Lca5 (lebercilin LCA5) - Rat Genome Database

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Gene: Lca5 (lebercilin LCA5) Rattus norvegicus
Analyze
Symbol: Lca5
Name: lebercilin LCA5
RGD ID: 1308555
Description: Predicted to be involved in intraciliary transport. Predicted to act upstream of or within photoreceptor cell maintenance. Located in ciliary basal body and photoreceptor connecting cilium. Human ortholog(s) of this gene implicated in Leber congenital amaurosis 5. Orthologous to human LCA5 (lebercilin LCA5); INTERACTS WITH 1-naphthyl isothiocyanate; 2,3,7,8-tetrachlorodibenzodioxine; aflatoxin B1.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LCA5, lebercilin; Leber congenital amaurosis 5; Leber congenital amaurosis 5 (human); leber congenital amaurosis 5 protein homolog; Lebercilin; LOC300866; RGD1308555; similar to RIKEN cDNA 4930431B11 gene
RGD Orthologs
Human
Mouse
Chinchilla
Bonobo
Dog
Squirrel
Pig
Green Monkey
Naked Mole-Rat
Alliance Genes
More Info more info ...
Latest Assembly: mRatBN7.2 - mRatBN7.2 Assembly
Position:
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8893,187,735 - 93,255,060 (-)NCBIGRCr8
mRatBN7.2884,307,696 - 84,375,025 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl884,317,659 - 84,374,956 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx889,929,315 - 89,986,500 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0888,151,561 - 88,208,851 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0886,020,981 - 86,078,357 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0890,926,309 - 90,984,271 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl890,926,311 - 90,984,224 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0890,435,348 - 90,503,675 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4888,464,748 - 88,522,568 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1888,484,204 - 88,542,023 (-)NCBI
Celera883,973,822 - 84,031,009 (-)NCBICelera
Cytogenetic Map8q31NCBI
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
axoneme  (IBA,IEA,ISO)
ciliary basal body  (IDA,ISO)
cilium  (ISO,ISS)
neuron projection  (ISO)
photoreceptor connecting cilium  (IDA,ISO)

Molecular Function

References

References - curated
# Reference Title Reference Citation
1. Mutations in LCA5, encoding the ciliary protein lebercilin, cause Leber congenital amaurosis. den Hollander AI, etal., Nat Genet. 2007 Jul;39(7):889-95. doi: 10.1038/ng2066. Epub 2007 Jun 3.
2. Phylogenetic-based propagation of functional annotations within the Gene Ontology consortium. Gaudet P, etal., Brief Bioinform. 2011 Sep;12(5):449-62. doi: 10.1093/bib/bbr042. Epub 2011 Aug 27.
3. OMIM Disease Annotation Pipeline OMIM Disease Annotation Pipeline
4. ClinVar Automated Import and Annotation Pipeline RGD automated import pipeline for ClinVar variants, variant-to-disease annotations and gene-to-disease annotations
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
6. Generation and initial analysis of more than 15,000 full-length human and mouse cDNA sequences. Strausberg RL, etal., Proc Natl Acad Sci U S A. 2002 Dec 24;99(26):16899-903. Epub 2002 Dec 11.
Additional References at PubMed
PMID:15489334   PMID:19800048   PMID:21606596   PMID:24833722  


