Validating internal controls for quantitative plant gene expression studies

BMC Plant Biology

Table 2 Description of poplar genes and primers for real-time PCR.

Name^a	GenBank accession number^b	*Arabidopsis*homolog locus^c	*Arabidopsis*locus description	BLASTX score/ E value	Primer sequences (forward/reverse)
ACT11	CA824001	AT3G12110	Actin 11	363/ e-101	CACACTGGAGTGATGGTTGG / ATTGGCCTTGGGGTTAAGAG
ACT2	BU879695	AT5G09810	Actin 2/7	320/ 5e-088	CCCATTGAGCACGGTATTGT / TACGACCACTGGCATACAGG
CYP	BU875027	AT2G21130	cyclophilin (CYP2)	284/ 6e-077	GGCTAATTTTGCCGATGAGA / ACGTCCATCCCTTCAACAAC
TUA	CA822230 CA825391	AT5G19780	tubulin alpha-3/alpha-5 chain	439/ e-130	AGGTTCTGGTTTGGGGTCTT / TTGTCCAAAAGCACAGCAAC
TUB	CA824237	AT4G20890	tubulin beta-9 chain	154/ 4e-038	GCACCAACTTGTTGAGAATGC / TTTCAACTGACCAGGGAACC
UBQ	BU879229	AT4G05050	polyubiquitin (UBQ11)	416/ e-117	GTTGATTTTTGCTGGGAAGC / GATCTTGGCCTTCACGTTGT
UBQ-L	BU871588	AT2G35635	ubiquitin-like (UBQ7)	291/ 4e-079	TGAGGCTTAGGGGAGGAACT / TGTAGTCGCGAGCTGTCTTG
EIF4B-L	CA825614	AT4G38710	similarity to eukaryotic translation initiation factor 4B	80/ 1e-015	AAAAAGGGGATTTGGGATTG / AACTTCGTCCTCGGTAGCAA
EF1β	BI125345	AT2G18110	elongation factor 1-beta, putative	122/ 1e-028	AAGAGGACAAGAAGGCAGCA / CTAACCGCCTTCTCCAACAC
18S	AF206999	18RRNA	18S ribosomal RNA	2949/ 0.0	AATTGTTGGTCTTCAACGAGGAA/ AAAGGGCAGGGACGTAGTCAA

^aAll poplar sequences except 18S are ESTs, and were named based on similarity to Arabidopsis proteins determined via BLASTX (Altschul et al. 1997). In most cases, the name indicates only a gene family or subfamily rather than a specific member of a gene family because partial poplar sequences and BLAST will not necessarily identify the putative Arabidopsis ortholog. ^bTwo accession numbers indicate that two EST sequences were used to design the primer set. ^cClosest Arabidopsis homolog identified using Tair BLAST 2.0 http://www.arabidopsis.org/Blast/. AGI proteins database was queried with poplar nucleotide sequences using BLASTX or in the case of 18S, Arabidopsis genome database with BLASTN.

ISSN: 1471-2229