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Gene Dmir\Lcp4

General Information
Symbol	Dmir\Lcp4	Species	D. miranda
Name	Larval cuticle protein 4	Annotation symbol
Feature type	gene	FlyBase ID	FBgn0012555
Gene Model Status	Unannotated	Stock availability	None publicly available
Also Known As	Lcp4
Genomic Location
Chromosome (arm)		Recombination map	X2
Cytogenetic map		Sequence location
Summary Information
Automatically generated summary See sections below for more information	The gene Larval cuticle protein 4 is referred to in FlyBase by the symbol Dmir\Lcp4 (FBgn0012555). It is a gene from Drosophila miranda. An electronic pipeline based on InterPro domains suggests that it has the molecular function: structural constituent of cuticle. The biological processes in which it is involved are not known. No alleles are reported. It has no annotated transcripts. Protein features are: Insect cuticle protein. Gene has not been localized to the genome sequence.
Recent Updates
Description	What does this section display? This section contains items that were added to this record for each release. It currently only tracks new links between this FlyBase report and other FlyBase data classes (e.g. genes, references, stocks) or controlled vocabulary terms (e.g. GO, anatomy terms). What does this section not display? This section does not currently display links that were removed or gene model changes.
Update Feed	Click the icon below to subscribe to this FlyBase record and receive updates automatically through your feed reader.
FB2013_03
FB2013_02
All updates	Click here to see a list of all updates to this record from FB2010_08 and on.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location
Experimentally Determined Cytological Location
Cytogenetic map Notes References   Located on Neo-X.   (Bachtrog and Andolfatto, 2006)
Experimentally Determined Recombination Data
Location	X2
Left of (cM)
Right of (cM)
Notes
Gene Model & Products
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa)
Additional Transcript Data & Comments
Reported size (kB)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kDa) Length (aa) Theoretical pI RefSeq ID GenBank protein
Additional Polypeptide Data & Comments
Reported size (kDa)
Comments
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Insect cuticle protein (IPR000618)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name M94252 AAA28670   X97815 CAA66395
UniProtKB/Swiss-Prot	Q01774
UniProtKB/TrEMBL
Mapped Features
Type Symbol & Location Additional Notes References
External Data
Linkouts
Crossreferences
Expression Data
Transcript Expression
Additional Descriptive Data
Marker for
Subcellular Localization
CV Term
Polypeptide Expression
Additional Descriptive Data
Marker for
Subcellular Localization (GO Cellular Component)
CV term Evidence References
Expression Deduced from Reporters
High-Throughput Expression Data
Associated Tools
Reference	See Gelbart and Emmert, 2010.10.13 for analysis details and data files for all genes.
FlyAtlas Anatomy Microarray
modENCODE Anatomy RNA-Seq
modENCODE Development RNA-Seq
modENCODE Cell Lines RNA-Seq
modENCODE Treatments RNA-Seq
Expression Clusters
External Data & Images
Linkouts
Alleles & Phenotypes
Summary of Allele Phenotypes
Phenotype manifest in Allele
Classical Alleles ( 0 )
For All Classical Alleles Show
Allele of Dmir\Lcp4 Class Mutagen Stocks Known lesion
Alleles Carried on Transgenic Constructs ( 0 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Dmir\Lcp4 Class Mutagen Stocks Known lesion
Aneuploid Aberrations
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data
Insertions
	Type of insertions Name Expression data
Gene Ontology: Function, Process & Cellular Component ( 1 unique term )
Terms Based on Experimental Evidence ( 0 terms )
Terms Based on Predictions or Assertions ( 1 term )
Molecular Function
CV term Evidence References
structural constituent of cuticle inferred from electronic annotation with InterPro:IPR000618 (FlyBase Curators et al., 2004-)
Biological Process ( 0 terms)
Cellular Component ( 0 terms)
Sequence Ontology: Class of Gene
	gene
Interactions & Pathways
Summary of Physical Interactions
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions Dmir\Lcp4 allele Gene References
External Data
Linkouts
Orthologs
OrthoDB Orthologs (0) - based on analysis using Dmel annotation version 5.41
OrthoDB Ortholog Groups
	OrthoDB orthology group searches (Waterhouse et al., 2011, Nucleic Acids Res. 39(Database issue): D283--D288) Drosophila inclusive ortholog search No orthologs identified Dipteran inclusive ortholog search No orthologs identified Insect inclusive ortholog search No orthologs identified Arthropod inclusive ortholog search No orthologs identified Metazoa inclusive ortholog search No orthologs identified
Ortholog(s) in Drosophila melanogaster (None identified)
No D. melanogaster orthologies identified
Human Orthologs (0)
Gene OMIM HGNC
AAA Orthologs (0) based on analysis using Dmel annotation version 4.3
No orthologs identified
Stocks & Reagents
Stocks Listed in FlyBase ( 0 )
Genomic Clones ( 0 )
