Lyzl4 (lysozyme-like 4) - Rat Genome Database

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Gene: Lyzl4 (lysozyme-like 4) Rattus norvegicus
Analyze
Symbol: Lyzl4
Name: lysozyme-like 4
RGD ID: 1308401
Description: Predicted to enable lysozyme activity. Predicted to be involved in fusion of sperm to egg plasma membrane involved in single fertilization. Located in sperm flagellum. Orthologous to human LYZL4 (lysozyme like 4); INTERACTS WITH 6-propyl-2-thiouracil; bisphenol A; Cuprizon.
Type: protein-coding
RefSeq Status: VALIDATED
Previously known as: LOC363168; lysozyme a; lysozyme like-4; lysozyme-4; lysozyme-like protein 4; Lyza; RGD1308401; similar to RIKEN cDNA 1810009N24
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
GRCr88130,125,641 - 130,132,872 (-)NCBIGRCr8
mRatBN7.28121,248,129 - 121,255,366 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8121,248,168 - 121,255,353 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8126,846,758 - 126,854,016 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08125,045,821 - 125,053,079 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08122,875,529 - 122,882,782 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08130,219,984 - 130,228,066 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8130,220,018 - 130,224,444 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08129,406,646 - 129,414,058 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48126,588,240 - 126,592,666 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18126,607,941 - 126,621,696 (-)NCBI
Celera8120,383,010 - 120,387,460 (-)NCBICelera
Cytogenetic Map8q32NCBI
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
acrosomal vesicle  (IBA,IEA,ISO,ISS)
extracellular space  (ISO,ISS)
membrane  (IEA)
sperm flagellum  (IBA,IDA,IEA,ISO)

Molecular Function
lysozyme activity  (IDA,IEA)

References

References - curated
# Reference Title Reference Citation
1. 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.
2. Rat ISS GO annotations from MGI mouse gene data--August 2006 MGD data from the GO Consortium
3. Characterization of a novel lysozyme-like 4 gene in the rat. Narmadha G, etal., PLoS One. 2011;6(11):e27659. doi: 10.1371/journal.pone.0027659. Epub 2011 Nov 15.
4. GOA pipeline RGD automated data pipeline
5. Data Import for Chemical-Gene Interactions RGD automated import pipeline for gene-chemical interactions
Additional References at PubMed
PMID:21444326   PMID:21630459   PMID:27821286  


