How to get the position of a transcript on chromosome with ncbi refseq_ncrna id?

Question

[hanchuanzhiyu]

I have a list of ncbi refseq_ncrna id, for example NR_046233, NR_015516, NR_102721...I need the position of the transcripts on chromosome.

I have tried to convert the refseq id to ensembl id, and use R package ensembldb to get the chromosome location of the transcript, but a lot of refseq_ncrna ids don't have corresponding ensembl id.

Is there any way to directly get the chromosome location of the transcript use refseq_ncrna id?

Answer 1

[c.chakraborty]

Use BioMart from ENSEMBL. 1. Go to the ENSEMBL BioMART tool. 2.Choose database- usually I choose ENSEMBL genes 3.On the right hand, you will find Filters, click on it and then choose genes. 4. In the second drop down you will find - Input External references. Tick this one. On the left, there is a drop down box, select RefSeq ncRNA ID (there you have it! :)), and paste all the RefSeq IDs of nc RNAs of your interest. 5. Then on the left you will see attributes, click on that. 6. Then select Gene- here you can select chromosome/scaffold name, strand, transcription start site or length of transcript. And hopefully now you will have almost all information for your ncRNAs.

[hanchuanzhiyu]

Thanks a lot! although it still doesn't work for ncRNAs without ensembl transcript id

[c.chakraborty]

Did you choose Refseq ncRNA ID from the dropbox menu?

[hanchuanzhiyu]

Yes I did, and it only gives results for those with ensemble transcript ids

Answer 2

[GenoMax]

A couple of different options using Entrezdirect.

$ esearch -db nuccore -query "NR_015516" | elink -target gene | efetch -format docsum | xtract -pattern DocumentSummary -element AssemblyAccVer,ChrAccVer,ChrStart,ChrStop
GCF_000001635.24        GCF_000001635.24        GCF_000001635.23        GCF_000001635.23        GCF_000002165.2 GCF_000001635.18        GCF_000002165.2 NC_000075.6     NC_000075.6     NW_004450259.NC_000075.6      NW_004450259.2  AC_000031.1     NT_166313.1     AC_000031.1     124423250       124423250       124423250       191494  124423250       170853  124647848       53408   124648095    124424855        124424855       194625  124424855       167722  124651402       56292   124651402

or

$ esearch -db nuccore -query "NR_015516" | elink -target gene | efetch -format ft

1. 4930526I15Rik
Official Symbol: 4930526I15Rik and Name: RIKEN cDNA 4930526I15 gene [Mus musculus (house mouse)]
Other Aliases: 1600027J15Rik
Chromosome: 9; Location: 9
Annotation: Chromosome 9 NC_000075.6 (124423251..124424856)
ID: 75135

[hanchuanzhiyu]

Thanks! I tried this, and it works for some of the ncRNAs

$ esearch -db nuccore -query "NR_102721" | elink -target gene | efetch -format ft

1. 4930526I15Rik
Official Symbol: 4930526I15Rik and Name: RIKEN cDNA 4930526I15 gene [Mus musculus (house mouse)]
Other Aliases: 1600027J15Rik
Chromosome: 9; Location: 9
Annotation: Chromosome 9 NC_000075.6 (124423251..124424856)
ID: 75135

but shows a little information for others

$ esearch -db nuccore -query "NR_046233"  | elink -target gene | efetch -format ft

1. Rn45s
45S pre-ribosomal RNA [Mus musculus (house mouse)]
Chromosome: 17
ID: 100861531

I guess it just doesn't have the information of chromosome location for some of the ncRNAs.