Gene Dmel\sqd

General Information
Symbol	Dmel\sqd	Species	D. melanogaster
Name	squid	Annotation symbol	CG16901
Feature type	protein_coding_gene	FlyBase ID	FBgn0086897
Created / Updated	2007-10-12/2007-10-12
Genomic Location
Chromosome (arm)	3R	Recombination map
Cytogenetic map	87F5-87F6	Sequence location	3R:9,461,214..9,472,026 [-]
Map ( GBrowse )
Summary Information
Automatically generated summary See sections below for more information	The gene squid is referred to in FlyBase by the symbol sqd (CG16901, FBgn0086897). It has the cytological map location 87F5-87F6. Its sequence location is 3R:9461214..9472026. Its molecular function is described as: mRNA binding; mRNA 3'-UTR binding; nucleic acid binding; nucleotide binding. It is involved in the biological processes described with 16 unique terms, many of which group under: gamete generation; anterior/posterior axis specification; anatomical structure development; oocyte axis determination; nucleocytoplasmic transport; mRNA metabolic process; oocyte anterior/posterior axis determination; transport; regulation of metabolic process; intracellular mRNA localization. 32 alleles are reported. The phenotypes of these alleles are annotated with 16 unique terms, many of which group under: organ system; anatomical structure; egg; follicle cell; organism; chorion; acellular anatomical structure; germarium; ventral furrow; cell part; spiracle. It has 4 annotated transcripts and 4 annotated polypeptides.
External Summaries

Detailed Mapping Data
FlyBase Computed Cytological Location
Cytogenetic map Evidence for location 87F5-87F6 Limits computationally determined from genome sequence between P{PZ}CtBP⁰³⁴⁶³ and P{lacW}B52^s2249&P{lacW}flfl^L4179
Experimentally Determined Cytological Location
Cytogenetic map Notes References 87F2-87F3 (determined by in situ hybridisation) 87F3--4 (determined by in situ hybridisation) (Spradling et al., 1999) 87F3-87F4 (determined by in situ hybridisation) 87F2--3 (determined by in situ hybridisation) (Perrimon et al., 1996) 87F3-87F4 (BDGP Project Members, 1994-1999) 87F-87F (determined by in situ hybridisation) (Kelley, 1993) 87F-87F (determined by in situ hybridisation) (Matunis et al., 1992) 87F4-87F10 (determined by in situ hybridisation) (Kelley, 1992)
Experimentally Determined Recombination Data
Location
Left of (cM)
Right of (cM)
Notes
Molecular Map Data
Gene Order (in direction of increasing cytology) References In direction of increasing cytology: sqd- Hrb87F- B52+ (Peng and Mount, 1995) Gene Order (overall orientation not stated) References Overall orientation not stated: sqd- rin? (Kelley, 1993) Overall orientation not stated: sqd- rin+ Rbp4- Hrb87F- B52+ (Haynes et al., 1997) Overall orientation not stated: sqd- rin+ (Pazman et al., 2000)
Gene Model & Products
Please see the GBrowse view of Dmel\sqd for information on other features
Comments on Gene Model

