Sounds like you're trying to knit a few hazy concepts together too quickly - it might help to start by completely ignoring the RNA polymerase (the machinery that does the transcription in the "opposite" direction), and building up your understanding from scratch. Here is a stab at an explanation, hopefully it won't make things worse!

Start with the basics:

• DNA is double-stranded. By convention, for a reference chromosome, one whole strand is designated the "forward strand" and the other the "reverse strand". This designation is arbitrary. Sometimes the terms "plus strand" and "minus strand" are used instead.

• Visually (I'm not talking about the transcription machinery yet), you would typically read the sequence of a strand in the 5-3 direction. For the forward strand, this means reading left-to-right, and for the reverse strand it means right-to-left.

• A gene can live on a DNA strand in one of two orientations. The gene is said to have a coding strand (also known as its sense strand), and a template strand (also known as its antisense strand). For 50% of genes, its coding strand will correspond to the chromosome's forward strand, and for the other 50% it will correspond to the reverse strand.

• The mRNA (and protein) sequence of a gene corresponds to the DNA sequence as read (again, visually) from the gene's coding strand. So the mRNA sequence always corresponds to the 5-3 coding sequence of a gene.

• Now, the RNA polymerase machinery moves along the DNA in the 5-3 orientation of the coding strand (e.g. left-to-right for a forward strand gene). It reads the bases from the template strand (so it is reading in the 3-5 direction from the point-of-view of the template strand), and builds the mRNA as it goes. This means that the mRNA matches the coding sequence of the gene, not the template sequence. (This diagram from Wikipedia illustrates).

• Annotations such as Ensembl and UCSC are concerned with the coding sequences of genes, so when they say a gene is on the forward strand, it means the gene's coding sequence is on the forward strand. To follow through again, that means that during transcription of this forward-strand gene, the gene's template sequence is read from the reverse strand, producing an mRNA that matches the sequence on the forward strand.

Short answer - yes. A "gene" is on the forward strand if its mRNA is on the forward strand.

I placed quotation marks around "gene" because, perhaps surprisingly, it is not a very useful word. In the context of this question we're using "sequence of a gene" to mean the same as "sequence of the mRNA transcribed from the gene." So we're referring to the same strand because we're talking about the same object.

What is a gene though? Most "genes" give rise to multiple transcripts. So we might say a gene is a region of DNA that serves as a template for transcription. A gene is not really a single object with start and end. It will have a "minimum start" (the 5'-most base from which transcription occurs) and a "maximum end" (the 3'-most base at which transcription terminates). So perhaps it's best to forget about genes and think about transcripts and their properties.

I agree that the "start < end" convention takes some getting used to but it makes a lot of sense when it comes to performing range calculations with sequences. If you just name the strands "+" or "-" and set start < end, you can forget about all the other terminology (forward/reverse, 5'/3' and so on), it all "just works".

I often find myself looking up what forward and reverse strands represent (along with their various synonyms) so I decided to compile some of my research in one place. Please correct me if I'm off about anything, there's a lot of divergent and database/organism-specific information out there.

• Forward vs reverse – by convention, in Eukaryotes, the forward strand is defined as the strand with its 5' end at the tip of the short arm (p arm) of the chromosome. Databases store the sequence of the forward strand and genome browsers display it in 5' to 3' (left to right) orientation with the coordinates increasing from 1 (or 0) starting at the 5' end. The reverse strand uses the coordinates defined by the forward strand, so for the reverse strand, the 5' end has higher values than the 3' end.

5' ------X---------------------- 3' <-- forward strand, typically shown in this orientation by genome browsers
3' ------X---------------------- 5' <-- negative strand, typically not shown by genome browsers

• Coding (information) vs noncoding – as I understand it, these are relative terms that only apply in regions of the genome that code for proteins (that is, they are not absolute terms that apply to the full chromosome-length strand of DNA). A given region of the genome is defined as coding if the pre-mRNA sequence of the gene encoded there matches the sequence (aside from Thymine/Uracil) and orientation of the forward (plus) strand. In other words, a strand is called the coding strand if the other strand acts as the template during transcription. The coding strand contains codons, the noncoding strand contains anticodons.

• Nontemplate vs template – synonyms of coding and noncoding respectively.

• Plus (+) vs minus (-) – synonyms of forward and reverse respectively. A gene has a plus (+) orientation if its pre-mRNA sequence matches that of the plus strand.

• Positive vs negative – synonyms of forward and reverse respectively.

• Sense (positive-sense) vs antisense (negative-sense) – synonyms for coding and noncoding respectively.

• Top vs bottom – this is a convention for labeling SNPs that was invented by Illumina and was later adopted by dbSNP. It is not directly related to Fwd/Rev or (+/-). The rules for determining whether a SNP is Top/Bot are somewhat involved so I refer you to Illumina’s technical note on this.

• Watson vs Crick – synonyms of forward and reverse respectively.

To summarize:

• Forward = Plus = (+) = Positive = Watson
• Reverse = Minus = (-) = Negative = Crick
• Coding = Nontemplate = Information = Sense = Positive-sense
• Noncoding = Template = Antisense = Negative-sense

Here are the sources I used to compile the above, in decreasing order of scholarliness:

• Is ‘forward’ the same as ‘plus’?… and other adventures in SNP allele nomenclature
• The multiple personalities of Watson and Crick strands
• NCBI Molecular Biology Review
• DNA strand designations (Illumina bulletin)
• "TOP/BOT" Strand and "A/B" Allele (Illumina technical note)
• DNA strand orientation
• Sense (molecular biology)
• Coding strand

'...A gene is read in the 3' to 5' direction and so its REVERSE complementary strand in the 5' to 3' direction is the same as the mRNA transcript...'