Genomics

Comparative Map Data
Lca5
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr8893,187,735 - 93,255,060 (-)NCBIGRCr8
mRatBN7.2884,307,696 - 84,375,025 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl884,317,659 - 84,374,956 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx889,929,315 - 89,986,500 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.0888,151,561 - 88,208,851 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.0886,020,981 - 86,078,357 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.0890,926,309 - 90,984,271 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl890,926,311 - 90,984,224 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.0890,435,348 - 90,503,675 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.4888,464,748 - 88,522,568 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.1888,484,204 - 88,542,023 (-)NCBI
Celera883,973,822 - 84,031,009 (-)NCBICelera
Cytogenetic Map8q31NCBI
LCA5
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38679,484,991 - 79,538,782 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl679,484,991 - 79,537,458 (-)EnsemblGRCh38hg38GRCh38
GRCh37680,194,708 - 80,247,147 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36680,251,427 - 80,303,866 (-)NCBINCBI36Build 36hg18NCBI36
Celera680,609,792 - 80,662,233 (-)NCBICelera
Cytogenetic Map6q14.1NCBI
HuRef677,415,318 - 77,467,734 (-)NCBIHuRef
CHM1_1680,292,226 - 80,344,664 (-)NCBICHM1_1
T2T-CHM13v2.0680,690,503 - 80,744,277 (-)NCBIT2T-CHM13v2.0
Lca5
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm39983,273,408 - 83,325,047 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl983,272,346 - 83,323,180 (-)EnsemblGRCm39 Ensembl
GRCm38983,391,355 - 83,442,994 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl983,390,293 - 83,441,127 (-)EnsemblGRCm38mm10GRCm38
MGSCv37983,284,962 - 83,334,734 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv36983,188,073 - 83,237,816 (-)NCBIMGSCv36mm8
Celera980,483,800 - 80,533,764 (-)NCBICelera
Cytogenetic Map9E2NCBI
cM Map945.42NCBI
Lca5
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_0049555027,325,103 - 7,376,368 (-)EnsemblChiLan1.0
ChiLan1.0NW_0049555027,325,650 - 7,373,641 (-)NCBIChiLan1.0ChiLan1.0
LCA5
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2599,570,353 - 99,622,886 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1697,449,680 - 97,502,161 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0677,366,248 - 77,418,718 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1680,636,181 - 80,688,609 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl680,636,181 - 80,688,609 (-)Ensemblpanpan1.1panPan2
LCA5
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.11240,443,759 - 40,527,300 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl1240,444,617 - 40,527,292 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha1240,316,651 - 40,400,202 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.01241,206,528 - 41,290,540 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl1241,206,511 - 41,259,652 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.11240,528,023 - 40,611,593 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.01240,503,437 - 40,587,080 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.01240,645,882 - 40,729,470 (-)NCBIUU_Cfam_GSD_1.0
Lca5
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_02440494675,767,861 - 75,828,214 (-)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_00493651010,671,297 - 10,703,618 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_00493651010,652,378 - 10,702,761 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LCA5
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl186,597,283 - 86,685,068 (+)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.1186,596,967 - 86,685,073 (+)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.2197,295,188 - 97,383,456 (+)NCBISscrofa10.2Sscrofa10.2susScr3
LCA5
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1134,197,522 - 4,230,274 (-)NCBIChlSab1.1ChlSab1.1chlSab2
ChlSab1.1 Ensembl134,197,371 - 4,248,854 (-)EnsemblChlSab1.1ChlSab1.1 EnsemblchlSab2
Vero_WHO_p1.0NW_023666040180,411,968 - 180,464,589 (-)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lca5
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla_female_1.0 EnsemblNW_0046248196,141,740 - 6,199,624 (-)EnsemblHetGla_female_1.0HetGla_female_1.0 EnsemblhetGla2
HetGla 1.0NW_0046248196,143,586 - 6,199,436 (-)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lca5
322 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:284
Count of miRNA genes:171
Interacting mature miRNAs:184
Transcripts:ENSRNOT00000044931
Prediction methods:Microtar, Miranda, Rnahybrid
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1581557Eae16Experimental allergic encephalomyelitis QTL 163.8nervous system integrity trait (VT:0010566)experimental autoimmune encephalomyelitis incidence/prevalence measurement (CMO:0001046)88462195110921472Rat
631650Stl6Serum triglyceride level QTL 640.0019blood triglyceride amount (VT:0002644)plasma triglyceride level (CMO:0000548)810378157112202585Rat
631271Lecl1Lens clarity QTL 10.001lens clarity trait (VT:0001304)age of onset/diagnosis of cataract (CMO:0001584)81898416884531599Rat
731182Uae24Urinary albumin excretion QTL 246.4urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)81933115293965294Rat
1358892Kidm26Kidney mass QTL 263.69kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)82720571599103503Rat
1358896Bp262Blood pressure QTL 2622.89arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)82720571599103503Rat
1358907Cm40Cardiac mass QTL 401.89heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)82720571599103503Rat