Genomics

Comparative Map Data
Lyzl4
(Rattus norvegicus - Norway rat)
Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCr88130,125,641 - 130,132,872 (-)NCBIGRCr8
mRatBN7.28121,248,129 - 121,255,366 (-)NCBImRatBN7.2mRatBN7.2
mRatBN7.2 Ensembl8121,248,168 - 121,255,353 (-)EnsemblmRatBN7.2 Ensembl
UTH_Rnor_SHR_Utx8126,846,758 - 126,854,016 (-)NCBIRnor_SHRUTH_Rnor_SHR_Utx
UTH_Rnor_SHRSP_BbbUtx_1.08125,045,821 - 125,053,079 (-)NCBIRnor_SHRSPUTH_Rnor_SHRSP_BbbUtx_1.0
UTH_Rnor_WKY_Bbb_1.08122,875,529 - 122,882,782 (-)NCBIRnor_WKYUTH_Rnor_WKY_Bbb_1.0
Rnor_6.08130,219,984 - 130,228,066 (-)NCBIRnor6.0Rnor_6.0rn6Rnor6.0
Rnor_6.0 Ensembl8130,220,018 - 130,224,444 (-)EnsemblRnor6.0rn6Rnor6.0
Rnor_5.08129,406,646 - 129,414,058 (-)NCBIRnor5.0Rnor_5.0rn5Rnor5.0
RGSC_v3.48126,588,240 - 126,592,666 (-)NCBIRGSC3.4RGSC_v3.4rn4RGSC3.4
RGSC_v3.18126,607,941 - 126,621,696 (-)NCBI
Celera8120,383,010 - 120,387,460 (-)NCBICelera
Cytogenetic Map8q32NCBI
LYZL4
(Homo sapiens - human)
Human AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCh38342,360,764 - 42,410,610 (-)NCBIGRCh38GRCh38hg38GRCh38
GRCh38.p14 Ensembl342,397,083 - 42,410,610 (-)EnsemblGRCh38hg38GRCh38
GRCh37342,438,575 - 42,452,102 (-)NCBIGRCh37GRCh37hg19GRCh37
Build 36342,413,579 - 42,427,069 (-)NCBINCBI36Build 36hg18NCBI36
Build 34342,413,578 - 42,427,069NCBI
Celera342,378,992 - 42,392,482 (-)NCBICelera
Cytogenetic Map3p22.1NCBI
HuRef342,482,777 - 42,496,267 (-)NCBIHuRef
CHM1_1342,389,883 - 42,403,363 (-)NCBICHM1_1
T2T-CHM13v2.0342,378,784 - 42,445,904 (-)NCBIT2T-CHM13v2.0
Lyzl4
(Mus musculus - house mouse)
Mouse AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
GRCm399121,406,907 - 121,471,187 (-)NCBIGRCm39GRCm39mm39
GRCm39 Ensembl9121,406,909 - 121,471,162 (-)EnsemblGRCm39 Ensembl
GRCm389121,577,841 - 121,642,121 (-)NCBIGRCm38GRCm38mm10GRCm38
GRCm38.p6 Ensembl9121,577,843 - 121,642,096 (-)EnsemblGRCm38mm10GRCm38
MGSCv379121,486,961 - 121,550,684 (-)NCBIGRCm37MGSCv37mm9NCBIm37
MGSCv369121,426,541 - 121,490,264 (-)NCBIMGSCv36mm8
Celera9122,047,977 - 122,114,890 (-)NCBICelera
Cytogenetic Map9F4NCBI
cM Map972.45NCBI
Lyzl4
(Chinchilla lanigera - long-tailed chinchilla)
Chinchilla AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChiLan1.0 EnsemblNW_00495542028,336,162 - 28,344,635 (+)EnsemblChiLan1.0
ChiLan1.0NW_00495542028,333,984 - 28,344,180 (+)NCBIChiLan1.0ChiLan1.0
LYZL4
(Pan paniscus - bonobo/pygmy chimpanzee)
Bonobo AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
NHGRI_mPanPan1-v2242,321,193 - 42,435,726 (-)NCBINHGRI_mPanPan1-v2
NHGRI_mPanPan1342,325,955 - 42,440,488 (-)NCBINHGRI_mPanPan1
Mhudiblu_PPA_v0342,302,237 - 42,378,700 (-)NCBIMhudiblu_PPA_v0Mhudiblu_PPA_v0panPan3
PanPan1.1342,565,535 - 42,579,033 (-)NCBIpanpan1.1PanPan1.1panPan2
PanPan1.1 Ensembl342,565,535 - 42,579,033 (-)Ensemblpanpan1.1panPan2
LYZL4
(Canis lupus familiaris - dog)
Dog AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
CanFam3.12311,526,560 - 11,540,724 (-)NCBICanFam3.1CanFam3.1canFam3CanFam3.1
CanFam3.1 Ensembl2311,526,697 - 11,540,554 (-)EnsemblCanFam3.1canFam3CanFam3.1
Dog10K_Boxer_Tasha2311,564,493 - 11,582,132 (-)NCBIDog10K_Boxer_Tasha
ROS_Cfam_1.02311,814,715 - 11,832,371 (-)NCBIROS_Cfam_1.0
ROS_Cfam_1.0 Ensembl2311,814,840 - 11,832,366 (-)EnsemblROS_Cfam_1.0 Ensembl
UMICH_Zoey_3.12311,616,455 - 11,634,094 (-)NCBIUMICH_Zoey_3.1
UNSW_CanFamBas_1.02311,758,878 - 11,776,523 (-)NCBIUNSW_CanFamBas_1.0
UU_Cfam_GSD_1.02311,763,105 - 11,780,752 (-)NCBIUU_Cfam_GSD_1.0
Lyzl4
(Ictidomys tridecemlineatus - thirteen-lined ground squirrel)
Squirrel AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HiC_Itri_2NW_024405118200,312,428 - 200,322,446 (+)NCBIHiC_Itri_2
SpeTri2.0 EnsemblNW_0049366952,668,444 - 2,674,605 (+)EnsemblSpeTri2.0SpeTri2.0 Ensembl
SpeTri2.0NW_0049366952,668,444 - 2,674,605 (+)NCBISpeTri2.0SpeTri2.0SpeTri2.0
LYZL4
(Sus scrofa - pig)
Pig AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
Sscrofa11.1 Ensembl1325,987,314 - 25,995,089 (-)EnsemblSscrofa11.1susScr11Sscrofa11.1
Sscrofa11.11325,987,662 - 25,992,607 (-)NCBISscrofa11.1Sscrofa11.1susScr11Sscrofa11.1
Sscrofa10.21328,656,765 - 28,664,020 (-)NCBISscrofa10.2Sscrofa10.2susScr3
LYZL4
(Chlorocebus sabaeus - green monkey)
Green Monkey AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
ChlSab1.1223,803,258 - 3,855,368 (-)NCBIChlSab1.1ChlSab1.1chlSab2
Vero_WHO_p1.0NW_023666041163,347,442 - 163,356,876 (+)NCBIVero_WHO_p1.0Vero_WHO_p1.0
Lyzl4
(Heterocephalus glaber - naked mole-rat)
Naked Mole-Rat AssemblyChrPosition (strand)SourceGenome Browsers
JBrowseNCBIUCSCEnsembl
HetGla 1.0NW_00462473077,220,928 - 77,224,946 (+)NCBIHetGla_female_1.0HetGla 1.0hetGla2

