KIAA0046

Product ID	ORK00383
Accession No	D28475
Description	chloride channel, voltage-sensitive 6, transcript variant 1
Clone name	ha00519s1
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 (5567 bp) Predicted protein sequence (872 aa)
HaloTag ORF Clone	FHC00383
Flexi ORF Clone	FXC00383
Source	Myeloblast cell line (KG-1)
Rouge ID	mKIAA0046 by Kazusa Mouse cDNA Project
Note	We replaced ha00519, former representative clones for KIAA0046 with ha00519s1. (2002/5/10)

Length: 5567 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	2905 bp
Genome contig ID	gi89161185f_11688855
PolyA signal sequence (AATAAA,-18)	+--------+--------+----*----+---- TAACCCTAACATGTGAGAATAAAATGTCTTCTGTC
Flanking genome sequence (136919 - 136968)	----+--------+--------+--------+--------+----* TCCTCTGTCTCCTTTAGCCTTTTGTCTCCATGCTGCTTTCTTTCTTTCTT

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

	Chr	f/r	start	end	exon	identity	class
Ensembl gnome browser	1	f	11788855	11825772	23	99.4	Perfect prediction

Length: 872 aa

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

Entry	ID%	Protein	Source
P51797	100.0	Chloride channe...	Homo sapiens
CAI15895	99.9	chloride channe...	Homo sapiens
XP_001104721	99.4	chloride channe...	Macaca mulatta
EAW71716	99.5	chloride channe...	Homo sapiens
XP_001491791	98.2	similar to Chlo...	Equus caballus

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)

[ zoom out (x2) ]

Result of InterProScan

Search method	interpro_ID	From	To	Entry	Definition
FPrintScan	IPR002248	5	17	PR01117	Chloride channel CLC-6
	IPR002248	81	90	PR01117	Chloride channel CLC-6
	IPR002248	101	113	PR01117	Chloride channel CLC-6
	IPR001807	155	172	PR00762	Chloride channel
	IPR001807	186	205	PR00762	Chloride channel
	IPR002248	206	215	PR01117	Chloride channel CLC-6
	IPR002248	217	226	PR01117	Chloride channel CLC-6
	IPR001807	250	269	PR00762	Chloride channel
	IPR001807	487	507	PR00762	Chloride channel
	IPR001807	522	538	PR00762	Chloride channel
	IPR001807	540	559	PR00762	Chloride channel
	IPR001807	578	592	PR00762	Chloride channel
HMMPfam	IPR014743	139	575	PF00654	Chloride channel
HMMPfam	IPR000644	606	861	PF00571	Cystathionine beta-synthase
HMMSmart	IPR000644	611	660	SM00116	Cystathionine beta-synthase
HMMSmart	IPR000644	813	861	SM00116	Cystathionine beta-synthase

Prediction of transmembrane (TM) segments

Method	No.	N terminal	transmembrane region	C terminal	type	length
SOSUI2	1	6	GCRGSLCCCCRWCCCCG	22	SECONDARY	17
	2	84	WMVVFAIGVCTGLVGLFVDFFVR	106	PRIMARY	23
	3	130	ALSLLELLGFNLTFVFLASLLVL	152	PRIMARY	23
	4	175	PGIVRLRTLLCKVLGVLFSVAGG	197	PRIMARY	23
	5	245	VSAGAAAGVAAAFGAPIGGTLFS	267	SECONDARY	23
	6	274	FWNQGLTWKVLFCSMSATFTLNF	296	SECONDARY	23
	7	333	TAMDLGFFVVMGVIGGLLGATFN	355	PRIMARY	23
	8	377	RVLESLLVSLVTTVVVFVASMVL	399	PRIMARY	23
	9	462	TFSPVTLALFFVLYFLLACWTY	483	PRIMARY	22
	10	490	GLFVPSLLCGAAFGRLVANVLKS	512	SECONDARY	23
	11	524	FALIGAAAFLGGVVRMTISLTVI	546	PRIMARY	23

Primer_f
Primer_r
PCR conditions	test

Panel name	Stanford G3
Primer_f	CCAGATAAGCCCAAAGAC
Primer_r	GTGATGGGGCTGCTAATG
PCR product length	124 bp
PCR conditions	95 °C15 sec56 °C60 sec30 cycles