KIAA0468

Product ID	ORK06744
Accession No	AB007937
Description	syndecan 3
Clone name	hg01596
Vector information	The cDNA fragment was inserted at the SalI-NotI site of the ... The cDNA fragment was inserted at the SalI-NotI site of the pBluescript II SK(+) vector (GenBank Accession No. X52328, AmpR). The 5' end of the cDNA was repaired and ligated with the SalI adapter (5'TCGACCCACG CGTCCG3') and inserted at the SalI site of the vector. The 3'end of the cDNA was inserted at the NotI site of the vector.
cDNA sequence	DNA sequence (6400 bp) Predicted protein sequence (410 aa)
Source	Human adult brain
Rouge ID	mKIAA0468 by Kazusa Mouse cDNA Project

Length: 6400 bp

Physical map

Restriction map

Prediction of protein coding region (GeneMark analysis).

	N-terminal truncation	Coding interruption
cloned DNA seq	No warning	Warning

Integrity of 3' end

Length of 3'UTR	3742 bp
Genome contig ID	gi89161185r_31014901
PolyA signal sequence (AATAAA,-20)	+--------+--------+----*----+---- CCATTTATAAGAGGAAATAAAATTAAGCTGAAATG
Flanking genome sequence (100000 - 99951)	----+--------+--------+--------+--------+----* ATGTGCCGTGTCCAGAGTATGAGATAAATATGGTCATTTGGGGAGGGCAG

Ensembl ContigView (Add our DAS server as a DAS source)

	Chr	f/r	start	end	exon	identity	class
Ensembl gnome browser	1	r	31114901	31124176	3	99.0	Terminal No-hit

Length: 410 aa

Result of homology search against nr database (FASTA output, Multiple alignment)

Entry	Exp	ID%	Protein	Source
CAI22245	1.5e-108	100.0	syndecan 3 [Hom...	Homo sapiens
O75056	1.1e-99	89.3	Syndecan-3; Sho...	Homo sapiens
AAK39969	2.2e-99	89.1	syndecan 3 [Hom...	Homo sapiens
XP_001149044	2.8e-98	99.2	similar to SDC3...	Pan troglodytes
EAX07637	8.5e-97	100.0	syndecan 3 (N-s...	Homo sapiens

The numbers on the left and right sides of a black line in the graphical overview indicate the lengths (in amino acid residues) of the non-homologous N-terminal and C-terminal portions flanking the homologous region (indicated by the black line), respectively.

Result of homology search against HUGE database (FASTA output, Multiple alignment)

No significant homologues

Result of motif / domain search (InterProScan and SOSUI)

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Result of InterProScan

Search method	interpro_ID	From	To	Entry	Definition
HMMPfam	IPR001050	19	408	PF01034	Syndecan
HMMSmart	IPR003585	376	394	SM00294	Neurexin/syndecan/glycophorin C
ScanRegExp	IPR001050	377	387	PS00964	Syndecan

Prediction of transmembrane (TM) segments

Method	No.	N terminal	transmembrane region	C terminal	type	length
SOSUI2	1	19	RGLGDLILMAIAYLGSSCP	37	SECONDARY	19
SOSUI2	2	352	EVLVAVIVGGVVGALFAAFLVTL	374	PRIMARY	23

Primer_f
Primer_r
PCR conditions	°C sec °C sec cycles

Panel name	GeneBridge 4
Primer_f	GGGCTCTGGGGATGATGACTC
Primer_r	CCCGTGGGCTTCTCAGAGTTG
PCR product length	149 bp
PCR conditions	95 °C15 sec68 °C60 sec30 cycles