Variants

.
Variants in Lyzl4
12 total Variants
miRNA Target Status

Predicted Target Of
Summary Value
Count of predictions:61
Count of miRNA genes:55
Interacting mature miRNAs:59
Transcripts:ENSRNOT00000026173
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.


QTLs in Region (mRatBN7.2)
The following QTLs overlap with this region.    Full Report CSV TAB Printer Gviewer
RGD IDSymbolNameLODP ValueTraitSub TraitChrStartStopSpecies
1554321Bmd3Bone mineral density QTL 37.90.0001femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)840952565123900184Rat
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
738011Anxrr9Anxiety related response QTL 96.1exploratory behavior trait (VT:0010471)number of entries into a discrete space in an experimental apparatus (CMO:0000960)893535351123900184Rat
1358893Bp263Blood pressure QTL 2635.01arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
1358903Bp252Blood pressure QTL 25270.0001arterial blood pressure trait (VT:2000000)mean arterial blood pressure (CMO:0000009)893965141123900184Rat
738014Anxrr15Anxiety related response QTL 153.60.005locomotor behavior trait (VT:0001392)amount of experiment time spent in a discrete space in an experimental apparatus (CMO:0000958)895718998123900184Rat
2300182Bmd56Bone mineral density QTL 565.4femur mineral mass (VT:0010011)volumetric bone mineral density (CMO:0001553)895718998123900184Rat


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 5 8
Low 2 16 8 25 9
Below cutoff 1 22 11 5 8 5 2 2 28 6 5 1 2

