# How do I find the genomic H2-L sequence?

**URL:** <https://community.alliancegenome.org/t/how-do-i-find-the-genomic-h2-l-sequence/8541>\
**Category:** Scientific Discussion\
**Created:** [October 22, 2025, 2:02pm UTC](https://community.alliancegenome.org/t/how-do-i-find-the-genomic-h2-l-sequence/8541 "2025-10-22T14:02:04Z")\
**Posts on this page:** 1\
**Page:** 1

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**Author:** ![clapcote](https://community.alliancegenome.org/letter_avatar_proxy/v4/letter/c/71c47a/32.png) [@clapcote](https://community.alliancegenome.org/u/clapcote)\
**Post date:** [October 22, 2025, 2:02pm UTC](https://community.alliancegenome.org/t/how-do-i-find-the-genomic-h2-l-sequence/8541/1 "2025-10-22T14:02:04Z")

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I understand from the Mouse Genome Informatics website that the [H2-L](https://www.informatics.jax.org/marker/MGI:95912) gene is present in BALB/c but null in C57BL/6, and protects neurological tissue against _Toxoplasma gondii_ infection.

In accord with this, [Blanchard et al. (2015)](https://www.sciencedirect.com/science/article/pii/S2211124719306801) says: “Consequently, C57BL/6 mice, which are devoid of _H-2 Ld_, are a good model to study the pathogenesis of _T. gondii_ encephalitis while mice expressing _H-2 Ld_ (e.g., BALB/c or congenic B6.H-2d mice) are TE-resistant.”

Because of this, I wish to introgress the _H-2 Ld_ gene from the BALB/c strain into a KO mouse line that has a C57BL/6 genetic background. I wish to design a PCR assay that will detect the _H-2 Ld_ gene from BALB/c and distinguish it from the null allele in C57BL/6.

The problem I am having is that I am not confident that I have accessed the correct genomic DNA sequence for this gene, in order to design primers. If I design primers for the wrong gene, C57BL/6 won’t be null for it. A search for ‘H2-L’ on the UCSC Genome Browser directs me [here](https://genome.ucsc.edu/cgi-bin/hgTracks?db=mm39&lastVirtModeType=default&lastVirtModeExtraState=&virtModeType=default&virtMode=0&nonVirtPosition=&position=chr17%3A35482099%2D35485706&hgsid=3265233801_trHSMNXd1qTaQj1LKZA1i7VbaA5O), while Ensembl doesn’t seem to find ‘H2-L’ at all.

Furthermore, I cannot find the original reporting paper or any DNA evidence to support that C57BL/6 mice really are H2-L null, as briefly mentioned on the [MGI website](https://www.informatics.jax.org/marker/MGI:95912) and tables posted [here](https://www.biolegend.com/Files/Images/media_assets/support_resource/BL_MouseAlloantigens_041116.pdf) and [here](https://documents.thermofisher.com/TFS-Assets/LSG/brochures/Mouse_Haplotype_Table.pdf). Is it that the gene is deleted from the C57BL/6 genome, or another reason why it’s apparently not expressed?

Any advice you can provide to me on this would be much appreciated.

Many thanks,

Steve Clapcote

University of Leeds, UK