IKMC Project Report - KOMP-CSD (ID: 100234)

Cd40 MGI:88336 ENSMUSG00000017652 OTTMUSG00000016424
Pre-pipeline Designs Vectors ES Cells Mice
ES Cells - Targeting Confirmed

Mice no data available

Mutagenesis Predictions

This gene has 7 wild type transcripts, of which 4 are protein-coding. Following removal of the floxed region, 4 transcripts are 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
ENSMUST00000017799 protein_coding Residual C-terminal product view

Predicted translation: 

MRALLVIPVVMGILITIFGVFLYIKKVVKKPKDNEILPPAARRQDPQEMEDYPGHNTAAPVQETLHGCQPVTQEDGKESR
ISVQERQVTDSIALRPLV*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00001024540 UTR + start codon + CDS
ENSMUSE00000973574 TNFR/NGFR_Cys_rich_reg (18/34 aa) CDS Deleted
ENSMUSE00001036418 TNFR/NGFR_Cys_rich_reg (17/34 aa) CDS Deleted
ENSMUSE00001071475 CDS Deleted
ENSMUSE00001088445 CDS Deleted
ENSMUSE00001088443 CDS
ENSMUSE00001029545 CDS UTR + start codon + CDS
ENSMUSE00000967725 CDS CDS
ENSMUSE00000801038 CDS + stop codon + UTR CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000081310 protein_coding Novel C-terminal product view

Predicted translation: 

MGLLVDSGLKSRMRALLVIPVVMGILITIFGVFLYIKKVVKKPKDNEILPPAARR

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000797119 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000973574 TNFR/NGFR_Cys_rich_reg (18/34 aa) CDS Deleted
ENSMUSE00001036418 TNFR/NGFR_Cys_rich_reg (17/34 aa) CDS Deleted
ENSMUSE00001071475 CDS Deleted
ENSMUSE00001088445 CDS Deleted
ENSMUSE00001003811 CDS CDS
ENSMUSE00001089404 CDS + stop codon + UTR CDS
ENSMUSE00000767996 UTR CDS
Legend: in frame deleted frameshifted
ENSMUST00000073707 protein_coding Novel C-terminal product view

Predicted translation: 

MGLLVDSAVRIRTWRSYRKERVRLMSSVKRWSRNQRIMRSYPLRLDGKIPRRWKIIPVITPLLQCRRRCTGVSLSHRRMV
KRVASQCRSGR*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000422617 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000973574 TNFR/NGFR_Cys_rich_reg (18/34 aa) CDS Deleted
ENSMUSE00001036418 TNFR/NGFR_Cys_rich_reg (17/34 aa) CDS Deleted
ENSMUSE00001071475 CDS Deleted
ENSMUSE00001088445 CDS Deleted
ENSMUSE00001088443 CDS CDS
ENSMUSE00000967725 CDS CDS
ENSMUSE00000550700 CDS + stop codon + UTR CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000140951 protein_coding No analysis available: incomplete transcript
ENSMUST00000146825 nonsense_mediated_decay No analysis available: incomplete transcript
ENSMUST00000153105 retained_intron No analysis available: incomplete transcript
ENSMUST00000154443 processed_transcript No analysis available: incomplete 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 EPD0901_3_A02 HTGR06019_A_3_D10 Cd40tm1a(KOMP)Wtsi Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen pass 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 -

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 EPD0901_3_E01 HTGR06019_A_3_D10 Cd40tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen pass LoxP Screen not confirmed 3' Screen not confirmed
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 EPD0901_3_H02 HTGR06019_A_3_D10 Cd40tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen pass LoxP Screen not confirmed 3' Screen not confirmed
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 EPD0901_3_C02 HTGR06019_A_3_D10 Cd40tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen pass LoxP Screen not confirmed 3' Screen not confirmed
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 EPD0901_3_F01 HTGR06019_A_3_D10 Cd40tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen pass LoxP Screen not confirmed 3' Screen not confirmed
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 -
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Targeting Vectors

Genome Browsers: Ensembl (mouse) - UCSC (mouse)
Tools: LRPCR Genotyping Primers
Design ID Vector Type Targeting Vector Cassette Backbone Genbank File
order 209292 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) HTGR06019_A_3_D10 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 209292 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) HTGR06019_A_2_D10 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 209292 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) HTGR06019_A_8_D10 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 209292 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) HTGR06019_A_6_D10 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 209292 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) HTGR06019_A_7_D10 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 209292 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) HTGR06019_A_5_D10 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 209292 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) HTGR06019_A_4_D10 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 209292 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) HTGRS06019_A_D10 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 209292 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) HTGR06019_A_1_D10 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
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Intermediate Vectors

Design ID Vector Type Intermediate Vector
209292 Knockout-First - Reporter Tagged Insertion PCS06019_A_D10