8662823Vetf5Vascular elastic tissue fragility QTL 51.9artery integrity trait (VT:0010639)patent ductus arteriosus score (CMO:0002566)82824291299525068Rat
1549908Neudeg1Neurodegradation QTL 15.50nervous system integrity trait (VT:0010566)logarithm of the ratio of the lesioned side motor neuron count to contralateral side motor neuron count (CMO:0001986)83018886794457446Rat
1578755Pur5Proteinuria QTL 53.30.0001urine total protein amount (VT:0000032)urine total protein excretion rate (CMO:0000756)830848154101699754Rat
1578765Klgr1Kidney lesion grade QTL 13.30.0001kidney morphology trait (VT:0002135)organ lesion measurement (CMO:0000677)830848154101699754Rat
1578769Uae31Urinary albumin excretion QTL 313.30.001urine albumin amount (VT:0002871)urine albumin excretion rate (CMO:0000757)830848154101699754Rat
2316950Scl66Serum cholesterol level QTL 664.1blood cholesterol amount (VT:0000180)plasma total cholesterol level (CMO:0000585)830848259105647037Rat
1331838Niddm61Non-insulin dependent diabetes mellitus QTL 613.530.0004blood insulin amount (VT:0001560)plasma insulin level (CMO:0000342)83646953599083736Rat
1358906Bp253Blood pressure QTL 25340.0004arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)84071306693965294Rat
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
1298079Activ2Activity QTL 29.50.000001voluntary movement trait (VT:0003491)rearing measurement (CMO:0001515)84186687686866876Rat
70161Bp62Blood pressure QTL 622.90.001arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)84269268490165460Rat
12879882Am8Aortic mass QTL 80.001aorta mass (VT:0002845)aorta weight to aorta length to body weight ratio (CMO:0002722)84329616998968765Rat
12879878Bw183Body weight QTL 1830.001body mass (VT:0001259)body weight (CMO:0000012)84329616998968765Rat
12879879Cm99Cardiac mass QTL 990.001heart mass (VT:0007028)heart weight to body weight ratio (CMO:0000074)84329616998968765Rat
12879880Cm100Cardiac mass QTL 1000.001heart left ventricle mass (VT:0007031)heart left ventricle weight to body weight ratio (CMO:0000530)84329616998968765Rat
12879881Cm101Cardiac mass QTL 1010.001heart right ventricle mass (VT:0007033)heart right ventricle weight to body weight ratio (CMO:0000914)84329616998968765Rat
12879883Kidm65Kidney mass QTL 650.001kidney mass (VT:0002707)both kidneys wet weight to body weight ratio (CMO:0000340)84329616998968765Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)pulse pressure (CMO:0000292)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)absolute change in systolic blood pressure (CMO:0000607)846531639119088626Rat
70197BpQTLcluster8Blood pressure QTL cluster 83.482arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)846531639119088626Rat
1331837Bw23Body weight QTL 234.190.00007body mass (VT:0001259)body weight (CMO:0000012)84653172299083736Rat
2303570Gluco48Glucose level QTL 482blood glucose amount (VT:0000188)blood glucose level (CMO:0000046)84980583194805831Rat
1358912Bw51Body weight QTL 512.95body mass (VT:0001259)body weight (CMO:0000012)851351728107062046Rat
10402857Bp380Blood pressure QTL 3800.95arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2301402Bp316Blood pressure QTL 3160.005arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)85396876598968765Rat
2293697Bmd39Bone mineral density QTL 39femur strength trait (VT:0010010)femur total energy absorbed before break (CMO:0001677)85404374498968765Rat
1582243Bw66Body weight QTL 663.40.0048body mass (VT:0001259)body weight (CMO:0000012)85423764485365202Rat
1582254Kidm31Kidney mass QTL 313kidney mass (VT:0002707)both kidneys wet weight (CMO:0000085)85423764485365202Rat
631664Hcar3Hepatocarcinoma resistance QTL 32.90.0005liver integrity trait (VT:0010547)volume of individual liver tumorous lesion (CMO:0001078)85423764499103503Rat
1300177Cm2Cardiac mass QTL 23.65heart mass (VT:0007028)heart weight (CMO:0000017)854259986100382532Rat
2303171Bp331Blood pressure QTL 3315.570.005arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)861290298119084929Rat
631653Bp125Blood pressure QTL 1253.3arterial blood pressure trait (VT:2000000)systolic blood pressure (CMO:0000004)866142385111142385Rat
631210Bw3Body weight QTL35.9mesenteric fat pad mass (VT:0010427)mesenteric fat pad weight to body weight ratio (CMO:0000654)869349194112783834Rat
1300171Bp184Blood pressure QTL 1843.66arterial blood pressure trait (VT:2000000)blood pressure time series experimental set point of the baroreceptor response (CMO:0002593)870513503118219066Rat
8694446Bw170Body weight QTL 17012.070.001retroperitoneal fat pad mass (VT:0010430)retroperitoneal fat pad weight to body weight ratio (CMO:0000635)871888757116888757Rat
9590292Uminl3Urine mineral level QTL 33.620.001urine mineral amount (VT:0015086)urine electrolyte level (CMO:0000593)871888757116888757Rat
8694200Abfw4Abdominal fat weight QTL 49.070.001visceral adipose mass (VT:0010063)abdominal fat pad weight to body weight ratio (CMO:0000095)871888757116888757Rat
8694392Bw161Body weight QTL 1618.060.001body lean mass (VT:0010483)lean tissue morphological measurement (CMO:0002184)871888757116888757Rat
1549909Stresp11Stress response QTL 116.830.0019stress-related behavior trait (VT:0010451)number of approaches toward negative stimulus before onset of defensive burying response (CMO:0001960)873473045118473045Rat
10450865Bw175Body weight QTL 1754.1total fat pad mass (VT:0015008)adipose tissue molecular composition measurement (CMO:0000484)87531177784531599Rat
2300181Bmd55Bone mineral density QTL 555.70.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)876468691121468691Rat
61437Cia6Collagen induced arthritis QTL 6joint integrity trait (VT:0010548)joint inflammation composite score (CMO:0000919)882460758122812818Rat