Transcript Data
Annotated Transcripts
Name FlyBase ID RefSeq ID Length (nt) Associated CDS (aa) sqd-RA FBtr0082854 NM_169529 2654 321 sqd-RB FBtr0082855 NM_169528 2322 344 sqd-RC FBtr0082856 NM_143952 2214 308 sqd-RD FBtr0082857 NM_206481 1974 178
Additional Transcript Data & Comments
Reported size (kB)	4.8, 3.5, 2.3, 1.9, 1.7, 1.5 (northern blot) (Kelley, 1993)
Comments	The 1.7kb and 1.9kb sqd transcripts differ in the site of polyadenylation. (Kelley, 1993, Kelley, 1993) The structure of the 3.5kb and 4.8kb transcripts has not been determined. (Kelley, 1993, Kelley, 1993)
External Data
Crossreferences
Polypeptide Data
Annotated Polypeptides
Name FlyBase ID Predicted MW (kD) Length (aa) Theoretical pI RefSeq ID GenBank protein sqd-PA FBpp0082319 35.0 321 6.54 NP_731826 AAF54964 sqd-PB FBpp0082320 36.2 344 7.62 NP_731825 AAF54963 sqd-PC FBpp0082321 33.1 308 6.96 NP_652209 AAN13570 sqd-PD FBpp0089309 18.3 178 9.97 NP_996203 AAS65146
Additional Polypeptide Data & Comments
Reported size (kD)	40 (kD observed) (Matunis et al., 1992) 345, 321 (aa); 40 (kD observed); 36, 35 (kD predicted) (Matunis et al., 1992) 321, 308 (aa) (Kelley, 1993)
Comments	sqd protein has two amino-terminal RNP-CS RNA-binding domains and a carboxy-terminal glycine-rich auxiliary domain. (Matunis et al., 1992, Matunis et al., 1992) hnRNP-specific mAbs were obtained and used to purify hnRNP complexes from S2 cells. hnRNP proteins were identified on the basis of nucleoplasmic localization, association with nascent transcripts, crosslinking to poly(A)-containing RNA in living cells, and amino acid sequence. Staining of polytene chromosomes reveals that sqd protein is associated with actively transcribing loci. (Matunis et al., 1992, Matunis et al., 1992)
External Data
Linkouts
Crossreferences	InterPro domains - A database of protein families, domains, and functional sites • RNA recognition motif, RNP-1 (IPR000504) Nucleotide-binding, alpha-beta plait (IPR012677)
Sequences Consistent with the Gene Model
DDBJ / EMBL / GenBank	DNA sequence Protein sequence Name AA201415 AA202270 AA202458 AA202666 AA246282 AA246607 AA246877 AA264842 AA264867 AA264928 AA264942 AA390435 AA390595 AA390689 AA390972 AA391566 AA391583 AA392187 AA392333 AA439002 AA439641 AA439700 AA440283 AA440353 AA441121 AA441154 AA441634 AA538773 AA541243 AA696732 AA698813 AA801875 AA802095 AA802391 AA802548 AA802610 AA816339 AA816784 AA821013 AA940588 AA940675 AA942304 AA942415 AA949460 AA950361 AA950386 AA951322 AA952277 AE003701 AAF54963 AE003701 AAF54964 AE003701 AAN13570 AE003701 AAS65146 AI063527 AI108821 AI135335 AI238292 AI257981 AI259148 AI293344 AI295398 AI389050 AI404245 AI455041 AI512756 AI514607 AI514647 AI514806 AI515121 AI516263 AI516409 AI516717 AI516912 AI519107 AI519766 AI519909 AI520340 AI520342 AI534676 AI534846 AI542808 AI543069 AI546091 AI946265 AI947163 AQ025143 AQ026331 AQ034130 AQ073021 AQ073075 AQ073154 AQ254622 AQ254681 AW942080 AW942084 AY069386 AAL39531 AY070527 AY118501 AAM49870 BF486415 BF488428 BF493136 BG637727 BG638009 BG638558 BG638655 BG641328 BI162797 BI162954 BI164087 BI164692 BI164712 BI164890 BI165203 BI165288 BI166403 BI166769 BI167853 BI168263 BI168305 BI169652 BI169910 BI171311 BI171603 BI172252 BI172426 BI172831 BI173463 BI173586 BI173756 BI173865 BI212123 BI213076 BI213204 BI214022 BI215308 BI216318 BI216401 BI227899 BI228260 BI229591 BI231363 BI234372 BI235121 BI235201 BI235253 BI236632 BI236801 BI237599 BI237987 BI238057 BI239044 BI239119 BI239183 BI239449 BI239761 BI239873 BI239926 BI240100 BI240455 BI240683 BI240775 BI240984 BI241260 BI241890 BI241960 BI242025 BI242028 BI242716 BI243299 BI355384 BI355445 BI356107 BI356108 BI357060 BI357296 BI358228 BI358474 BI361607 BI361769 BI362284 BI362581 BI362636 BI362832 BI362934 BI363733 BI363734 BI363750 BI364181 BI365765 BI366032 BI366033 BI366047 BI366498 BI366598 BI367793 BI367921 BI367922 BI368056