene; 17alpha-ethynylestradiol; 6-propyl-2-thiouracil.
Type: protein-coding
RefSeq Status: VALIDATED
Also known as: cysteine-rich secretory protein LCCL domain-containing 2; late gestation lung protein 1; Lcrisp2; Lgl1
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
mRatBN7.21948,053,153 - 48,111,485 (+)NCBI
Rnor_6.0 Ensembl1952,647,070 - 52,705,131 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01952,647,038 - 52,705,118 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01963,394,645 - 63,452,571 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41950,313,710 - 50,378,031 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11950,287,944 - 50,381,888 (+)NCBI
Celera1947,326,756 - 47,367,597 (+)NCBICelera
Cytogenetic Map19q12NCBI
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
1,1,1-trichloro-2,2-bis(4-hydroxyphenyl)ethane  (ISO)
1,2,4-trimethylbenzene  (EXP)
1,2-dichloroethane  (ISO)
17alpha-ethynylestradiol  (EXP,ISO)
17beta-estradiol  (ISO)
17beta-hydroxy-5alpha-androstan-3-one  (ISO)
2,3,7,8-tetrachlorodibenzodioxine  (ISO)
2-hydroxypropanoic acid  (ISO)
3-isobutyl-1-methyl-7H-xanthine  (ISO)
4,4'-sulfonyldiphenol  (ISO)
4-hydroxyphenyl retinamide  (ISO)
6-propyl-2-thiouracil  (EXP)
aflatoxin B1  (ISO)
all-trans-retinoic acid  (EXP,ISO)
ammonium chloride  (EXP)
amphetamine  (EXP)
arsane  (ISO)
arsenic atom  (ISO)
atrazine  (ISO)
benzo[a]pyrene  (ISO)
benzo[a]pyrene diol epoxide I  (ISO)
bis(2-ethylhexyl) phthalate  (ISO)
bisphenol A  (EXP,ISO)
bisphenol F  (ISO)
butan-1-ol  (ISO)
cadmium dichloride  (ISO)
calcitriol  (ISO)
candesartan  (EXP)
carbon nanotube  (ISO)
chromium atom  (ISO)
chrysene  (ISO)
cisplatin  (ISO)
clodronic acid  (ISO)
copper atom  (EXP,ISO)
copper(0)  (EXP,ISO)
corticosterone  (EXP)
crocidolite asbestos  (ISO)
cytarabine  (ISO)
dexamethasone  (ISO)
diazinon  (ISO)
dibutyl phthalate  (EXP)
diethylstilbestrol  (ISO)
disulfiram  (ISO)
dorsomorphin  (ISO)
doxorubicin  (ISO)
estriol  (ISO)
fipronil  (EXP)
formaldehyde  (ISO)
furan  (EXP)
genistein  (EXP)
GW 4064  (ISO)
hydroquinone  (ISO)
indometacin  (ISO)
isobutanol  (ISO)
lead diacetate  (ISO)
malathion  (EXP)
methimazole  (EXP)
methylmercury chloride  (ISO)
mifepristone  (ISO)
nickel atom  (ISO)
nitrobenzenes  (EXP)
nitrofen  (EXP)
oxaliplatin  (EXP)
paracetamol  (EXP)
paraquat  (EXP)
potassium chromate  (ISO)
potassium dichromate  (ISO)
progesterone  (EXP,ISO)
rac-lactic acid  (ISO)
raloxifene  (ISO)
SB 431542  (ISO)
serpentine asbestos  (ISO)
silicon dioxide  (ISO)
sodium arsenate  (ISO)
Soman  (EXP)
sulforaphane  (ISO)
tamoxifen  (ISO)
tert-butyl hydroperoxide  (ISO)
tetrachloromethane  (EXP,ISO)
thioacetamide  (EXP)
titanium dioxide  (ISO)
topotecan  (EXP)
trichostatin A  (ISO)
triclosan  (ISO)
trimellitic anhydride  (ISO)
triptonide  (ISO)
urethane  (ISO)
valproic acid  (ISO)
zinc atom  (ISO)
zinc(0)  (ISO)

Gene Ontology Annotations     Click to see Annotation Detail View

Biological Process

Cellular Component

Molecular Function

References

Additional References at PubMed
PMID:8889548   PMID:10971586   PMID:12880386   PMID:16492977   PMID:18757743   PMID:20057335   PMID:21069352   PMID:21254358   PMID:21856246   PMID:23038739   PMID:23533145  


