IKMC Project Report - KOMP-CSD (ID: 39707)

Msx1 MGI:97168 ENSMUSG00000048450 OTTMUSG00000021309
Pre-pipeline Designs Vectors ES Cells Mice
Mice - Genotype confirmed

Mice

Microinjection Status Allele Allele Type ES Cell Clone Genetic Background QC Data MI/Distribution Centre
contact distributor Genotype confirmed Msx1tm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) EPD0334_7_D05 C57BL/6N;C57BL/6NJ;C57BL/6N-Atm1Brd/a view
( about ) 		JAX/UCD
Southern Blot na TV Backbone Assay na 5' LR-PCR na
Loss of WT Allele (LOA) qPCR pass Homozygous Loss of WT Allele (LOA) SR-PCR na Neo Count (qPCR) na
LacZ SR-PCR na 5' Cassette Integrity Neo SR-PCR na
Mutant Specific SR-PCR na LoxP Confirmation na 3' LR-PCR
Genotyping Comment -

Mutagenesis Predictions

This gene has 1 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 with conditional potential'. 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
ENSMUST00000063116 protein_coding Residual N-terminal, unknown C-terminal view

Predicted translation: 

MAPAAAMTSLPLGVKVEDSAFAKPAGGGVGQAPGAAAATATAMGTDEEGAKPKVPASLLPFSVEALMADHRKPGAKESVL
VASEGAQAAGGSVQHLGTRPGSLGAPDAPSSPRPLGHFSVGGLLKLPEDALVKAESPEKLDRTPWMQSPRFSPPPA

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000355418 UTR + start codon + CDS
ENSMUSE00000376402 Homeodomain (57/57 aa) CDS + stop codon + UTR Deleted
Legend: in frame deleted frameshifted

ES Cell Clones With Knockout First Mutation (Reporter Tagged Insertion 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 EPD0334_7_D05 PRPGS00162_B_G04 Msx1tm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8A1.N3 view yes view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen pass 3' Screen pass
Loss of WT Allele (LOA) - Vector Integrity pass
Distribution Centre
Karyotype 0.8 - 0.71 Copy Number pass Cells Thawed Correctly -
5' LR-PCR pass 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 -
order EPD0334_7_A05 PRPGS00162_B_G04 Msx1tm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen pass 3' Screen pass
Loss of WT Allele (LOA) - Vector Integrity pass
Distribution Centre
Karyotype 0.7 - 0.61 Copy Number pass Cells Thawed Correctly -
5' LR-PCR pass 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 -
order EPD0334_7_E06 PRPGS00162_B_G04 Msx1tm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen pass 3' Screen pass
Loss of WT Allele (LOA) - Vector Integrity pass
Distribution Centre
Karyotype 0.5 - 0.41 Copy Number pass Cells Thawed Correctly -
5' LR-PCR pass 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 -
order EPD0334_7_C07 PRPGS00162_B_G04 Msx1tm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen pass 3' Screen pass
Loss of WT Allele (LOA) - Vector Integrity pass
Distribution Centre
Karyotype - Copy Number pass Cells Thawed Correctly -
5' LR-PCR fail 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 -
order EPD0334_7_F07 PRPGS00162_B_G04 Msx1tm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen pass 3' Screen pass
Loss of WT Allele (LOA) - 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 -
order EPD0334_7_H07 PRPGS00162_B_G04 Msx1tm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen pass 3' Screen pass
Loss of WT Allele (LOA) - 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 -
show/hide more ES cells

Targeting Vectors

Genome Browsers: Ensembl (mouse) - UCSC (mouse)
Tools: LRPCR Genotyping Primers
Design ID Vector Type Targeting Vector Cassette Backbone Genbank File
order 221080 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00162_Y_6_G04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 221080 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00162_Z_6_G04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 221080 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00162_Y_1_G03 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 221080 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00162_Y_1_H04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 221080 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00162_Z_5_H04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 221080 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00162_Z_1_H04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 221080 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PRPGS00162_A_G04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 221080 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00162_Y_5_H04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 221080 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PRPGS00162_B_G04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
show/hide more targeting vectors

Intermediate Vectors

Design ID Vector Type Intermediate Vector
221080 Knockout First, Reporter-tagged insertion with conditional potential PCS00162_A_G04