Comparative mapping of the 22q11.2 deletion region and the potential of simple model organisms

Guna, Alina; Butcher, Nancy J.; Bassett, Anne S.

doi:10.1186/s11689-015-9113-x

Journal of Neurodevelopmental Disorders

Table 1 Conservation status and available knockout (KO)/knockdown (KD) models of 22q11.2 deletion region protein-coding genes

From: Comparative mapping of the 22q11.2 deletion region and the potential of simple model organisms

Human protein- coding gene^a	C. elegans			D. melanogaster			D. rerio			M. musculus
Human protein- coding gene^a	Homologue (n = 17)	%	Model^b	Homologue (n = 22)	%	Model^b	Homologue (n = 37)	%	Model^b	Homologue (n = 40)	%	Model^b
DGCR6				gdl	37	KO	dgcr6	65	−	Dgcr6	92	−
PRODH	CELE_B0513.5	46	KD	slgA	46	KO, KD	LOC100537991	69	−	Prodh	82	KO
PRODH	CELE_B0513.5	46	KD	slgA	46	KO, KD	prodha	63	KO	Prodh	82	KO
DGCR2							dgcr2	64	KO	Dgcr2	93	KO
DGCR14	ess-2	30	KO, KD	Es2	35	KD	dgcr14	67	−	Dgcr14	93	KO
TSSK2										Tssk2	92	KO
GSC2							LOC101885810	52	−	Gsc2	76	KO
SLC25A1	K11H3.3	65	KD	sea	67	KO, KD	slc25a1a	78	KD	Slc25a1	94	KO
SLC25A1	K11H3.3	65	KD	sea	67	KO, KD	slc25a1b	84	−	Slc25a1	94	KO
HIRA	K10D2.1	33	KO, KD	Hira	60	KO, KD	hira	78	KD	Hira	96	KO
MRPL40	mrpl-40	30	KD	mRpL40	40	KO, KD	mrpl40	50	−	Mrpl40	75	KO
C22orf39				CG15908	32	KO, KD	si:ch211..51 h9.6	49	−	2510002D24Rik	72	KO
UFD1L	ufd-1	41	KD	Ufd1-like	56	KO, KD	ufd1l	87	KO	Ufd1l	99	KO
CDC45	evl-18	29	KO, KD	CDC45L	39	KO, KD	cdc45	74	KO	Cdc45	92	KO
CLDN5							cldn5a	57	KO, KD	Cldn5	92	KO
CLDN5							cldn5b	54	−	Cldn5	92	KO
SEPT5							sept5a	84	−	Sept5	99	KO
SEPT5							sept5b	85	−	Sept5	99	KO
GP1BB							gp1bb	46	−	Gp1bb	90	KO
TBX1	mls-1	53	KO, KD	org-1	58	KO, KD	tbx1	72	KO, KD	Tbx1	91	KO
GNB1L				CG13192	30	KO, KD	gnb1l	53	−	Gnb1l	82	KO
TXNRD2	trxr-2	49	KO, KD	Trxr-2	55	KD	si:ch1073-179p4.3	71	−	Txnrd2	86	KO
COMT							comta	53	−	Comt	80	KO
COMT							comtb	54	−	Comt	80	KO
ARVCF							arvcfb	64	KO	Arvcf	92	KO
TANGO2	R186.1	29	KD	Tango2	30	KO, KD	tango2	64	−	Tango2	88	−
DGCR8	pash-1	25	KO, KD	pasha	37	KO, KD	dgcr8	72	KO	Dgcr8	95	KO
TRMT2A	H24K24.4	27	KD	CG3808	37	KO, KD	trmt2a	56	KO	Trmt2a	83	KO
RANBP1							ranbp1	73	KO	Ranbp1	93	KO
ZDHHC8							zdhhc8b	57	KO	Zdhhc8	92	KO
LOC388849										Gm7873	72	−
RTN4R							rtn4r	45	KD	Rtn4r	89	KO
SCARF2							scarf2	52	−	Scarf2	82	KO
KLHL22				CG1812	30	KO, KD	klhl22	60	−	Klhl22	95	−
MED15	mdt-15^c	26	KO, KD	MED15	32	KO, KD	med15^b	60	KD	Med15	90	−
PI4KA	CELE_Y75B8A.24	38	KO, KD	PI4KIIIalpha	45	KO, KD	pi4kaa	84	KD	Pi4ka	98	KO
SERPIND1							serpind1	54	−	Serpind1	82	KO
SNAP29	snap-29	28	KO, KD	Snap29	32	KO, KD	snap29	51	KD	Snap29	83	KO
CRKL							crkl	82	KD	Crkl	97	KO
AIFM3	F20D6.11	34	KD	CG4199	38	KO, KD	LOC100150876	66	−	Aifm3	96	−
LZTR1				CG3711	51	KO, KD	lztr1	81	−	Lztr1	95	KO
THAP7							thap7	42	KO	Thap7	93	−
P2RX6										P2rx6	86	KO
SLC7A4	C50D2.2	43	KD	CG13248	43	KO, KD	slc7a4	64	KO	Slc7a4	84	−
LRRC74B							si:ch211-173a9.8	41	−	Lrrc74b	68	−

^aGenes ordered by proximal to distal 22q11.2 locus position. Genes CLTCL1, C22orf29, DGCR6L, USP41, LOC101927859, and ZNF74 have no putative homologues, and are therefore not shown
^bKnockout indicates a homozygous knockout model (heterozygous knockout models can be generated by crossing a homozygous knockout with a wild-type strain)
^cIncluded due to confirmed functional homology [98], although did not meet minimal protein sequence coverage requirement at 50 %
Italicized genes have putative homologues across all four model organisms (n = 17). Blank cells indicate no identified homologue; − indicates no knockout (KO) or knockdown (KD) model available. Percent (%) indicates sequence similarity to human protein. Homologues were identified using blastp using the UniProtKB database. KO and KD models were identified from WormBase (http://www.wormbase.org/), FlyBase (http://flybase.org/), ZFin (http://zfin.org/), and MGI (http://www.informatics.jax.org/) for C. elegans, D. melanogaster, D. rerio, and M. musculus, respectively. Data are current to 2 December 2014

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ISSN: 1866-1955

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