Genomics

Comparative Map Data
Crispld2
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
mRatBN7.21948,053,153 - 48,111,485 (+)NCBI
Rnor_6.0 Ensembl1952,647,070 - 52,705,131 (+)EnsemblRnor6.0rn6Rnor6.0
Rnor_6.01952,647,038 - 52,705,118 (+)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_5.01963,394,645 - 63,452,571 (+)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.41950,313,710 - 50,378,031 (+)NCBIRGSC3.4rn4RGSC3.4
RGSC_v3.11950,287,944 - 50,381,888 (+)NCBI
Celera1947,326,756 - 47,367,597 (+)NCBICelera
Cytogenetic Map19q12NCBI
CRISPLD2
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38.p13 Ensembl1684,819,985 - 84,920,768 (+)EnsemblGRCh38hg38GRCh38
GRCh381684,819,981 - 84,909,510 (+)NCBIGRCh38GRCh38hg38GRCh38
GRCh371684,853,591 - 84,943,114 (+)NCBIGRCh37GRCh37hg19GRCh37
Build 361683,411,113 - 83,500,615 (+)NCBINCBI36hg18NCBI36
Celera1669,155,851 - 69,245,341 (+)NCBI
Cytogenetic Map16q24.1NCBI
HuRef1670,606,440 - 70,695,722 (+)NCBIHuRef
CHM1_11686,265,158 - 86,354,661 (+)NCBICHM1_1
Crispld2
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm398120,719,177 - 120,779,533 (+)NCBIGRCm39mm39
GRCm39 Ensembl8120,719,177 - 120,779,532 (+)Ensembl
GRCm388119,992,438 - 120,052,794 (+)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl8119,992,438 - 120,052,793 (+)EnsemblGRCm38mm10GRCm38
MGSCv378122,516,370 - 122,576,693 (+)NCBIGRCm37mm9NCBIm37
MGSCv368122,878,453 - 122,937,551 (+)NCBImm8
Celera8124,213,551 - 124,273,013 (+)NCBICelera
Cytogenetic Map8E1NCBI
Crispld2
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_004955541336,558 - 367,817 (+)EnsemblChiLan1.0
ChiLan1.0NW_004955541324,623 - 369,690 (+)NCBIChiLan1.0ChiLan1.0
CRISPLD2
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
PanPan1.11684,828,816 - 84,916,183 (+)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl1684,828,816 - 84,916,183 (+)Ensemblpanpan1.1panPan2
Mhudiblu_PPA_v01665,488,965 - 65,578,502 (+)NCBIMhudiblu_PPA_v0panPan3
CRISPLD2
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.1567,643,225 - 67,707,438 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl567,645,179 - 67,692,122 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha567,657,270 - 67,722,081 (-)NCBI
ROS_Cfam_1.0567,875,237 - 67,940,166 (-)NCBI
UMICH_Zoey_3.1567,891,163 - 67,955,381 (-)NCBI
UNSW_CanFamBas_1.0567,725,561 - 67,790,266 (-)NCBI
UU_Cfam_GSD_1.0568,140,460 - 68,205,242 (-)NCBI
Crispld2
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440934927,475,244 - 27,523,841 (-)NCBI
SpeTri2.0NW_0049366413,228,791 - 3,277,379 (-)NCBISpeTri2.0SpeTri2.0SpeTri2.0
CRISPLD2
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl63,881,725 - 3,944,580 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.163,881,715 - 3,944,592 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.264,412,912 - 4,458,663 (+)NCBISscrofa10.2Sscrofa10.2susScr3
CRISPLD2
(Chlorocebus sabaeus - African green monkey)
Vervet AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1570,225,791 - 70,314,763 (+)NCBI
ChlSab1.1 Ensembl570,225,883 - 70,314,974 (+)Ensembl
Crispld2
(Heterocephalus glaber - naked mole-rat)
Molerat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_0046247461,648,753 - 1,691,722 (+)NCBI


QTLs in Region (Rnor_6.0)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
724566Uae12Urinary albumin excretion QTL 125urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19243296362275575Rat
1331737Uae29Urinary albumin excretion QTL 295.5urine albumin amount (VT:0002871)urine albumin level (CMO:0000130)19650676160220581Rat
1578764Stresp19Stress response QTL 193.60.001blood renin amount (VT:0003349)plasma renin activity level (CMO:0000116)191899398262275575Rat
7411549Bw130Body weight QTL 13050.001body mass (VT:0001259)body weight gain (CMO:0000420)191917749562275575Rat
2298478Eau8Experimental allergic uveoretinitis QTL 80.0163uvea integrity trait (VT:0010551)experimental autoimmune uveitis score (CMO:0001504)192140778762275575Rat
61350Bp32Blood pressure QTL 320.012arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)192481825762275575Rat
724546Kidm3Kidney mass QTL 33.1kidney mass (VT:0002707)calculated kidney weight (CMO:0000160)193299439262275575Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum insulin level (CMO:0000358)193791679960220451Rat
1358200Insglur2Insulin/glucose ratio QTL 24.1blood glucose amount (VT:0000188)serum glucose level (CMO:0000543)193791679960220451Rat
5135224Leukc1Leukocyte quantity QTL 1eosinophil quantity (VT:0002602)blood eosinophil count (CMO:0000033)194883071260220581Rat

miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:627
Count of miRNA genes:291
Interacting mature miRNAs:371
Transcripts:ENSRNOT00000068389
Prediction methods:Microtar, 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 2 31 2 2 2 2 1 4 4 24 34 11 1
Low 1 12 47 31 17 31 7 7 70 11 7 7
Below cutoff 8 8 8

