Gene Dmel\Scm

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General Information

Symbol

Dmel\Scm

Species

D. melanogaster

Name

Sex comb on midleg

Annotation symbol

CG9495

Feature type

protein_coding_gene

FlyBase ID

FBgn0003334

Created / Updated

2003-12-01/2003-12-01

Genomic Location

Chromosome (arm)

Recombination map

3-48.5

Cytogenetic map

85E2-85E2

Sequence location

3R:5,459,081..5,463,329 [-]

Map ( GBrowse )

Summary Information

Automatically generated summary

See sections below for more information

The gene Sex comb on midleg is referred to in FlyBase by the symbol Scm (CG9495, FBgn0003334). It has the cytological map location 85E2. Its sequence location is 3R:5459081..5463329. Its molecular function is described as: specific RNA polymerase II transcription factor activity; zinc ion binding. It is involved in the biological processes: gene silencing; regulation of transcription; germarium-derived female germ-line cyst encapsulation; ovarian follicle cell stalk formation; neurogenesis. 38 alleles are reported. The phenotypes of these alleles are annotated with 30 unique terms, many of which group under: adult segment; larval abdominal segment; thoracic segment; adult; anatomical structure; larval thorax; organ system; abdominal segment 7; adult mesothoracic segment; peripheral nervous system. It has one annotated transcript and one annotated polypeptide.

External Summaries

Phenotypic Description from the Red Book (Lindsley & Zimm 1992)

Gene/Allele symbols may differ from current usage

Scm: Sex combs on midleg

Presumably Scm/+ males form sex combs on the mesothoracic legs; does not appear to have been explicitly described. Homozygous embryos show posteriorly directed transformations; A1 resembles A2 and A2-7 transformed into more posterior segments, head and thorax normal. Pcl Scm double homozygotes exhibit transformation of all segments toward A8; Keilin's organs retained in thoracic segments; head involution does not occur; prominant abdominal denticle band seen on dorsal surface of head. Homozygous embryos derived from transplanted homozygous maternal germ-cell precursors display A8 morphology in all thoracic and abdominal segments; head seems to resemble that of Pcl Scm double homozygotes produced by heterozygous mothers; heterozygous adults from homozygous oocytes show patchy transformations of A4 to A5 and of A6 and A7 to A8; similar transformation infrequently seen in heterozygous offspring of heterozygous mothers.

ScmK1

Strong dominant enhancer of the extra sex combs phenotype of Pc heterozygotes. Allelism to Scm inferred from phenotype and location.

Detailed Mapping Data

FlyBase Computed Cytological Location

Cytogenetic map

Evidence for location

85E2-85E2

Limits computationally determined from genome sequence between P{EP}Crc^EP3006 and P{lacW}s2681

Experimentally Determined Cytological Location

Cytogenetic map

Notes

References

85F-85F

Location from complementation analysis with deficiency and duplication chromosomes (details unspecified).

(Kennison and Tamkun, 1988)

Experimentally Determined Recombination Data

Location

3-48.5

(Tearle and Nusslein-Volhard, 1987)

3-49

(Jurgens, 1985, Kennison and Tamkun, 1988)

Left of (cM)

l(3)85Eb

(Lindsley and Zimm, 1992)

Right of (cM)

l(3)85Ec

(Lindsley and Zimm, 1992)

Notes

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\Scm for information on other features

Comments on Gene Model

EST data suggest additional 3' exon(s)

Transcript Data

Annotated Transcripts

Name

FlyBase ID

RefSeq ID

Length (nt)

Associated CDS (aa)

Scm-RA

FBtr0082102

NM_169299

4065

877

Additional Transcript Data & Comments

Reported size (kB)

4.1, 3.8 (longest cDNA)

(Bornemann et al., 1996)

Comments

The 4.1 and 3.8 kb Scm transcripts differ only in the use of alternative polyadenylation sites. Both transcripts are expressed maternally, while the 4.1 kb transcript is the predominant zygotic form.

(Bornemann et al., 1996)

The 4.1 and 3.8 kb Scm transcripts differ only in the use of alternative polyadenylation sites. Both transcripts are expressed maternally, while the 4.1 kb Scm transcript is the predominant zygotic form.

