KIAA0476

Product ID	ORK00087
Accession No	AB007945
Description	DENN/MADD domain containing 4B
Clone name	ah04654
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 (5688 bp) Predicted protein sequence (1626 aa)
HaloTag ORF Clone	FHC00087
Flexi ORF Clone	FXC00087
Source	Human brain (amygdala)
Rouge ID	mKIAA0476 by Kazusa Mouse cDNA Project
Note	We replaced hh00487, former representative clones for KIAA0476 with ah04654. (2005/08/06)

Length: 5688 bp

Physical map

Restriction map

Prediction of protein coding region (GeneMark analysis).

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

Integrity of 3' end

Length of 3'UTR	796 bp
Genome contig ID	gi89161185r_152068601
PolyA signal sequence (AGTAAA,-25)	+--------+--------+----*----+---- ATGTAAATATAGTAAAAGCTGCTTCTGTCTTTTTC
Flanking genome sequence (100000 - 99951)	----+--------+--------+--------+--------+----* CTTCGGCCTCCTGTTCCCTGGGTCTGGGGTAATGCGGGGATACCTTTCAT

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

	Chr	f/r	start	end	exon	identity	class
Ensembl gnome browser	1	r	152168601	152185778	28	99.9	Perfect prediction

Length: 1626 aa

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

Entry	ID%	Protein	Source
XP_513830	97.3	DENN/MADD domai...	Pan troglodytes
O75064	100.0	DENN domain-con...	Homo sapiens
XP_001493908	95.2	DENN/MADD domai...	Equus caballus
XP_001929547	94.8	DENN/MADD domai...	Sus scrofa
BAE33359	93.6	unnamed protein...	Mus musculus

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)

Entry	Exp	ID%	HUGE_ID
AB051553	1.2e-08	28.4	KIAA1766
AB029014	3.8e-05	24.2	KIAA1091
AB033103	0.00023	24.7	KIAA1277

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 motif / domain search (InterProScan and SOSUI)

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Result of InterProScan

Search method	interpro_ID	From	To	Entry	Definition
HMMPfam	IPR005113	321	409	PF03456	uDENN
	IPR001194	443	627	PF02141	DENN
	IPR005112	692	766	PF03455	dDENN
	IPR002885	944	978	PF01535	Pentatricopeptide repeat
HMMSmart	IPR005113	302	409	SM00800	uDENN
	IPR001194	443	627	SM00799	DENN
	IPR005112	692	766	SM00801	dDENN
HMMTigr	IPR002885	944	978	TIGR00756	Pentatricopeptide repeat
ProfileScan	IPR005113	136	415	PS50946	uDENN
	IPR001194	443	627	PS50211	DENN
	IPR005112	692	766	PS50947	dDENN

Prediction of transmembrane (TM) segments

Method	No.	N terminal	transmembrane region	C terminal	type	length
SOSUI2	1	527	SFLQLLQSLGPELAITLLLAVLT	549	SECONDARY	23
	2	560	PDLLTSVCEALVSMIFPLHWQCP	582	SECONDARY	23
	3	586	LCPLVLADVLSAPVPFIVGIHSS	608	PRIMARY	23

Primer_f
Primer_r
PCR conditions	°C sec °C sec cycles

Panel name	GeneBridge 4
Primer_f	CTCCATAAGAACCTCATAAGC
Primer_r	AATAATGGTCCCTCTTCCCTG
PCR product length	135 bp
PCR conditions	95 °C15 sec62 °C60 sec30 cycles