A high throughput messenger RNA differential display screen identifies discrete domains of gene expression and novel patterning processes along the developing neural tube

Chambers, David; Mason, Ivor

doi:10.1186/1471-213X-6-9

Table 1 Summary of cDNA fragments isolated by differential display of mRNA from fore/mid and hindbrain regions of a HH st10 chick embryo

From: A high throughput messenger RNA differential display screen identifies discrete domains of gene expression and novel patterning processes along the developing neural tube

Clone	Accession	BBSRC	Encoded	Function	Remark
A	Q05916 [SP]	603103425F1	Engrailed 1	TF	See figure 3A
B	No match	603743047F1	mafB	TF	See figure 3K
C [x3]	Bankit754392	603407923F1	SPARC-related 1	Cell adhesion	See figure 3H 2.8 kb cDNA from 5' RACE
D	gi\|4929813	603118757F1	Sprouty2	Intracellular signaling	See figure 3B [42]
E	gi\|17440991	603139218F1	KIAA0007	Unknown	See figure 3N
F	Bankit754394	No match	Similar to HB GAM*	Heparin-binding	See figure 3K 3.2 kb cDNA from library
G	Bankit754396	603856249F1	Unknown	Unknown	See figure 3E 1.6 kb cDNA from library
H	Bankit754406	No match	Unknown	Unknown	DD: Up in Midbrain
I	gi\|12407844	603127196F1	Peroxiredoxin	Redox signaling	DD: Up in Midbrain
J	Bankit754410	No match	Unknown	Unknown	DD: Up in R1 & Hindbrain
L [X2]	gi\|12729652	603488169F1	L1CAM	Cell adhesion	See figure 3F
N	Bankit754412	No match	Unknown	Unknown	DD: Up in Hindbrain
O	No match	602554245F1	Unknown	Unknown	DD: Up in Hindbrain
P	Bankit754414	No match	Unknown	Unknown	DD: Up in Hindbrain
Q	gi\|1710781	604136738F1	LRP37/p40	Cell adhesion	See figure 3M
S	gi\|550024	603129809F1	Ribosomal protein	Translation	DD: Up in R1 & Hindbrain
U	Bankit754420	No match	Unknown	Unknown	DD: Up in R1 & Hindbrain
V	gi\|12653908	603762906F1	exoribonuclease	RNA processing	DD: Up in Forebrain
W	gi\|13489085	603493341F1	Ubiquitin-conjucating enzyme	Protein turnover	DD: Down in Midbrain
X	Bankit741871	No match	Unknown	Unknown	DD: Up in Hindbrain
Y	Bankit754720	No match	Unknown	Unknown	DD: Up in Hindbrain
Z	Bankit741629	No match	Unknown	Unknown	DD: Up in R1 and Midbrain
β	Bankit754422	603124149F1	Pax2*	TF	See figure 3D 2.8 kb cDNA from library
1	gi\|550024	603129809F1	ribosomal s10	Translation	DD: Up in Midbrain
2	gi\|441123	603788872F1	RTPzeta	Intracellular signaling	See figure 3C
3	Bankit741889	No match	Unknown	Unknown	See figure 3I
4	Q90835 [SP]	603120688F1	EF1α	Translation	See figure 3J 2 kb cDNA from library
5	Q90749 [SP]	603848654F1	FGFR2	Intracellular signaling	See figure 3G [56]
6	No match	603408919F1	Unknown	Unknown	DD: Up [weak] in Midbrain
7	gi\|14211561	603373072F1	GLP1	G-protein signaling	DD: Up in R1 & Midbrain
8	gi\|15281514	603217934F1	Roundabout1	Axon guidance	DD: Up in Hindbrain
9	AAK55455	604170469F1	hypothetical protein 127.7 kDa	Putative TF regulator	DD: Up in R1 & Midbrain
10	No match	603107258F1	Unkown	Unkown	DD: Up [weak] in Hindbrain
11	Q9Y2L0 [SP]	603499417F1	KIAA1007 protein	Unknown	DD: Up [weak] in Midbrain
12	Q9NR13 [SP]	603951558F1	ALR-like	cytokine	DD: Up [weak] in Midbrain
13	Q9P278 [SP]	603610122F1	KIAA1450 protein	unknown	DD: Up in R1 and Hindbrain
14	No match	603005063F1	unknown	unknown	DD: Up in Fore and Midbrain
15	P08125	603848942F1	Collagen Alpha 1[X]	connective tissue	DD: Up in Hindbrain
16	X67778	604141228F1	Claustrin	Cell adhesion	DD: Up in F & M
17	No match	No match	EF2⁺	Translation	DD: H on
18	No match	603401645F1	EiF3zeta	Translation	DD: R1 & H on

Where an unequivocal identity is found for the differential display clone in BBSRC, Genbank or SWISSPROT databases, it is shown in the appropriate column. SP = Swiss-Prot Database, TF = Transcription Factor, RTP = Receptor Tyrosine Phosphatase, FGFR = Fibroblast Growth Factor Receptor, GLP = Glugacon-like Peptide, EF = Elongation Factor, LRP = Laminin Receptor Protein, L1CAM = L1-like Cell Adhesion Molecule, mafB ~ kreisler, 5' RACE = rapid amplification of 5' cDNA end. Where no identity for a cDNA is found in the sequence repositories, the sequence is given in Supplementary Information. F = forebrain, M = midbrain, R1 = rhombomere 1, H = hindbrain (rhombomeres 2–7). * denotes clones whose identity has been derived from significant matches with the chick genome sequence (see Results). ⁺ denotes identity derived from similarity to an ortholog. Where a 100% match with an EST from the UMIST collection was found the fragment sequence was not submitted to Genbank.

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ISSN: 1471-213X

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