(Bornemann et al., 1996)

External Data

Crossreferences

Polypeptide Data

Annotated Polypeptides

Name

FlyBase ID

Predicted MW (kD)

Length (aa)

Theoretical pI

RefSeq ID

GenBank protein

Scm-PA

FBpp0081580

93.6

877

8.71

NP_731385

AAF54419

Additional Polypeptide Data & Comments

Reported size (kD)

100 (kD observed)

(Bornemann et al., 1998)

877 (aa); 94 (kD predicted)

(Bornemann et al., 1996)

Comments

The Scm protein shares homology with the phl protein in the C-terminal SAM domain, and in the class of zinc fingers. The Scm protein also shares a region of homology with the l(3)mbt protein, a 100 aa stretch which is repeated twice in the Scm protein and thrice in the l(3)mbt protein.

(Bornemann et al., 1996)

External Data

Linkouts

PANTHER - Protein classification by function, families, and pathways

•

FBgn0003334

Crossreferences

InterPro domains - A database of protein families, domains, and functional sites

•

Sterile alpha motif SAM (IPR001660)

Mbt repeat (IPR004092)

Sterile alpha motif homology (IPR010993)

Zinc finger, FCS-type (IPR012313)

Sterile alpha motif-type (IPR013761)

Sequences Consistent with the Gene Model

DDBJ /
EMBL /
GenBank

DNA sequence

Protein sequence

Name

Q9VHA0

Maps to

Does NOT map to

Identified with

LD09463

(Salvaing et al., 2003)

RE16782

(BDGP Project Members, 2000-)

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

point mutation

Scm[Suz302]
3R:5,462,177..5,462,177

evidence=experimental
na_change=G5462177A
pr_change=D215N|Scm-PA
reported_na_change=G?A|FBrf0104734
reported_pr_change=D215N|FBrf0104734

(Bornemann et al., 1998)

point mutation

Scm[5]
3R:5,462,140..5,462,140

comment=Site of nucleotide substitution in mutant inferred by FlyBase based on reported amino acid change.
evidence=experimental
na_change=T5462140A
pr_change=V227E|Scm-PA
reported_pr_change=V227E|FBrf0104734

(Bornemann et al., 1998)

point mutation

Scm[H1]
3R:5,462,073..5,462,074

comment=G to A nucleotide change at the second or third position of the Trp codon leads to a nonsense mutation. (exact site of mutation unspecified). Site of nucleotide substitution in mutant inferred by FlyBase based on reported amino acid change.
evidence=experimental
na_change=G?A
pr_change=W249@|Scm-PA
reported_pr_change=W249@|FBrf0104734

(Bornemann et al., 1998)

point mutation

Scm[ET50]
3R:5,461,996..5,461,996

na_change=G5461996A
pr_change=G275E|Scm-PA
reported_pr_change=G275E|FBrf0104734
comment=Site of nucleotide substitution in mutant inferred by FlyBase based on reported amino acid change.
evidence=experimental

(Bornemann et al., 1998)

point mutation

Scm[K2]
3R:5,461,545..5,461,545

comment=Site of nucleotide substitution in mutant inferred by FlyBase based on reported amino acid change.
evidence=experimental
na_change=C5461545G
pr_change=C425W|Scm-PA
reported_pr_change=C425Y|FBrf0104734

(Bornemann et al., 1998)

point mutation

Scm[M36]
3R:5,461,223..5,461,223

comment=Site of nucleotide substitution in mutant inferred by FlyBase based on reported amino acid change.
evidence=experimental
na_change=G5461223A
pr_change=C511Y|Scm-PA
reported_pr_change=C511Y|FBrf0104734

(Bornemann et al., 1998)

sequence variant

Scm[R5-13]
3R:5,462,001..5,462,012

comment=12 bp in-frame deletion
evidence=experimental

(Bornemann et al., 1998)

sequence variant

Scm[4]
3R:5,460,019..5,460,269

comment=deletion of 251 bp, plus insertion of 4 nucleotides (CTGA)
evidence=experimental

(Bornemann et al., 1996)

External Data

Linkouts

DEDB - Drosophila exon database: splicing graphs

•

8814

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

oogenesis stage,adult stage

ovary

(Bornemann et al., 1996)

embryonic stage | >12 hr

embryonic central nervous system

(Bornemann et al., 1996)

embryonic stage-pupal stage

(Bornemann et al., 1996)

Marker for

Subcellular Localization

CV Term

Summary of Polypeptide Expression

Stage

Tissue/Position

Reference

adult stage

adult head

(Bornemann et al., 1998)

adult stage | male

(Bornemann et al., 1998)

larval stage

(Bornemann et al., 1998)

embryonic stage-adult stage

(Bornemann et al., 1998)

adult stage | female

ovary

(Bornemann et al., 1998)