Markers in Region
BE115256  
Rat AssemblyChrPosition (strand)SourceJBrowse
mRatBN7.2884,318,940 - 84,319,090 (+)MAPPERmRatBN7.2
Rnor_6.0890,927,593 - 90,927,742NCBIRnor6.0
Rnor_5.0890,446,838 - 90,446,987UniSTSRnor5.0
RGSC_v3.4888,466,032 - 88,466,181UniSTSRGSC3.4
Celera883,975,106 - 83,975,255UniSTS
RH 3.4 Map8976.2UniSTS
Cytogenetic Map8q31UniSTS


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 7
Low 3 27 23 15 19 15 1 1 70 35 34 11 1
Below cutoff 16 34 26 26 7 9 7

Sequence

Nucleotide Sequences
RefSeq Transcripts NM_001393917 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  NR_172050 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766249 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766251 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766252 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766253 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766255 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766256 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766257 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766258 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_008766259 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_017595575 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081163 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081164 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_039081165 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063265188 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063265189 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063265191 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XM_063265192 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005487787 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_005487788 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  XR_010053951 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
GenBank Nucleotide BC083657 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  BC085805 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  CH473954 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles
  JAXUCZ010000008 (Get FASTA)   NCBI Sequence Viewer   Search GEO for Microarray Profiles

