Gene Function Search

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HelpThis tool allows users to search for genes from various datasets available in GDC (Genomic Database for Cannabis). Users can search for genes and transcripts predicted from whole genome assemblies by accession, name, location, and/or function keyword. For keyword, enter any protein name of homologs, GO term, or InterPro term. A query is constrained by all selected items from the available options. The C. sativa assembly and annotation items are used for genes/transcripts not associated with a specific assembly (e.g. GenBank or Uniprot curated genes). The lookup table for chromosome name to NCBI sequence accession ID is available here
Cultivar
Annotation
Chromosome/Contig
between
and
Gene/Transcript Name/Accession
Keyword
(eg. terpene, cannabidiolic, ATP binding, zinc finger)

 

Data sources  (Guide to Cultivar, Annotation and Genome Assembly fields)

Cutivar Annotation Type Genome Assembly RNA-Seq/transcripts dataset Method Reference

Cannabis sativa (CBDRx, cs10)

 CS10 gene, mRNA GCF_900626175.2   NCBI RefSeq Refseq

Cannabis sativa (Purple Kush, pkv5)

 PKGMv1 gene, mRNA GCA_000230575.5   GeneMark EP gene prodection, besthit blastp with NCBI NR van Bakel 2011

Cannabis sativa (Purple Kush, pkv5)

 PKFDv1 gene, mRNA GCA_000230575.5 PRJNA73819 (SRR352195, SRR352196, SRR352198, SRR352200, SRR352201, SRR352202, SRR352203, SRR352205, SRR352208, SRR352210)

Finder gene prediction, blasp with Swissprot/Trembl, Uniref100

Banerjee 2021 10.1186/s12859-021-04120-9

 van Bakel 2011

Cannabis sativa (Finola, fnv2)

 FNFDv1 gene, mRNA GCA_003417725.2

PRJNA73819 (SRR351932,SRR351933)

PRJNA483805 (SRR7630400-SRR7630408)

Finder gene prediction, blasp with Swissprot/Trembl, Uniref100

Banerjee 2021 10.1186/s12859-021-04120-9

van Bakel 2011

Livingston 2020
Cannabis sativa (Purple Kush, pkv5) Csativa mRNA   Assembled transcripts from canSat3_transcriptome-representative.fa.gz   van Bakel 2011
Cannabis sativa (Finola, fnv2) Csativa mRNA   Assembled transcripts from finola1_transcriptome-representative.fa.gz   van Bakel 2011
Cannabis sativa L. Csativa mRNA no specific assembly C sativa mRNAs from NCBI Genes    
Cannabis sativa (CBDRx, cs10) cs10g21t gene, mRNA GCF_900626175.2 21 trichomes (trichome_rnaseq in CannSeek genotype viewer) RNASpades transcript assembly, Transdecoder /GMAP ORF detection and mapping. blastp with UniProt