• Home
• Tools
  • BLAST
  • GBrowse
  • QueryBuilder
  • TermLink
  • ImageBrowse
  • Interactions Browser
  • Apollo
  • CytoSearch
  • QuickSearch
  • Batch Download
  • Coordinate Converter
  • Google™ FlyBase
  • Find A Person
  • Update An Address
  • Add A New Person
• Files
  • Downloads:
  • Precomputed files
  • Archived data
  • Releases FTP
  • Genomes FTP
  • Lists:
  • Transposons (Dmel)
  • Transposons (other)
  • Vectors & Constructs
  • Anatomical Terms
  • Map Conversion
• Species
  • Phylogeny
  • Synteny Table
  • Drosophilidae
  • Abbreviations
• Documents
  • About FlyBase
  • Reference Manual:
  • Sections
  • Contents
  • Nomenclature
  • Release Notes
• Resources
  • All resources
  • Interactive Fly
  • Textpresso for Fly
  • AAA site
  • BDGP
  • DHGP
  • DGRC
  • Model Organisms
  • Stock Collections:
  • Bloomington
  • DrosDel
  • Ehime
  • Exelixis (Harvard)
  • GDP (Baylor)
  • Kyoto
  • NIG-Fly
  • Szeged
  • Tucson
  • VDRC
• News
  • News
  • FlyBase Forum
  • FlyBase Positions
  • Meetings
  • Courses
  • Fly Board
  • White papers
  • Funding
  • bionet.dros
• Help
  • Google™ FlyBase
  • Site Map
  • FAQs
  • Report help
  • New to Flies
  • Pers. comm.
  • Author guidelines
  • Known Problems
  • Contact FlyBase
• Archives
  • Prior Home Page
  • R4.3 BLAST
  • R4.3 GBrowse
  • Older Archives

Gene Dmel\Ama

General Information
Symbol	Dmel\Ama	Species	D. melanogaster
Name	Amalgam	Annotation symbol	CG2198
Feature type	protein_coding_gene	FlyBase ID	FBgn0000071
Created / Updated	2003-12-01/2003-12-01
Genomic Location
Chromosome (arm)	3R	Recombination map	3-
Cytogenetic map	84A5-84A5	Sequence location	3R:2,588,315..2,590,983 [+]
Map ( GBrowse )	Decorated FastA GenBankGFF Gene region Extended Gene region CDSIntronsExonsTranslationsTranscripts3' UTR5' UTR
Summary Information
Automatically generated summary See sections below for more information	The gene Amalgam is referred to in FlyBase by the symbol Ama (CG2198, FBgn0000071). It has the cytological map location 84A5. Its sequence location is 3R:2588315..2590983. Its molecular function is described as antigen binding. It is involved in the biological process cell adhesion. 7 alleles are reported. No phenotypic data is available. It has 3 annotated transcripts and 3 annotated polypeptides.
External Summaries
Phenotypic Description from the Red Book (Lindsley & Zimm 1992)
Gene/Allele symbols may differ from current usage	Ama: Amalgam Antibody staining first detects Amalgam in the mesoderm during gastrulation; as neuroblasts delaminate from the ectoderm staining appears in a row of mesectodermal cells along the ventral midline of the extended germ band. Amalgam appears in the first neurons generated from the ganglion-mother cells, but not in the neuroblast precursors of these cells. Neuronal accumulation of Ama gene product increases during CNS development, but appears to be confined to the CNS and initially does not extend to axons exiting the CNS in segmental, intersegmental, or peripheral nerves; with time three rows of PNS-associated cells accumulate Ama protein; staining heavy around spiracle sensory organ and several cephalic sensory structures. Simultaneously there is a complicated temporal and spatial sequence of staining of mesodermal derivatives. Embryonic phenotype of deletion of Ama attributable to simultaneous deletion of zen; no effect of Ama- detectable.
Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 84A5-84A5   Limits computationally determined from genome sequence between P{PZ}pb04498 and P{lacW}l(3)L2100L2100
Experimentally Determined Cytological Location
Cytogenetic map Notes References
Experimentally Determined Recombination Data
Location	3- (Hill et al., 1995)
Left of (cM)	th (Liebl et al., 2003) cu (Hill et al., 1995)
Right of (cM)	st (Hill et al., 1995, Liebl et al., 2003)
Notes	3-47 (Liebl et al., 2003)
Molecular Map Data
Gene Order (in direction of increasing cytology) References Gene Order (overall orientation not stated) References
Gene Model & Products
Please see the GBrowse view of Dmel\Ama for information on other features
Comments on Gene Model
Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) Ama-RA FBtr0081619  NM_057231   1540   333 Ama-RB FBtr0081618  NM_169160   1833   341 Ama-RC FBtr0081620  NM_176412   1524   333
Additional Transcript Data & Comments
Reported size (kB)	1.5 (northern blot) (Seeger et al., 1988)
Comments
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein Ama-PA   FBpp0081136   36.4   333   7.04     NP_476579   AAF54084 Ama-PB   FBpp0081135   37.4   341   7.28     NP_731114   AAN13372 Ama-PC   FBpp0081137   36.4   333   7.04     NP_788589   AAO41515
Additional Polypeptide Data & Comments
Reported size (kD)	333 (aa) (Seeger et al., 1988)
Comments
External Data
Linkouts	PANTHER - Protein classification by function, families, and pathways • FBgn0000071
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • Immunoglobulin-like fold (IPR013783) Immunoglobulin subtype 2 (IPR003598) Immunoglobulin subtype (IPR003599) Immunoglobulin-like (IPR007110) Immunoglobulin I-set (IPR013098)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA439246   AA952131   AC002512   AE001572 AAD19797   AE003674 AAF54084   AE003674 AAN13372   AE003674 AAO41515   AI256902   AI258973   AI295266   AI520006   AW943486   AY051911 AAK93335   BI162749   BI162750   BI163832   BI213346   BI238382   BI239690   BI241944   BI355943   BI356712   BI356768   BI370700   BI371550   BI373259   BI373311   BI373486   BI484712   BI485705   BI580896   BI632423   BQ103205   CK132139   CK658286   CO192249   CO272022   CO282802   CO295983   CO298207   CO302094   CO323280   CO333941   CO337067   CO337137   EC073572   EC087126   EC197656   EC245900   EC247684   EC250405   EC251310   EC261520   EC264254   EL873919   FF579073   FF579478   M23561 AAA28367   RE01978
UniProtKB/Swiss-Prot	P15364
UniProtKB/TrEMBL	Q7KSX2 A4V2I0
Maps to	DS00276 (FlyBase, 1992-)
Does NOT map to
Identified with	LD39923 (BDGP Project Members, 2000-) D1347 (BDGP Project Members, 1994-1999)
Mapped Features & Mutations
Please see GBrowse or insertion reports for information on insertions of transgenic constructs and features not listed here Type Symbol & Location Additional Notes References deletion Ama[R1]-2 3R:2,589,901..2,589,929 comment=29bp deletion which begins with the first base of codon P114. Causes a frameshift followed by 54 novel amino acid residues before early termination. The Ama[R1] allele also contains a R103C missense mutation. evidence=experimental (Liebl et al., 2003, Liebl, 2005.5.20) point mutation Ama[M109] 3R:2,589,698..2,589,698 comment=Site of nucleotide substitution in mutant inferred by FlyBase based on reported amino acid change. evidence=experimental na_change=G2589698A pr_change=C54Y|Ama-PB,C46Y|Ama-PA,C46Y|Ama-PC reported_pr_change=C46Y (Liebl et al., 2003) point mutation Ama[R1]-1 3R:2,589,868..2,589,868 comment=Site of nucleotide substitution in mutant inferred by FlyBase based on reported amino acid change. The Ama[R1] allele also contains a 29bp deletion beginning in codon P114, which causes a frameshift. evidence=experimental na_change=C2589868T pr_change=R111C|Ama-PB,R103C|Ama-PA,R103C|Ama-PC reported_pr_change=R103C (Liebl et al., 2003)
External Data
Linkouts	DEDB - Drosophila exon database: splicing graphs • 8526
Crossreferences
Expression Data
FlyBase-Curated Data
Transcript and Protein data	Please see the FlyBase Gene Expression Report for details of gene expression from the literature.