Reference Sequences
RefSeq Acc Id: ENSRNOT00000044931   ⟹   ENSRNOP00000046841
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl884,317,659 - 84,374,956 (-)Ensembl
Rnor_6.0 Ensembl890,926,311 - 90,984,224 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000086426   ⟹   ENSRNOP00000074416
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl884,319,294 - 84,374,956 (-)Ensembl
Rnor_6.0 Ensembl890,926,311 - 90,962,470 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000090139   ⟹   ENSRNOP00000075180
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl884,320,911 - 84,366,310 (-)Ensembl
Rnor_6.0 Ensembl890,927,156 - 90,975,599 (-)Ensembl
RefSeq Acc Id: NM_001393917   ⟹   NP_001380846
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,200,950 - 93,246,414 (-)NCBI
mRatBN7.2884,320,907 - 84,366,373 (-)NCBI
RefSeq Acc Id: NR_172050
RefSeq Status: VALIDATED
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,197,700 - 93,254,991 (-)NCBI
mRatBN7.2884,317,657 - 84,374,956 (-)NCBI
RefSeq Acc Id: XM_008766249   ⟹   XP_008764471
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,200,950 - 93,246,360 (-)NCBI
mRatBN7.2884,320,907 - 84,366,310 (-)NCBI
Rnor_6.0890,929,553 - 90,975,534 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766251   ⟹   XP_008764473
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,200,950 - 93,255,060 (-)NCBI
mRatBN7.2884,320,907 - 84,375,025 (-)NCBI
Rnor_6.0890,929,553 - 90,984,271 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766252   ⟹   XP_008764474
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,200,950 - 93,246,367 (-)NCBI
mRatBN7.2884,320,907 - 84,366,227 (-)NCBI
Rnor_6.0890,929,553 - 90,975,451 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766255   ⟹   XP_008764477
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,200,950 - 93,255,038 (-)NCBI
mRatBN7.2884,320,907 - 84,374,985 (-)NCBI
Rnor_6.0890,929,553 - 90,984,271 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766256   ⟹   XP_008764478
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,200,950 - 93,246,412 (-)NCBI
mRatBN7.2884,320,907 - 84,366,371 (-)NCBI
Rnor_6.0890,929,553 - 90,975,619 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766257   ⟹   XP_008764479
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,200,950 - 93,235,025 (-)NCBI
mRatBN7.2884,320,907 - 84,362,303 (-)NCBI
Rnor_6.0890,929,553 - 90,964,584 (-)NCBI
Sequence:
RefSeq Acc Id: XM_008766258   ⟹   XP_008764480
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,200,950 - 93,245,516 (-)NCBI
mRatBN7.2884,320,907 - 84,366,054 (-)NCBI
Rnor_6.0890,929,553 - 90,972,767 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039081163   ⟹   XP_038937091
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,198,925 - 93,255,060 (-)NCBI
mRatBN7.2884,318,882 - 84,375,025 (-)NCBI
RefSeq Acc Id: XM_039081164   ⟹   XP_038937092
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,198,925 - 93,255,060 (-)NCBI
mRatBN7.2884,318,882 - 84,375,025 (-)NCBI
RefSeq Acc Id: XM_039081165   ⟹   XP_038937093
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,198,925 - 93,255,060 (-)NCBI
mRatBN7.2884,318,882 - 84,375,025 (-)NCBI
RefSeq Acc Id: XM_063265188   ⟹   XP_063121258
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,198,925 - 93,246,360 (-)NCBI
RefSeq Acc Id: XM_063265189   ⟹   XP_063121259
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,198,925 - 93,235,025 (-)NCBI
RefSeq Acc Id: XM_063265191   ⟹   XP_063121261
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,198,925 - 93,246,429 (-)NCBI
RefSeq Acc Id: XM_063265192   ⟹   XP_063121262
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,198,925 - 93,246,411 (-)NCBI
