Amplicon Information:

Amplicon ID:

An identifier for this amplicon.

HFA Amplicon ID:

The identifier for the corresponding amplicon from the Paro Lab.

Amplicon Nickname:

The nickname is the former term for the oligos of the amplicon. It was also used to refer to the amplicon as a whole. The name is usually based on the amplicon's intended target gene.

"R" Primer:

The primer on the 5' end of the amplicon relative to its orientation to its corresponding transcript. Because the the sequence presented here is derived from genomic sequence, the "R" primer is not necessarily on the 5' end of the amplicon as it is represented here.

"S" Primer:

The primer on the 3' end of the amplicon relative to its orientation to its corresponding transcript. Because the the sequence presented here is derived from genomic sequence, the "S" primer is not necessarily on the 3' end of the amplicon as it is represented here.

Amplicon Length:

The number of base pairs in the amplicon based on one of the amplicon's predicted sequences.

First PCR:

The results of the initial PCR to create the amplicon.

Intended 2.0 Gene Target:

The original gene target to which this amplicon was designed. If this field is blank, it indicates that this amplicon was designed to target a computationally predicted gene that was not yet publicly annotated.

Intended 3.1 Gene Target:

The symbol for the intended gene target for the amplicon based on BDGP 3.1 annotations.

Sequence:

The nucleotide sequence of the amplicon. Usually, this is based on an extraction from genomic sequence based on the alignment of the two oligos. In rare cases there may be more than one valid amplicon sequence, but this web page just shows one of these (This occurs if the amplicon targets a repetitive element instead of a typical gene.). Use the "Click here for more sequence information and fragment analysis" link to see all predicted sequences for an amplicon.

Gene Information:

• Gene information is derived by using Blast analysis of the amplicon sequence. The amplicon is "blasted" to a genomic/chromosomal database from BDGP. In this way, the position(s) of the amplicon along one or more fly chromosomes is determined and stored in the database. Position information of chromosome annotations such as genes, exons, transposable elements, etc. are also stored in the database. All genes and other annotations that the amplicon overlaps are displayed on this page.
• There can be more than one gene match per amplicon as long as all matches meet the above criteria. These genes are not necessarily the same as the original intended gene target of the primer pair.
• In some cases an overlaps a transposable element insertion rather than a gene. In this case less Flybase information is displayed.

Symbol:

The official gene symbol for this gene.

Flybase ID:

The Flybase identifier for this gene (or transposon).

Gene Name:

The gene name for this field. Corresponds to the "NAM" field of Flybase.

Amplicon Matches An Exon?:

If this value is "Yes", this indicates that there was a match to an exon from the same gene as the matching genomic annotation region. If the value is "No", this indicates that there were no matches to any exons from the gene region. This can occur if the amplicon corresponds to an intron of the gene.

Synonyms:

These are synonyms for the gene. They correspond to values of the "SYN" field from Flybase.

Old Flybase IDs:

These are deprecated Flybase identifiers for this gene. They correspond to values of the "ID2" field from Flybase.

Genomic Sequence Analysis:

FBan identifiers associated with this gene. They correspond to the "ASQ" field from Flybase:

NCBI Nucleotide Accs:

These are Genbank accessions associated with this gene based on "NA" values of the "DBA" field of Flybase.

NCBI Protein Accs:

These are GenPept accessions associated with this gene based on "PA" values of the "DBA" and "PAC" fields of Flybase.

Swiss-Prot Accs:

These are Swiss-Prot and SPTREMBL accessions associated with this gene based on the "SWP" and "SPTREMBL" values of the "PAC" field of Flybase.

Gene Ontology IDs:

Gene Ontology Database Identifiers. They are parsed from Flybase data.

Other External Accs:

These are miscellaneous accessions from the "DBA" and "PAC" fields from Flybase.

Amplicon Matches To Transcripts and Exons:

This is a list of all the annotated transcripts associated with this gene for which this amplicon overlaps. If there are none, then the "Amplicon Matches An Exon?" value will be "No".

Transcript Name:

The name of the transcript is used as a header followed by a list of overlapping exons.

Exon ## Length:

This indicates which exon of the transcript overlaps the amplicon and how long that exon is.

Amplicon Position Relative to Exon ##:

This indicates what parts of the exon the amplicon overlaps. If there are arrow symbols, the amplicon extends beyond the position of the exon.

Amplicon Matches To Genes And Other Annotations:

This is the genomic region corresponding to this gene which this amplicon has overlaps. Generally, there should be only one of these per gene. (Although an amplicon may have more than one gene to which it matches since some amplicons are designed to target transposable elements and other repeats.)

Annotation Name:

The name of the genomic region annotation is used as header.

Genomic Annotation Region Database:

The BDGP genomic annotation region database that was used by the Blast analysis. This should have the same release number as the transcript database.

Annotation Length:

This is the length of the entire genomic annotation region.

Amplicon Position Relative to Name:

This the position along the Genomic Annotation Region where the amplicon overlaps. If there are arrow symbols, the amplicon extends beyond the position of the gene region.

Chromosome Location Information:

• The chromosome location information provides information as to where in the genome the amplicon lies. A few amplicons target repetitive elements and may correspond to more than one location in the fly genome.