Marker for

Subcellular Localization

CV Term

nucleus

(Bornemann et al., 1998)

External Data & Images

Linkouts

FLIGHT - Cell culture data for RNAi and other high-throughput technologies

•

FBgn0003334

FlyAtlas - Adult expression by tissue, using Affymetrix Dros2 array

•

FBgn0003334

GEO (NCBI) - Gene expression data: microarray and other high-throughput technologies

•

FBgn0003334

Alleles & Phenotypes

Summary of Allele Phenotypes

Lethality

Allele

viable | female, with Scer\GAL4^prd.RG1

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

viable, with Scer\GAL4^71B

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

viable, with Scer\GAL4^A9

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

viable, with Scer\GAL4^ap-md52

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

lethal | recessive

lethal | male, with Scer\GAL4^prd.RG1

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

lethal | embryonic stage (with Scm⁴)

Scm^H1

lethal | embryonic stage (with Scm^H1)

Scm⁴

lethal | embryonic stage | recessive

Scm^unspecified

lethal | embryonic stage | conditional - heat sensitive, with Scer\GAL4^da.G32

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

lethal | larval stage

lethal | larval stage | recessive

Scm⁵

lethal | pupal stage (with Scm^ET50)

Scm^H1

lethal | pupal stage (with Scm^H1)