RefSeq Acc Id: XR_005487787
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,187,735 - 93,255,060 (-)NCBI
mRatBN7.2884,307,696 - 84,375,025 (-)NCBI
RefSeq Acc Id: XR_005487788
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,197,700 - 93,255,060 (-)NCBI
mRatBN7.2884,317,657 - 84,375,025 (-)NCBI
RefSeq Acc Id: XR_010053951
Type: NON-CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr8893,187,735 - 93,255,060 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: XP_008764473   ⟸   XM_008766251
- Peptide Label: isoform X1
- UniProtKB: Q5XIM2 (UniProtKB/Swiss-Prot),   Q5U2Y9 (UniProtKB/Swiss-Prot),   A6I1R3 (UniProtKB/TrEMBL),   A0A8L2RA12 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008764477   ⟸   XM_008766255
- Peptide Label: isoform X1
- UniProtKB: Q5XIM2 (UniProtKB/Swiss-Prot),   Q5U2Y9 (UniProtKB/Swiss-Prot),   A6I1R3 (UniProtKB/TrEMBL),   A0A8L2RA12 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008764478   ⟸   XM_008766256
- Peptide Label: isoform X1
- UniProtKB: Q5XIM2 (UniProtKB/Swiss-Prot),   Q5U2Y9 (UniProtKB/Swiss-Prot),   A6I1R3 (UniProtKB/TrEMBL),   A0A8L2RA12 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008764471   ⟸   XM_008766249
- Peptide Label: isoform X1
- UniProtKB: Q5XIM2 (UniProtKB/Swiss-Prot),   Q5U2Y9 (UniProtKB/Swiss-Prot),   A6I1R3 (UniProtKB/TrEMBL),   A0A8L2RA12 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008764474   ⟸   XM_008766252
- Peptide Label: isoform X1
- UniProtKB: Q5XIM2 (UniProtKB/Swiss-Prot),   Q5U2Y9 (UniProtKB/Swiss-Prot),   A6I1R3 (UniProtKB/TrEMBL),   A0A8L2RA12 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008764480   ⟸   XM_008766258
- Peptide Label: isoform X1
- UniProtKB: Q5XIM2 (UniProtKB/Swiss-Prot),   Q5U2Y9 (UniProtKB/Swiss-Prot),   A6I1R3 (UniProtKB/TrEMBL),   A0A8L2RA12 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_008764479   ⟸   XM_008766257
- Peptide Label: isoform X1
- UniProtKB: Q5XIM2 (UniProtKB/Swiss-Prot),   Q5U2Y9 (UniProtKB/Swiss-Prot),   A6I1R3 (UniProtKB/TrEMBL),   A0A8L2RA12 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000075180   ⟸   ENSRNOT00000090139
RefSeq Acc Id: ENSRNOP00000046841   ⟸   ENSRNOT00000044931
RefSeq Acc Id: ENSRNOP00000074416   ⟸   ENSRNOT00000086426
RefSeq Acc Id: XP_038937093   ⟸   XM_039081165
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K802 (UniProtKB/TrEMBL),   A6I1R1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038937091   ⟸   XM_039081163
- Peptide Label: isoform X1
- UniProtKB: Q5U2Y9 (UniProtKB/Swiss-Prot),   Q5XIM2 (UniProtKB/Swiss-Prot),   A6I1R3 (UniProtKB/TrEMBL),   A0A8L2RA12 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_038937092   ⟸   XM_039081164
- Peptide Label: isoform X1
- UniProtKB: Q5U2Y9 (UniProtKB/Swiss-Prot),   Q5XIM2 (UniProtKB/Swiss-Prot),   A6I1R3 (UniProtKB/TrEMBL),   A0A8L2RA12 (UniProtKB/TrEMBL)
RefSeq Acc Id: NP_001380846   ⟸   NM_001393917
- UniProtKB: Q5U2Y9 (UniProtKB/Swiss-Prot),   Q5XIM2 (UniProtKB/Swiss-Prot),   A6I1R3 (UniProtKB/TrEMBL),   A0A8L2RA12 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063121261   ⟸   XM_063265191
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K802 (UniProtKB/TrEMBL),   A6I1R1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063121262   ⟸   XM_063265192
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K802 (UniProtKB/TrEMBL),   A6I1R1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063121258   ⟸   XM_063265188
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K802 (UniProtKB/TrEMBL),   A6I1R1 (UniProtKB/TrEMBL)
RefSeq Acc Id: XP_063121259   ⟸   XM_063265189
- Peptide Label: isoform X2
- UniProtKB: A0A0G2K802 (UniProtKB/TrEMBL),   A6I1R1 (UniProtKB/TrEMBL)
Protein Domains
Lebercilin

