Genes Not Annotated in the Current Assemblies

S. purpuratus

cox17

This gene has been characterized in the lab of Kate Buckley by Nick Kraieski.

The cox17 protein sequence was identified using BLAST of the human COX17 protein sequence against Echinoderm protein which returned a hit to P. miniata LOC119744863/XP_038076971.1 with the description cytochrome c oxidase copper chaperone-like.

The P. miniata protein sequence, XP_038076971.1, was then BLASTed against S. purpuratus with a hit to scaffold 21, NW_022145607.1.

The H. sapiens protein sequence, AAF82569.1, hit 2 regions of scaffold 21, NW_022145607.1.

A hypothetical ORF was constructed from this location information, and then PCR amplified it from cDNA.

ORF:ATG CCT GAT AAG AAA GAA ATT GAA GGT TCC GTG AAT GGA GAG GGG GAT GCA AAG CCC AAG TTG AAG CCG TGT TGT GCT TGT CCA GAA ACG AAG AAA GTT CGA GAT GCA TG|C ATA ATG GAG AAT GGA GAA GCA GAG TGT GGT GAC CTT ATT GAA GCG CAT AAA GAA TGC ATG AGG TCT CTG GGG TTC AAC ATC TGA

*The exon junction is marked with "|" (TG|C to code for a cysteine residue).

Gene Location

The ORF is located in the minus strand of scaffold 21 (in 5.0 version)

Coding region of Exon 1: 25740048-25739939

Coding region of Exon 2: 25735568-25735484

Primers were designed to amplify a 290 bp amplicon encompassing the entire 195 bp ORF.

This gel shows in lane 1, 100 bp molecular weight ladder, lane 2, NTC (no RT) and lane 3, 24 hpf cDNA.

The amplicon was sequenced and confirmed the predicted ORF sequence.

L. variegatus

P. miniata

A. planci