Sequence


Reference Sequences
RefSeq Acc Id: ENSRNOT00000026173   ⟹   ENSRNOP00000026173
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8121,248,168 - 121,255,353 (-)Ensembl
Rnor_6.0 Ensembl8130,220,018 - 130,224,444 (-)Ensembl
RefSeq Acc Id: ENSRNOT00000106654   ⟹   ENSRNOP00000089851
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
mRatBN7.2 Ensembl8121,248,168 - 121,255,353 (-)Ensembl
RefSeq Acc Id: NM_001246183   ⟹   NP_001233112
RefSeq Status: VALIDATED
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,125,642 - 130,132,872 (-)NCBI
mRatBN7.28121,248,135 - 121,255,366 (-)NCBI
Rnor_6.08130,220,018 - 130,224,444 (-)NCBI
Rnor_5.08129,406,646 - 129,414,058 (-)NCBI
Celera8120,383,010 - 120,387,460 (-)NCBI
Sequence:
RefSeq Acc Id: XM_006244125   ⟹   XP_006244187
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,125,641 - 130,132,850 (-)NCBI
mRatBN7.28121,248,129 - 121,255,332 (-)NCBI
Rnor_6.08130,219,984 - 130,226,132 (-)NCBI
Rnor_5.08129,406,646 - 129,414,058 (-)NCBI
Sequence:
RefSeq Acc Id: XM_039081816   ⟹   XP_038937744
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,125,641 - 130,132,856 (-)NCBI
mRatBN7.28121,248,129 - 121,255,332 (-)NCBI
RefSeq Acc Id: XM_063265853   ⟹   XP_063121923
Type: CODING
Position:
Rat AssemblyChrPosition (strand)Source
GRCr88130,125,641 - 130,132,838 (-)NCBI
Reference Protein Sequences
RefSeq Acc Id: NP_001233112   ⟸   NM_001246183
- Peptide Label: precursor
- UniProtKB: D4ABW7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: XP_006244187   ⟸   XM_006244125
- Peptide Label: isoform X1
- UniProtKB: D4ABW7 (UniProtKB/TrEMBL)
- Sequence:
RefSeq Acc Id: ENSRNOP00000026173   ⟸   ENSRNOT00000026173
RefSeq Acc Id: XP_038937744   ⟸   XM_039081816
- Peptide Label: isoform X1
- UniProtKB: D4ABW7 (UniProtKB/Swiss-Prot)
RefSeq Acc Id: ENSRNOP00000089851   ⟸   ENSRNOT00000106654
RefSeq Acc Id: XP_063121923   ⟸   XM_063265853
- Peptide Label: isoform X1
Protein Domains
C-type lysozyme   Glycosyl hydrolases family 22 (GH22)

Protein Structures
Name Modeler Protein Id AA Range Protein Structure
AF-D4ABW7-F1-model_v2 AlphaFold D4ABW7 1-145 view protein structure

Transcriptome

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


Additional Information

Database Acc Id Source(s)
AGR Gene RGD:1308401 AgrOrtholog
BioCyc Gene G2FUF-28688 BioCyc
Ensembl Genes ENSRNOG00000019350 Ensembl, ENTREZGENE, UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Ensembl Transcript ENSRNOT00000026173.7 UniProtKB/Swiss-Prot
  ENSRNOT00000106654.1 UniProtKB/TrEMBL
Gene3D-CATH 1.10.530.10 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
InterPro Glyco_hydro_22 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glyco_hydro_22_CS UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Glyco_hydro_22_lys UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  Lysozyme-like_dom_sf UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
KEGG Report rno:363168 UniProtKB/Swiss-Prot
NCBI Gene 363168 ENTREZGENE
PANTHER PTHR11407 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  PTHR11407:SF21 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Pfam Lys UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PhenoGen Lyzl4 PhenoGen
PRINTS LYSOZYME UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
  LYZLACT UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
PROSITE GLYCOSYL_HYDROL_F22_1 UniProtKB/TrEMBL
  GLYCOSYL_HYDROL_F22_2 UniProtKB/TrEMBL
  LACTALBUMIN_LYSOZYME_1 UniProtKB/Swiss-Prot
  LACTALBUMIN_LYSOZYME_2 UniProtKB/Swiss-Prot
RatGTEx ENSRNOG00000019350 RatGTEx
SMART LYZ1 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
Superfamily-SCOP SSF53955 UniProtKB/Swiss-Prot, UniProtKB/TrEMBL
UniProt A0A8I6ACK3_RAT UniProtKB/TrEMBL
  D4ABW7 ENTREZGENE, UniProtKB/Swiss-Prot


Nomenclature History
Date Current Symbol Current Name Previous Symbol Previous Name Description Reference Status
2008-04-30 Lyzl4  lysozyme-like 4   Lyzl4_predicted  lysozyme-like 4 (predicted)  'predicted' is removed 2292626 APPROVED
2006-03-30 Lyzl4_predicted  lysozyme-like 4 (predicted)  RGD1308401_predicted  similar to RIKEN cDNA 1810009N24 (predicted)  Symbol and Name updated 1299863 APPROVED
2005-01-20 RGD1308401_predicted  similar to RIKEN cDNA 1810009N24 (predicted)  LOC363168_predicted    Symbol and Name status set to approved 1331353 APPROVED
2005-01-12 LOC363168_predicted  similar to RIKEN cDNA 1810009N24 (predicted)      Symbol and Name status set to provisional 70820 PROVISIONAL