Hi Si-Yu,

I hope I got this correctly, but this is the 3'UTR of the hemoglobin ß, adult s chain :

accccc tttcctgctc ttgcctgtga acaatggtta attgttccca agagagcatc tgtcagttgt tggcaaaatg ataaagacat ttgaaaatct gtcttctgac aaataaaaag catttatttc actgcaatga tgtttt

in a BC57BL/6J encoded by the HBB-bs gene

this would be the 3'UTR of the hemoglobin ß, adult t chain:

gc cccttttctg ctattgtcta tgcacaaagg ttatatgtcc cctagagaaa aactgtcaat tgtggggaaa tgatgaagac ctttgggcat ctagctttta tctaataaat gatatttact gtcatctcaa

in a BC57BL/6J encoded by the HBB-bt gene

I haven't checked is but I think the gene sequence is very similar (or the same) but the 3'UTR differs

To check this out use the following links:

https://www.ncbi.nlm.nih.gov/nuccore/NC_000073.7?from=103475730&to=103477135&report=genbank&strand=true

and

https://www.ncbi.nlm.nih.gov/nuccore/NC_000073.7?from=103461731&to=103463130&report=genbank&strand=true

You can identifying the 3' UTR by comparing the Exons with the CD (you can mark this on the website)

Please be aware that

"In mouse, two major strain-specific haplotypes of the beta-globin gene cluster are found - a "single" haplotype found in C57BL/-type strains, which includes two highly similar adult beta-globin genes, beta s and beta t, and a "diffuse" haplotype found in strains such as BALB/c and 129Sv, which includes two somewhat diverse adult beta-globin genes, beta-major and beta-minor. This gene represents the beta t adult gene found in the "single" haplotype. Primary chromosome 7 of the mouse reference genome assembly, which is derived from C57BL/6 strain mice, represents the "single" haplotype, while the "diffuse" haplotype is represented in the reference genome collection by the BALB/c strain alternate contig, NT_095534.1.

Check with which gene you are truly working - However I thinks most likely for your approach both UTRs should work.

I hope this helps

Dörthe Andrea Kesper Thanks, Dörthe. It helps a lot! I also found the 3'UTR sequence in the following link: https://www.ncbi.nlm.nih.gov/nuccore/NM_001278161.1?report=graph

According to the online search, in the sequence at this link, the sequence after the stop codon is the 3'UTR part of Hbb-b1.

There is a little difference between your sequence (3'UTR of the hemoglobin ß, adult s chain) and this sequence.

But as what you said, all these sequences should be able to achieve my experimental purpose?

Thank you again!

Hi Si-Yu,

I have checked the sequence you have provided - the 3'UTR of this sequence is very similar to 3'UTR the hemoglobin ß, adult s chain in the C57BL/6J mouse background.

There is also a minor sequence deviation shortly before the stop codon (AGVATALAHKYH instead of AGVAAALAHKYH) however this might be due to variation because of another mouse strain.

This is what is mentioned on the website of the sequence you found:

"In mouse, two major strain-specific haplotypes of the beta-globin gene cluster are found - a 'single' haplotype found in C57BL/-type strains, which includes two highly similar adult beta-globin genes, beta s and beta t, and a 'diffuse' haplotype found in strains such as BALB/c and 129Sv, which includes two somewhat diverse adult beta-globin genes, beta-major and beta-minor. This gene represents the beta-major adult gene found in the 'diffuse' haplotype. Primary chromosome 7 of the mouse reference genome assembly, which is derived from C57BL/6 strain mice, represents the 'single' haplotype, while the 'diffuse' haplotype is represented in the reference genome collection by the BALB/c strain alternate contig, NT_095534.1. [provided by RefSeq, May 2013]."

As this sequence represent the "diffuse" haplotype I would conclude that the sequence you found comes from Balb/c mice.

I think all the sequences should be able to achieve you experimental goal - however small variations can not be excluded.

To be on the save site you might check your genomic background/the genomic background your sequence is derived from and (C57BL/-type mice) (BALB/c or 129SV type mice) choose the 3'UTR accordingly.

If you have additional question I am happy to help.

KR Dörthe