cDNA Clones ( 0 )
cDNA Clones, Fully Sequenced
BDGP DGC clones
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones
Other clones
RNAi & Array Information
Linkouts
Antibody Information
Other Information
Discoverer
Etymology
Identification
Relationship to Other Genes
Source for database identity of
Source for database merge of
Additional comments
Other Comments
	Comparison of the Lcp multigene family of the X2 and neo-Y chromosomes of D.miranda reveals massive rearrangements including insertions, deletions and a large duplication in the neo-Y cluster. (Steinemann and Steinemann, 1993) Located in a cluster of four Lcp genes on the X2 chromosome. The arrangement of genes and direction of transcription within the cluster are similar to those in the D.melanogaster Lcp cluster. (Steinemann and Steinemann, 1992) Comparison of the D.miranda Lcp gene cluster on the X2 chromosome (Dmir\Lcp1, Dmir\Lcp2, Dmir\Lcp3 and Dmir\Lcp4) and the Y sex chromosome (Dmir\Lcp1Ψ, Dmir\Lcp2Ψ, Dmir\Lcp3Ψ, Dmir\Lcp4Ψ and Dmir\Lcp2DΨ) reveal extensive DNA rearrangements in the latter gene cluster. (Steinemann and Steinemann, 1990)
External Crossreferences & Linkouts
Sequence Crossreferences
	DDBJ / EMBL / GenBank • AAA28670 CAA66395 M94252 X97815 UniProtKB/Swiss-Prot • Q01774
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites • Insect cuticle protein (IPR000618)
Linkouts
Synonyms & Secondary IDs ( 10 )
Reported As
Symbol Synonym	Dmir\Lcp4   Lcp (Bartolome and Charlesworth, 2006) Lcp 4 (Steinemann and Steinemann, 2005) Lcp4 (Steinemann and Steinemann, 2005, Bachtrog and Andolfatto, 2006, Steinemann and Steinemann, 2007) LCP4 (Karouzou et al., 2007) Lcp4miX   unnamed (Steinemann and Steinemann, 1990)
Name Synonym	Gene 4 (Steinemann and Steinemann, 1992) Larval cuticle protein 4 (Steinemann and Steinemann, 1993) larval cuticle protein 4 (Steinemann and Steinemann, 2007)
Secondary FlyBase IDs
References ( 17 )
Research paper	Steinemann and Steinemann, 2007, Insect Mol. Biol. 16(2): 167--174 Evolution of sex chromosomes: dosage compensation of the Lcp1-4 gene cluster on the evolving neo-X chromosome in Drosophila miranda. [FBrf0192468] Bachtrog and Andolfatto, 2006, Genetics 174(4): 2045--2059 Selection, recombination and demographic history in Drosophila miranda. [FBrf0193451] Bartolome and Charlesworth, 2006, Genetics 173(2): 779--791 Rates and patterns of chromosomal evolution in Drosophila pseudoobscura and D. miranda. [FBrf0193909] Bachtrog, 2003, Genetics 165(3): 1221--1232 Protein evolution and codon usage bias on the neo-sex chromosomes of Drosophila miranda. [FBrf0167628] Steinemann and Steinemann, 1998, Genetica 102-103(1-6): 409--420 Enigma of Y chromosome degeneration: neo-Y and neo-X chromosomes of Drosophila miranda a model for sex chromosome evolution. [FBrf0104518] Steinemann and Steinemann, 1997, Genetics 145(2): 261--266 The enigma of Y chromosome degeneration: TRAM, a novel retrotransposon is preferentially located on the Neo-Y chromosome of Drosophila miranda. [FBrf0092695] Mandalaparthy et al., 1996, D. I. S. 77: 49--51 The cuticle proteins of Drosophila melanogaster: Sequence of Lcp5 in the third chromosome cluster. [FBrf0091421] Steinemann et al., 1996, J. Mol. Evol. 43(4): 405--412 Evolution of the larval cuticle proteins coded by the secondary sex chromosome pair: X2 and neo-Y of Drosophila miranda. [FBrf0090813] Steinemann et al., 1996, J. Mol. Evol. 43(4): 413--417 Evolution of the larval cuticle proteins coded by the secondary sex chromosome pair: X2 and neo-Y of Drosophila miranda. [FBrf0090812] Steinemann and Steinemann, 1993, Genetics 134(2): 497--505 A duplication including the Y allele of Lcp2 and the TRIM retrotransposon at the Lcp locus on the degenerating neo-Y chromosome of Drosophila miranda: molecular structure and mechanisms by which it may have arisen. [FBrf0058598] Steinemann et al., 1993, Proc. Natl. Acad. Sci. U.S.A. 90(12): 5737--5741 How Y chromosomes become genetically inert. [FBrf0059273] Steinemann and Steinemann, 1992, Proc. Natl. Acad. Sci. U.S.A. 89: 7591--7595 Degenerating Y chromosome of Drosophila miranda: a trap for retrotransposons. [FBrf0057553] Steinemann and Steinemann, 1990, Chromosoma 99(6): 424--431 Evolutionary changes in the organization of the major lcp gene cluster during sex chromosomal differentiation in the sibling species Drosophila persimilis, Drosophila pseudoobscura and Drosophila miranda. [FBrf0051452]
Supplementary material	Karouzou et al., 2007, Insect Biochem. Mol. Biol. 37(8): Tables S2-S5. [FBrf0200186]
Review	Steinemann and Steinemann, 2005, BioEssays 27(10): 1076--1083 Y chromosomes: born to be destroyed. [FBrf0189794]
Personal communication to FlyBase	FlyBase Curators et al., 2004-, Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. Gene Ontology annotation in FlyBase through association of InterPro records with GO terms. [FBrf0174215]
Abstract	Yi and Charlesworth, 1998, A. Dros. Res. Conf. 39: 602B Inferring the evolution of sex chromosomes from the Lcp genes on the newly evolving sex chromosomes of Drosophila miranda. [FBrf0101639]