Scm^ET50

lethal | pupal stage | recessive

lethal, with Scer\GAL4^Bx-MS1096

Scm^GD1526

lethal, with Scer\GAL4^dpp.blk1, Scm^H1

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

lethal, with Scer\GAL4^dpp.blk1, Scm^{SPM.Scer\UAS.T:Ivir\HA1}

Scm^H1

lethal, with Scer\GAL4^pnr-MD237

Scm^GD1526

lethal, with Scer\GAL4^GMR.PF, Scer\GAL4^ey.PH

Scm^GD1526

lethal, with Scer\GAL4^Act5C

Scm^GD1526

Other Phenotypes

Allele

visible | dominant | homeotic

Scm^D1

visible | homeotic

Scm^D1

visible | homeotic | male, with Scer\GAL4^dpp.blk1

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

visible | homeotic | male, with Scer\GAL4^ptc-559.1

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

visible | female | homeotic, with Scer\GAL4^prd.RG1

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

visible, with Scer\GAL4^71B

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

visible, with Scer\GAL4^A9

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

visible, with Scer\GAL4^A9, Scm^H1

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

visible, with Scer\GAL4^A9, Scm^{SPM.Scer\UAS.T:Ivir\HA1}

Scm^H1

visible, with Scer\GAL4^ap-md52

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

reduced cell number | somatic clone

Scm^D1

non-enhancer of variegation, with P{hsp26-pt-T}39C-5

Scm^ET50

non-enhancer of variegation, with P{hsp26-pt-T}39C-31

Scm^Suz302

suppressor of variegation | dominant, with P{wA}4-4

Scm^Suz302

suppressor of variegation | dominant, with P{hsp26-pt-T}39C-5

Scm^Suz302

suppressor of variegation | dominant, with P{hsp26-pt-T}39C-27

Scm^Suz302

suppressor of variegation | dominant, with P{SUPor-P.PRE#6}69

Scm^D1

suppressor of variegation | dominant, with P{SUPor-P.PRE#6}69M3

Scm^D1

suppressor of variegation | dominant, with P{SUPor-P.PRE#6}69M1

Scm^D1

suppressor of variegation | dominant, with P{SUPor-P.PRE#6}69M2

Scm^D1

suppressor of variegation | dominant, with P{SUPor-P.PRE#6}4

Scm^D1

non-suppressor of variegation, with P{hsp26-pt-T}39C-5

Scm^ET50

non-suppressor of variegation, with P{hsp26-pt-T}39C-31

Scm^Suz302

mitotic cell cycle defective | somatic clone

Scm^D1

Phenotype manifest in

Allele

larval abdominal segment 1

larval abdominal segment 2 | ectopic

Scm¹

larval abdominal segment 2

larval abdominal segment 3 | ectopic

Scm¹

larval abdominal segment 3

larval abdominal segment 4 | ectopic

Scm¹

larval abdominal segment 4

larval abdominal segment 5 | ectopic

Scm¹

larval abdominal segment 5

larval abdominal segment 6 | ectopic

Scm¹

larval abdominal segment 6

larval abdominal segment 7 | ectopic

Scm¹

larval abdominal segment 7

larval abdominal segment 8 | ectopic

Scm¹

larval abdominal segment 1 | germ-line clone

Scm¹

larval abdominal segment 2 | germ-line clone

Scm¹

larval abdominal segment 3 | germ-line clone

Scm¹

larval abdominal segment 4 | germ-line clone

Scm¹

larval abdominal segment 5 | germ-line clone

Scm¹

larval abdominal segment 6 | germ-line clone

Scm¹

larval abdominal segment 7 | germ-line clone

Scm¹

larval prothoracic segment | germ-line clone

Scm¹

larval mesothoracic segment | germ-line clone

Scm¹

larval metathoracic segment | germ-line clone

Scm¹

larval abdominal segment 8 | ectopic | germ-line clone

Scm¹

sex comb | ectopic

sex comb

Scm^Cas-Scm7

wing

Scm^Cas-Scm7

egg chamber

Scm^D1

interfollicle cell | ectopic

Scm^D1

mesothoracic leg

Scm^D1

embryonic/first instar larval cuticle

Scm^D1

adult abdominal segment 4

Scm^D1

adult abdominal segment 5 | ectopic

Scm^D1

abdominal tergite 4 | male

Scm^D1

adult abdominal segment 6

Scm^D1

adult abdominal segment 7 | ectopic

Scm^D1

abdominal tergite 6 | male

Scm^D1

embryonic segment

neuroblast | somatic clone

Scm^D1

larval prothoracic segment

Scm^D2

larval mesothoracic segment

Scm^D2

larval metathoracic segment

Scm^D2

wing, with Scer\GAL4^A9, Scm^{SPM.Scer\UAS.T:Ivir\HA1}

Scm^H1

pigment cell

wing, with Scer\GAL4^A9, Scm^H1

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

wing, with Scer\GAL4^71B

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

wing, with Scer\GAL4^A9

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

wing, with Scer\GAL4^ap-md52

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

haltere | ectopic, with Scer\GAL4^ap-md52

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

sex comb | ectopic, with Scer\GAL4^dpp.blk1

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

leg | male, with Scer\GAL4^dpp.blk1

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

antenna | female, with Scer\GAL4^prd.RG1

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

leg | ectopic | female, with Scer\GAL4^prd.RG1

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

sex comb | ectopic, with Scer\GAL4^ptc-559.1

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

leg | male, with Scer\GAL4^ptc-559.1

Scm^{SPM.Scer\UAS.T:Ivir\HA1}

embryo

Scm^unspecified

Classical Alleles ( 23 )

For All Classical Alleles Show

Allele of Scm	Class	Mutagen	Stocks	Known lesion
Scm¹		ethyl methanesulfonate	0	--
Scm^28-16			0	--
Scm²		ethyl methanesulfonate	0	--
Scm³		ethyl methanesulfonate	0	--
Scm⁴	loss of function	X ray	0	Yes
Scm⁵	hypomorph	ethyl methanesulfonate	0	Yes
Scm^D1	amorph, loss of function	X ray	3	Yes
Scm^D2	loss of function	X ray	0	--
Scm^ET50	hypomorph	ethyl methanesulfonate	0	Yes
Scm^H1	loss of function	ethyl methanesulfonate	0	Yes
Scm^K1		ethyl methanesulfonate	0	--
Scm^K2	hypomorph	ethyl methanesulfonate	0	Yes
Scm^LA01027		P-element activity	1	--
Scm^M36	hypomorph	ethyl methanesulfonate	0	Yes
Scm^M56	loss of function		0	Yes
Scm^P11		Δ2-3	0	Yes
Scm^P12		Δ2-3	0	Yes
Scm^P22		Δ2-3	0	--
Scm^P23		Δ2-3	0	Yes
Scm^R5-13	hypomorph	X ray	0	Yes
Scm^Suz302	hypomorph, gain of function	ethyl methanesulfonate	0	--
Scm^e01989		piggyBac transposase	1	--
Scm^unspecified			0	--

Alleles Carried on Transgenic Constructs ( 15 )

For All Alleles Carried on Transgenic Constructs Show

Allele of Scm	Mutagen	Stocks	Known lesion
Scm^Cas-Scm7	in vitro construct \| genomic fragment	0	Yes
Scm^{G31D.T:Zzzz\FLAG}	in vitro construct \| amino acid replacement	0	Yes
Scm^GD1526	in vitro construct \| RNAi in vitro construct \| regulatory fusion	2	Yes
Scm^{I29T.T:Zzzz\FLAG}