zebrafishREFSEQ {zebrafish}R Documentation

Mappings between probe identifiers and RefSeq identifiers


The Reference Sequence (RefSeq) database contains curated non-redundant set of sequences for genomic DNA, RNA, and protein for various organisms. zebrafishREFSEQ maps probe identifiers to all the RefSeq identifiers that are mapped by NCBI to genes represented by the probe identifiers


RefSeq ids differ in format according to the type of record the ids are for as shown below:

NG_XXXXX: RefSeq accessions for genomic region (nucleotide) records

NM_XXXXX: RefSeq accessions for mRNA records

NC_XXXXX: RefSeq accessions for chromosome records

NP_XXXXX: RefSeq accessions for protein records

XR_XXXXX: RefSeq accessions for model RNAs that are not associated with protein products

XM_XXXXX: RefSeq accessions for model mRNA records

XP_XXXXX: RefSeq accessions for model protein records

Where XXXXX is a sequence of integers.

NCBI http://www.ncbi.nlm.nih.gov/RefSeq/ allows users to query the RefSeq database using RefSeq ids.

Mappings were based on data provided by:

LocusLink:ftp://ftp.ncbi.nih.gov/refseq/LocusLink/LL_tmpl.gz. Built: September 16, 2004

Package built Fri Sep 17 09:37:03 2004


NCBI http://www.ncbi.nlm.nih.gov and RefSeQ http://www.ncbi.nlm.nih.gov/RefSeq/


    # Convert the environment to a list
    xx <- as.list(zebrafishREFSEQ)
    # Remove probe ids that do not map to any RefSeq
    xx <- xx[!is.na(xx)]
    if(length(xx) > 0){
    # The RefSeq for the first two elements of XX
    # Get the first one

[Package zebrafish version 1.6.5 Index]