IKMC Project Report - KOMP-CSD (ID: 49567)

Usf1 MGI:99542 ENSMUSG00000026641 OTTMUSG00000030990
Pre-pipeline Designs Vectors ES Cells Mice
ES Cells - Targeting Confirmed

Mice no data available

Mutagenesis Predictions

This gene has 10 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 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
ENSMUST00000161241 protein_coding Residual N-terminal, unknown C-terminal view

Predicted translation: 

MKGQQKTAETEEGTVQIQEGAVATGEDPTSVAIASIQSAATFPDPNVKYVFRTENGGQVMYRVIQVSEGQLDGQTEGSGA
ISGYPATQSMTQ

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000863220 UTR UTR
ENSMUSE00000992743 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001086528 CDS CDS
ENSMUSE00000987028 CDS CDS
ENSMUSE00001062071 CDS CDS
ENSMUSE00000992734 CDS Deleted
ENSMUSE00001093195 CDS Deleted
ENSMUSE00001032327 HLH_DNA-bd (7/55 aa) CDS Deleted
ENSMUSE00001088818 HLH_DNA-bd (49/55 aa) CDS Deleted
ENSMUSE00000865893 CDS + stop codon + UTR Deleted
Legend: in frame deleted frameshifted
ENSMUST00000167546 protein_coding Residual N-terminal, unknown C-terminal view

Predicted translation: 

MKGQQKTAETEEGTVQIQEGAVATGEDPTSVAIASIQSAATFPDPNVKYVFRTENGGQVMYRVIQVSEGQLDGQTEGSGA
ISGYPATQSMTQ

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000888634 UTR UTR
ENSMUSE00000992743 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001086528 CDS CDS
ENSMUSE00000987028 CDS CDS
ENSMUSE00001062071 CDS CDS
ENSMUSE00000992734 CDS Deleted
ENSMUSE00001093195 CDS Deleted
ENSMUSE00001032327 HLH_DNA-bd (7/55 aa) CDS Deleted
ENSMUSE00001088818 HLH_DNA-bd (49/55 aa) CDS Deleted
ENSMUSE00000884056 CDS + stop codon + UTR Deleted
Legend: in frame deleted frameshifted
ENSMUST00000160486 protein_coding Residual N-terminal, unknown C-terminal view

Predicted translation: 

MKGQQKTAETEEGTVQIQEGAVATGEDPTSVAIASIQSAATFPDPNVKYVFRTENGGQVMYRVIQVSEGQLDGQTEGSGA
ISGYPATQSMTQ

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000425361 UTR UTR
ENSMUSE00000992743 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001086528 CDS CDS
ENSMUSE00000987028 CDS CDS
ENSMUSE00001062071 CDS CDS
ENSMUSE00000992734 CDS Deleted
ENSMUSE00001093195 CDS Deleted
ENSMUSE00001032327 HLH_DNA-bd (7/55 aa) CDS Deleted
ENSMUSE00000870083 HLH_DNA-bd (49/55 aa) CDS + stop codon + UTR Deleted
Legend: in frame deleted frameshifted
ENSMUST00000159207 protein_coding No analysis available: incomplete transcript
ENSMUST00000001284 nonsense_mediated_decay Residual N-terminal, unknown C-terminal view

Predicted translation: 

MKGQQKTAETEEGTVQIQEGAVATGEDPTSVAIASIQSAATFPDPNVK*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000863220 UTR UTR
ENSMUSE00000992743 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001086528 CDS CDS
ENSMUSE00000872242 CDS CDS
ENSMUSE00000965554 CDS + stop codon + UTR CDS + stop codon + UTR
ENSMUSE00000971414 UTR Deleted
ENSMUSE00001064679 UTR Deleted
ENSMUSE00001046012 UTR Deleted
ENSMUSE00001068756 UTR Deleted
ENSMUSE00000658694 UTR Deleted
Legend: in frame deleted frameshifted
ENSMUST00000160335 retained_intron No analysis available: incomplete transcript
ENSMUST00000159371 retained_intron No analysis available: incomplete transcript
ENSMUST00000159929 retained_intron No analysis available: incomplete transcript
ENSMUST00000161297 processed_transcript Target region does not overlap transcript
ENSMUST00000159466 retained_intron Target region does not overlap 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 EPD0246_8_D03 PRPGS00100_B_A01 Usf1tm1a(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 EPD0246_8_G03 PRPGS00100_B_A01 Usf1tm1a(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 EPD0246_8_G02 PRPGS00100_B_A01 Usf1tm1a(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

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 EPD0246_8_E04 PRPGS00100_B_A01 Usf1tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen not confirmed 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 -
order EPD0246_8_F02 PRPGS00100_B_A01 Usf1tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A1.N3 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 EPD0246_8_C03 PRPGS00100_B_A01 Usf1tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen pass 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 -
order EPD0246_8_H02 PRPGS00100_B_A01 Usf1tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A1.N3 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 EPD0246_8_G04 PRPGS00100_B_A01 Usf1tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A1.N3 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 EPD0246_8_D04 PRPGS00100_B_A01 Usf1tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A1.N3 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 EPD0246_8_E02 PRPGS00100_B_A01 Usf1tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen not confirmed 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 -
order EPD0246_8_H01 PRPGS00100_B_A01 Usf1tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen pass 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 -
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 96672 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PRPGS00100_B_A01 L1L2_Pgk_P L3L4_pD223_DTA_T_spec view

Intermediate Vectors

Design ID Vector Type Intermediate Vector
96672 Knockout First, Reporter-tagged insertion with conditional potential PCS00100_B_A01