Summary of Transcript Expression
Stage Tissue/Position Reference  embryonic stage   (Seeger et al., 1988)  pupal stage   (Seeger et al., 1988)
Marker for
Subcellular Localization
CV Term
Summary of Polypeptide Expression
Stage Tissue/Position Reference  embryonic stage | stage >=10  embryonic central nervous system | presumptive (Seeger et al., 1988)  embryonic stage | stage >=13  peripheral nervous system (Seeger et al., 1988)  embryonic stage | stage 16  larval labral sense organ | presumptive (Seeger et al., 1988)  embryonic stage | stage 8  mesoderm (Seeger et al., 1988)  embryonic stage | stage 13  spiracular sensory organ (Seeger et al., 1988)  embryonic stage | stage 10  amnioserosa (Seeger et al., 1988)  embryonic stage | stage 16  fat body (Seeger et al., 1988)  embryonic stage | stage 16  embryonic/larval dorsal vessel (Seeger et al., 1988)  embryonic stage | stage 13  visceral mesoderm (Seeger et al., 1988)  embryonic stage | stage 16  hypophysis (Seeger et al., 1988)  embryonic stage | stage 10  neuron (Seeger et al., 1988)
Marker for
Subcellular Localization
CV Term	plasma membrane axon cell body (Seeger et al., 1988)
Microarray Data
	Developmental timecourse, Costello et al., 2008 (Original data from Arbeitman et al., 2002) AI520006
External Data & Images
Linkouts	FLIGHT - Cell culture data for RNAi and other high-throughput technologies • FBgn0000071 FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array • FBgn0000071 GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies • FBgn0000071 BDGP expression data • Show all BDGP original images, annotations and embryonic microarray data for Ama FlyExpress - Embryonic expression images (BDGP data) • Show all FlyExpress processed images for Ama Stage(s) 1-3 Stage(s) 4-6 Stage(s) 7-8 Stage(s) 9-10 Stage(s) 11-12 Stage(s) 13-16
Alleles & Phenotypes
Summary of Allele Phenotypes
Phenotype manifest in Allele
Classical Alleles ( 2 )
For All Classical Alleles Show
Allele of Ama Class Mutagen Stocks Known lesion AmaM109 ethyl methanesulfonate 0 Yes AmaR1 ethyl methanesulfonate 0 Yes
Alleles Carried on Transgenic Constructs ( 5 )
For All Alleles Carried on Transgenic Constructs Show
Allele of Ama Class Mutagen Stocks Known lesion AmaGD12733 in vitro construct | RNAi in vitro construct | regulatory fusion 2 Yes AmaM109.MtnA in vitro construct | regulatory fusion 0 Yes AmaMtnA.PL in vitro construct | regulatory fusion 0 Yes AmadsRNA.cLa in vitro construct | RNAi 0 Yes Amahs.PK in vitro construct | regulatory fusion 1 Yes
Aneuploid Aberrations
Useful deficiency	Df(3R)MAP117
Useful duplication	Dp(3;Y)77ab
Disrupted in	Df(3R)D830 (Fremion et al., 2000) Df(3R)MAP11 (Liebl et al., 2003) Df(3R)MAP117 (Kaufman et al., 1990) Df(3R)SCB-XL2 (Kaufman, 1994.10.5) Df(3R)ama (Fremion et al., 2000)
Not disrupted in	Df(3R)MAP8 (Kaufman et al., 1990)
Transgenic Constructs & Insertions
Transgenic Constructs
	Type of construct Name Expression data UAS construct P{GD12733} NA heat-shock construct P{Hsp70-Ama} NA
Insertions
	Type of insertions Name Expression data
Related Comments
	Please look at the allele reports for the complete phenotype data Embryonic phenotype of deletion of Ama attributable to simultaneous deletion of zen; no effect of Ama- detectable. (Lindsley and Zimm, 1992)
Gene Ontology: Function, Process & Cellular Component ( 3 )
Molecular Function
CV term Evidence References
antigen binding non-traceable author statement (Swiss-Prot Project Members, 1990.4.1)
Biological Process
CV term Evidence References
cell adhesion non-traceable author statement (Lindsley and Zimm, 1992) non-traceable author statement (FlyBase, 1992-)
Cellular Component
CV term Evidence References
plasma membrane inferred from direct assay AND inferred from sequence or structural similarity (Seeger et al., 1988)
Sequence Ontology: Class of Gene
	protein_coding_gene   nuclear_gene
