IKMC Project Report - KOMP-CSD (ID: 24629)

Foxa2 MGI:1347476 ENSMUSG00000037025 OTTMUSG00000015678
Pre-pipeline Designs Vectors ES Cells Mice
ES Cells - Targeting Confirmed

Mice no data available

Mutagenesis Predictions

This gene has 4 wild type transcripts, of which 3 are protein-coding. Following removal of the floxed region, 3 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 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
ENSMUST00000047315 protein_coding Residual N-terminal, unknown C-terminal view

Predicted translation: 

MLGAVKMEGHEPSDWSSYYAEPE

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000247098 UTR UTR
ENSMUSE00000247095 Fork-head_N (6/142 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000682215 TF_fork_head (96/96 aa) | Fork-head_N (136/142 aa) | Forkhead_box_C (75/75 aa) CDS + stop codon + UTR Deleted
Legend: in frame deleted frameshifted
ENSMUST00000109964 protein_coding Residual N-terminal, unknown C-terminal view

Predicted translation: 

MHSASSMLGAVKMEGHEPSDWSSYYAEPE

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000682216 Fork-head_N (6/142 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000682215 TF_fork_head (96/96 aa) | Fork-head_N (136/142 aa) | Forkhead_box_C (75/75 aa) CDS + stop codon + UTR Deleted
Legend: in frame deleted frameshifted
ENSMUST00000172928 protein_coding Residual N-terminal, unknown C-terminal view

Predicted translation: 

MLGAVKMEGHEPSDWSSYYAEPE

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000937018 UTR UTR
ENSMUSE00000247095 TF_fork_head (5/62 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000927274 Forkhead_box_C (75/75 aa) | TF_fork_head (57/62 aa) CDS + stop codon + UTR Deleted
Legend: in frame deleted frameshifted
ENSMUST00000146242 processed_transcript No analysis available: incomplete transcript
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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 EPD0379_1_A04 PRPGS00162_A_G02 Foxa2tm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (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) pass Vector Integrity pass
Distribution Centre
Karyotype - Copy Number pass Cells Thawed Correctly -
5' LR-PCR pass 5' SR-PCR - 3' SR-PCR pass
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 EPD0966_4_C06 PG00162_Y_6_G02 Foxa2tm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen - LoxP Screen not confirmed 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 -
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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 EPD0379_1_H04 PRPGS00162_A_G02 Foxa2tm1e(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 pass
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 - 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 EPD0379_1_H01 PRPGS00162_A_G02 Foxa2tm1e(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 pass
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 - 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 EPD0379_1_B04 PRPGS00162_A_G02 Foxa2tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen not confirmed 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 - 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 EPD0379_1_C01 PRPGS00162_A_G02 Foxa2tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen no reads detected LoxP Screen no reads detected 3' Screen no reads detected
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 - 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 EPD0379_1_G03 PRPGS00162_A_G02 Foxa2tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen not confirmed 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 - 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 214649 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00162_Z_6_G02 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 214649 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PRPGS00162_A_G02 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 214649 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00162_Y_6_G02 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 214649 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PRPGS00162_B_G02 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 214649 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00162_Y_5_G02 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 214649 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00162_Y_7_G02 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
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Intermediate Vectors

Design ID Vector Type Intermediate Vector
214649 Knockout First, Reporter-tagged insertion with conditional potential PCS00162_A_G02