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-Q5U2Y9-F1-model_v2 AlphaFold Q5U2Y9 1-727 view protein structure

Transcriptome

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

Promoters
RGD ID:13696158
Promoter ID:EPDNEW_R6677
Type:multiple initiation site
Name:Lca5_1
Description:LCA5, lebercilin
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_6.0890,975,602 - 90,975,662EPDNEW

Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308555 AgrOrtholog
BioCyc Gene G2FUF-29692 BioCyc
Ensembl Genes ENSRNOG00000009580 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000044931 ENTREZGENE
  ENSRNOT00000044931.5 UniProtKB/Swiss-Prot
  ENSRNOT00000086426 ENTREZGENE
  ENSRNOT00000086426.2 UniProtKB/TrEMBL
  ENSRNOT00000090139.2 UniProtKB/TrEMBL
IMAGE_CLONE IMAGE:7112021 IMAGE-MGC_LOAD
InterPro Lebercilin-like UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lebercilin_dom UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:300866 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
MGC_CLONE MGC:93865 IMAGE-MGC_LOAD
NCBI Gene 300866 ENTREZGENE
PANTHER PTHR16650 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR16650:SF10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Lebercilin UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lca5 PhenoGen
RatGTEx ENSRNOG00000009580 RatGTEx
UniProt A0A0G2K802 ENTREZGENE, UniProtKB/TrEMBL
  A0A8L2RA12 ENTREZGENE, UniProtKB/TrEMBL
  A6I1R1 ENTREZGENE, UniProtKB/TrEMBL
  A6I1R3 ENTREZGENE, UniProtKB/TrEMBL
  LCA5_RAT UniProtKB/Swiss-Prot, ENTREZGENE
  Q5XIM2 ENTREZGENE
UniProt Secondary Q5XIM2 UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2019-04-10 Lca5  lebercilin LCA5  Lca5  LCA5, lebercilin  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2016-06-01 Lca5  LCA5, lebercilin  Lca5  Leber congenital amaurosis 5  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2012-01-17 Lca5  Leber congenital amaurosis 5  Lca5  Leber congenital amaurosis 5 (human)  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2008-02-26 Lca5  Leber congenital amaurosis 5 (human)  RGD1308555  similar to RIKEN cDNA 4930431B11 gene  Nomenclature updated to reflect human and mouse nomenclature 1299863 APPROVED
2005-12-06 RGD1308555  similar to RIKEN cDNA 4930431B11 gene  RGD1308555_predicted  similar to RIKEN cDNA 4930431B11 gene (predicted)  Symbol and Name updated 1559027 APPROVED
2005-01-20 RGD1308555_predicted  similar to RIKEN cDNA 4930431B11 gene (predicted)  LOC300866_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC300866_predicted  similar to RIKEN cDNA 4930431B11 gene (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL