IKMC Project Report - KOMP-CSD (ID: 24025)

Alg13 MGI:1914824 ENSMUSG00000041718 OTTMUSG00000018919
Pre-pipeline Designs Vectors ES Cells Mice
Mice - Phenotype Data Available

Mice

Microinjection Status Allele Allele Type ES Cell Clone Genetic Background QC Data MI/Distribution Centre
contact distributor Genotype confirmed Alg13tm1a(KOMP)Wtsi Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) EPD0161_5_G06 C57BL/6NTac;C57BL/6NTac;C57BL/6N view
( about ) 		WTSI
Southern Blot na TV Backbone Assay pass 5' LR-PCR pass
Loss of WT Allele (LOA) qPCR pass Homozygous Loss of WT Allele (LOA) SR-PCR pass Neo Count (qPCR) pass
LacZ SR-PCR pass 5' Cassette Integrity Neo SR-PCR na
Mutant Specific SR-PCR pass LoxP Confirmation pass 3' LR-PCR
Genotyping Comment -

Mutagenesis Predictions

This gene has 11 wild type transcripts, of which 1 are protein-coding. Following removal of the floxed region, 1 transcript is predicted to produce a truncated protein product of which 0 may be subject to non-sense mediated decay (NMD). The original allele for this mutation is of type 'Knockout-First - Reporter Tagged Insertion'. The table below shows the predicted structure of the gene transcripts after application of Flp and Cre (forming a 'Knockout-First, Post-Flp and Cre - Deletion, No Reporter' allele - more information on IKMC alleles can be found here). Click the 'view' button for each transcript to see the full prediction for that transcript.

Ensembl transcript id Ensembl Biotype Floxed transcript description Details
ENSMUST00000070801 protein_coding Target region does not overlap transcript
ENSMUST00000154827 nonsense_mediated_decay No protein product (NMD) view

Predicted translation: 

MKRAFVTVGTTSFDELVARVVANDCVQILESLGYNHLVLQVGRGTVVPKPFRTESFTLDVYRYKDSLKEDLQQADLVISH
AGAGSCLESLEKGKPLVVVVNEKLMNNHQFELAKQLHKEGHLFYCTCRVLSCPAPVSLLLVLLGSAKILQQLPSA*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000766239 Glyco_trans_28_C (22/121 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000454648 Glyco_trans_28_C (55/121 aa) CDS CDS
ENSMUSE00001037174 Glyco_trans_28_C (45/121 aa) CDS CDS
ENSMUSE00001000033 CDS + stop codon + UTR CDS + stop codon + UTR
ENSMUSE00000745155 UTR UTR
ENSMUSE00000812845 UTR UTR
ENSMUSE00000742469 UTR Deleted
ENSMUSE00000788715 UTR UTR
ENSMUSE00000743694 UTR UTR
ENSMUSE00000780920 UTR UTR
ENSMUSE00000787332 UTR UTR
ENSMUSE00000785658 UTR UTR
ENSMUSE00000752305 UTR UTR
ENSMUSE00000737615 UTR UTR
ENSMUSE00000772740 UTR UTR
ENSMUSE00000747919 UTR UTR
ENSMUSE00000773562 UTR UTR
ENSMUSE00000729200 UTR UTR
ENSMUSE00000793152 UTR UTR
ENSMUSE00000831448 UTR UTR
ENSMUSE00000804620 UTR UTR
ENSMUSE00000731899 UTR UTR
ENSMUSE00000753674 UTR UTR
ENSMUSE00000750956 UTR UTR
ENSMUSE00000843947 UTR UTR
ENSMUSE00000740300 UTR UTR
ENSMUSE00000834022 UTR UTR
Legend: in frame deleted frameshifted
ENSMUST00000123710 nonsense_mediated_decay Target region does not overlap transcript
ENSMUST00000145724 nonsense_mediated_decay Target region does not overlap transcript
ENSMUST00000144185 nonsense_mediated_decay Target region does not overlap transcript
ENSMUST00000149330 nonsense_mediated_decay Target region does not overlap transcript
ENSMUST00000149427 processed_transcript No analysis available: incomplete transcript
ENSMUST00000132416 processed_transcript Target region does not overlap transcript
ENSMUST00000149811 processed_transcript Target region does not overlap transcript
ENSMUST00000040338 processed_transcript Target region does not overlap transcript
ENSMUST00000139260 processed_transcript Target region does not overlap transcript
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ES Cell Clones With Conditional Potential

Genome Browsers: Ensembl (mouse) - UCSC (mouse)
Tools: Southern Blot Tool - LRPCR Genotyping Primers
ES Cell Clone Targeting Vector Allele Allele Type Parental ES Cell Line Genbank File Mouse QC Data
order EPD0161_5_G06 PRPGS00066_A_B01 Alg13tm1a(KOMP)Wtsi Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) JM8.N4 view yes view    ( about )
Production Centre
5' Screen pass LoxP Screen pass 3' Screen not confirmed
Loss of WT Allele (LOA) pass Vector Integrity -
Distribution Centre
Karyotype - Copy Number - Cells Thawed Correctly -
5' LR-PCR - 5' SR-PCR - 3' SR-PCR -
LOA - LOXP - LACZ -
Chromosome 1 - Chromosome 8a - Chromosome 8b -
Chromosome 11a - Chromosome 11b - Chromosome Y -
User/Mouse Clinic
Southern Blot - Map Test - Karyotype -
TV Backbone Assay - 5' LR-PCR pass Loss of WT Allele (LOA) -
Neo Count (qPCR) - LacZ SR-PCR - 5' Cassette Integrity -
Neo SR-PCR - Mutant Specific SR-PCR - LoxP Confirmation -
3' LR-PCR -
order EPD0161_5_A06 PRPGS00066_A_B01 Alg13tm1a(KOMP)Wtsi Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) JM8.N4 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen pass 3' Screen not confirmed
Loss of WT Allele (LOA) pass Vector Integrity -
Distribution Centre
Karyotype - Copy Number - Cells Thawed Correctly -
5' LR-PCR - 5' SR-PCR - 3' SR-PCR -
LOA fail LOXP pass LACZ pass
Chromosome 1 fail Chromosome 8a pass Chromosome 8b -
Chromosome 11a - Chromosome 11b pass Chromosome Y pass
User/Mouse Clinic
Southern Blot - Map Test - Karyotype -
TV Backbone Assay - 5' LR-PCR - Loss of WT Allele (LOA) -
Neo Count (qPCR) - LacZ SR-PCR - 5' Cassette Integrity -
Neo SR-PCR - Mutant Specific SR-PCR - LoxP Confirmation -
3' LR-PCR -
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ES Cell Clones Without Conditional Potential

Note: Mutations of type "Without Conditional Potential" are correctly targeted clones that have lost the 3' LoxP site. These mutations cannot be converted into conditional alleles.

Genome Browsers: Ensembl (mouse) - UCSC (mouse)
Tools: Southern Blot Tool - LRPCR Genotyping Primers
ES Cell Clone Targeting Vector Allele Allele Type Parental ES Cell Line Genbank File Mouse QC Data
order EPD0161_5_H06 PRPGS00066_A_B01 Alg13tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8.N4 view no view    ( about )
Production Centre
5' Screen pass LoxP Screen not confirmed 3' Screen not confirmed
Loss of WT Allele (LOA) fail Vector Integrity -
Distribution Centre
Karyotype - Copy Number - Cells Thawed Correctly -
5' LR-PCR - 5' SR-PCR - 3' SR-PCR -
LOA - LOXP - LACZ -
Chromosome 1 - Chromosome 8a - Chromosome 8b -
Chromosome 11a - Chromosome 11b - Chromosome Y -
User/Mouse Clinic
Southern Blot - Map Test - Karyotype -
TV Backbone Assay - 5' LR-PCR - Loss of WT Allele (LOA) -
Neo Count (qPCR) - LacZ SR-PCR - 5' Cassette Integrity -
Neo SR-PCR - Mutant Specific SR-PCR - LoxP Confirmation -
3' LR-PCR -

Targeting Vectors

Genome Browsers: Ensembl (mouse) - UCSC (mouse)
Tools: LRPCR Genotyping Primers
Design ID Vector Type Targeting Vector Cassette Backbone Genbank File
order 46913 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) PRPGS00066_A_B01 L1L2_Bact_P L3L4_pD223_DTA_spec view
order 46913 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) PG00066_Z_1_B01 L1L2_Bact_P L3L4_pD223_DTA_spec view
order 46913 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) PG00066_Z_1_C02 L1L2_Bact_P L3L4_pD223_DTA_spec view
order 46913 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) PG00066_Z_4_B01 L1L2_Bact_P L3L4_pD223_DTA_spec view
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Intermediate Vectors

Design ID Vector Type Intermediate Vector
46913 Knockout-First - Reporter Tagged Insertion PCS00066_A_B01