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000068389   ⟹   ENSRNOP00000059225
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1952,647,070 - 52,705,131 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000082754   ⟹   ENSRNOP00000070831
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1952,664,322 - 52,676,842 (+)Ensembl
RefSeq Acc Id: ENSRNOT00000087857   ⟹   ENSRNOP00000069254
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
Rnor_6.0 Ensembl1952,647,143 - 52,704,098 (+)Ensembl
RefSeq Acc Id: NM_138518   ⟹   NP_612527
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21948,070,339 - 48,111,485 (+)NCBI
Rnor_6.01952,664,073 - 52,705,118 (+)NCBI
Rnor_5.01963,394,645 - 63,452,571 (+)NCBI
RGSC_v3.41950,313,710 - 50,378,031 (+)RGD
Celera1947,326,756 - 47,367,597 (+)RGD
Sequence:
RefSeq Acc Id: XM_006255708   ⟹   XP_006255770
RefSeq Status:
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.21948,053,153 - 48,111,485 (+)NCBI
Rnor_6.01952,647,038 - 52,705,118 (+)NCBI
Rnor_5.01963,394,645 - 63,452,571 (+)NCBI
Sequence:
Protein Sequences
Protein RefSeqs NP_612527 (Get FASTA)   NCBI Sequence Viewer  
  XP_006255770 (Get FASTA)   NCBI Sequence Viewer  
GenBank Protein AAD16986 (Get FASTA)   NCBI Sequence Viewer  
  AAK55115 (Get FASTA)   NCBI Sequence Viewer  
  EDL92691 (Get FASTA)   NCBI Sequence Viewer  
  EDL92692 (Get FASTA)   NCBI Sequence Viewer  
Reference Sequences
RefSeq Acc Id: NP_612527   ⟸   NM_138518
- Peptide Label: precursor
- UniProtKB: G3V9T1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006255770   ⟸   XM_006255708
- Peptide Label: isoform X1
- UniProtKB: G3V9T1 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000070831   ⟸   ENSRNOT00000082754
RefSeq Acc Id: ENSRNOP00000069254   ⟸   ENSRNOT00000087857
RefSeq Acc Id: ENSRNOP00000059225   ⟸   ENSRNOT00000068389
Protein Domains
LCCL   SCP

Transcriptome

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

Promoters
RGD ID:13701189
Promoter ID:EPDNEW_R11710
Type:initiation region
Name:Crispld2_1
Description:cysteine-rich secretory protein LCCL domain containing 2
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_6.01952,647,072 - 52,647,132EPDNEW

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)
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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

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:620860 AgrOrtholog
Ensembl Genes ENSRNOG00000016752 Ensembl, ENTREZGENE, UniProtKB/TrEMBL
Ensembl Protein ENSRNOP00000059225 ENTREZGENE, UniProtKB/TrEMBL
  ENSRNOP00000069254 UniProtKB/TrEMBL
  ENSRNOP00000070831 UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000068389 UniProtKB/TrEMBL
  ENSRNOT00000082754 UniProtKB/TrEMBL
  ENSRNOT00000087857 UniProtKB/TrEMBL
Gene3D-CATH 2.170.130.20 UniProtKB/TrEMBL
  3.40.33.10 UniProtKB/TrEMBL
InterPro Allrgn_V5/Tpx1 UniProtKB/TrEMBL
  Allrgn_V5/Tpx1_CS UniProtKB/TrEMBL
  CAP_domain UniProtKB/TrEMBL
  CAP_sf UniProtKB/TrEMBL
  LCCL UniProtKB/TrEMBL
  LCCL_sf UniProtKB/TrEMBL
  V5_allergen UniProtKB/TrEMBL
KEGG Report rno:171547 UniProtKB/TrEMBL
NCBI Gene 171547 ENTREZGENE
PANTHER Allrgn_V5/Tpx1 UniProtKB/TrEMBL
Pfam CAP UniProtKB/TrEMBL
  LCCL UniProtKB/TrEMBL
PhenoGen Crispld2 PhenoGen
PRINTS V5ALLERGEN UniProtKB/TrEMBL
  V5TPXLIKE UniProtKB/TrEMBL
PROSITE CRISP_2 UniProtKB/TrEMBL
  LCCL UniProtKB/TrEMBL
SMART LCCL UniProtKB/TrEMBL
  SCP UniProtKB/TrEMBL
Superfamily-SCOP LCCL UniProtKB/TrEMBL
  SCP-like_extracellular UniProtKB/TrEMBL
UniProt A0A0G2JYX8_RAT UniProtKB/TrEMBL
  G3V9T1 ENTREZGENE, UniProtKB/TrEMBL
  Q9Z0U6_RAT UniProtKB/TrEMBL


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2005-11-17 Crispld2  cysteine-rich secretory protein LCCL domain containing 2      Symbol and Name updated 1299863 APPROVED
2005-01-20 Lgl1  late gestation lung protein 1      Symbol and Name status set to approved 1299863 APPROVED
2002-08-07 Lgl1  late gestation lung protein 1      Symbol and Name status set to provisional 70820 PROVISIONAL

RGD Curation Notes
Note Type Note Reference
gene_expression expressed in mesenchyme of fetal lungkidneyand intestine 633294
gene_product member of the CRISP family of cysteine-rich extracellular proteins 633294