Interactions & Pathways
Summary of Genetic Interactions
Interacts with	Please look at the allele data for full details of the genetic interactions Ama allele Gene References AmadsRNA.cLa Abl (Liebl et al., 2003) AmaM109 Abl (Liebl et al., 2001, Liebl et al., 2003) AmaR1 Abl (Liebl et al., 2003)
External Data
Linkouts	BioGRID - Interaction data, including yeast 2-hybrid and genetic interactions • 66029
Orthologs
Genome-wide drosophilid orthologs	Dana\GF17188 Dere\GG13665 Dgri\GH18131 Dper\GL21774 Dsec\GM10913 Dsim\Ama Dvir\GJ23304 Dwil\GK12252 Dyak\GE24882
Curated drosophilid orthologs	Dpse\Ama   Dsim\Ama
Linkouts	InParanoid orthologs - Eukaryotic orthologs • NEWSINFRUP00000178749 Takifugu rubripes (Ensembl) ENSGALP00000029822 Gallus gallus (Ensembl) ENSMODP00000000570 Monodelphis domestica (Ensembl)
Functional Complementation between Species
Inter-Species Misexpression Data
Produces phenotype in
Produces NO phenotype in
Stocks & Reagents
Stocks Listed in FlyBase ( 3 )
Bloomington	7439 w1118; P{Hsp70-Ama}2
VDRC	v22944 w1118 P{GD12733}v22944 v22945 w1118; P{GD12733}v22945/TM3
Genomic Clones ( 1 )
	BACR19D23
cDNA Clones ( 38 )
	Please Note This section lists cDNAs and ESTs that fall within the genomic extent of the gene model, which may include cDNAs and ESTs of genes within introns, or of overlapping genes. Please see GBrowse for alignment of the cDNAs and ESTs to the gene model.
cDNA Clones, Fully Sequenced
BDGP DGC clones	LD39923
Other clones
cDNA Clones, End Sequenced (ESTs)
BDGP DGC clones	RE60783 RE60514 RE37010 RE34804 RE60570 RE75143 LP08849 SD26196 RE58465 RE03346 LD29204 LP13424 LP02284 LD13756 LP15117 RE36257 RE42906 LP03618 RE57421 RE69040 RE42974 RE18729 RE67854 RE39150
Other clones	EK212437 RE01978 EK172529 UUGC0605 EK161242 EK308416 IP14004 EK190105 EN13910 EC33427 EK105518 EN13754 EK183041
RNAi & Array Information
Affy Oligo
Linkouts	DRSC - RNAi screening (Harvard): high-throughput cell culture data and design • FBgn0000071 GenomeRNAi - RNAi phenotypes (Heidelberg): high-throughput cell culture data • FBgn0000071
Antibody Information
	polyclonal (Seeger et al., 1988)
Other Information
Discoverer
Etymology
Identification
Position Effect Variegation Data
Relationship to Other Genes
Source for database identity of	Source for identity of: Ama CG2198 (Li, 1999.11)
Source for database merge of	Source for merge of: Ama M109 (Liebl et al., 2001)
Additional comments
Comments About Role
	Encodes a protein of the immunoglobulin super-family that may function as a cell-adhesion protein. (Lindsley and Zimm, 1992) Nrt is hypothesized to require Ama as its ligand. (Diano and Piovant, 1995)
Comments About Molecular Function
Other Comments
	The homologs of Antp, ftz, Scr, Dfd, Ama, bcd, zen, pb and lab, but not zen2 are all present in D.pseudoobscura.pseudoobscura, in the same linear order and similarly spaced along the chromosome as in D.melanogaster. (Randazzo et al., 1993) Haploinsufficiency dependent upon an Abl mutant background (HDA). (Hill et al., 1995) In a sample of 79 genes with multiple introns, 33 showed significant heterogeneity in G+C content among introns of the same gene and significant positive correspondence between the intron and the third codon position G+C content within genes. These results are consistent with selection adding against preferred codons at the start of genes. (Kliman and Eyre-Walker, 1998)
External Crossreferences & Linkouts
Sequence Crossreferences
	RefSeq (Transcripts) • NM_169160 NM_057231 NM_176412 RefSeq (Proteins) • NP_731114 NP_476579 NP_788589 DDBJ / EMBL / GenBank • AC002512 AE001572 AAD19797 AE003674 AAN13372 AAF54084 AAO41515 AI520006 AW943486 AY051911 AAK93335 M23561 AAA28367 UniProtKB/Swiss-Prot • P15364 UniProtKB/TrEMBL • Q7KSX2 A4V2I0
Other Crossreferences
	InterPro domains - A database of protein families, domains, and functional sites •