IKMC Project Report - EUCOMM (ID: 24365)

Brdt MGI:1891374 ENSMUSG00000029279 OTTMUSG00000017134
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 Brdttm1a(EUCOMM)Wtsi Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) EPD0126_2_D06 C57BL/6Dnk;C57BL/6Brd-Tyrc-Brd;C57BL/6N-Atm1Brd/a view
( about ) 		WTSI/Oulu
Southern Blot na TV Backbone Assay pass 5' LR-PCR na
Loss of WT Allele (LOA) qPCR na 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 4 wild type transcripts, of which 2 are protein-coding. Following removal of the floxed region, 2 transcripts are predicted to produce a truncated protein product of which 2 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
ENSMUST00000031215 protein_coding No protein product (NMD) view

Predicted translation: 

MSLPSRQTAIVNPPPPEYINTKKSGRLTNQLQFLQRVVLKALWKHGFSWPFQQPVDAVKLKLPDYYTIIKTPMDLNTIKK
RLENKYYEKASECIEDFNTMFSNCYLYNKISNKR*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000856958 UTR UTR
ENSMUSE00000305190 UTR UTR
ENSMUSE00000305184 Bromodomain (25/82 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000867267 Bromodomain (46/82 aa) CDS CDS
ENSMUSE00000851241 Bromodomain (11/82 aa) CDS Deleted
ENSMUSE00000851576 CDS CDS + stop codon + UTR
ENSMUSE00000187673 Bromodomain (47/88 aa) CDS
ENSMUSE00000187653 Bromodomain (41/88 aa) CDS
ENSMUSE00000187663 CDS
ENSMUSE00000187679 CDS
ENSMUSE00000187668 CDS
ENSMUSE00000187643 CDS
ENSMUSE00000515246 CDS
ENSMUSE00001068078 CDS
ENSMUSE00000187677 CDS
ENSMUSE00001089223 CDS
ENSMUSE00000541322 CDS
ENSMUSE00000982955 CDS
ENSMUSE00000509282 CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000112677 protein_coding No protein product (NMD) view

Predicted translation: 

MSLPSRQTAIVNPPPPEYINTKKSGRLTNQLQFLQRVVLKALWKHGFSWPFQQPVDAVKLKLPDYYTIIKTPMDLNTIKK
RLENKYYEKASECIEDFNTMFSNCYLYNKISNKR*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000692703 UTR UTR
ENSMUSE00000305190 UTR UTR
ENSMUSE00000305184 Bromodomain (25/82 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000867267 Bromodomain (46/82 aa) CDS CDS
ENSMUSE00000851241 Bromodomain (11/82 aa) CDS Deleted
ENSMUSE00000851576 CDS CDS + stop codon + UTR
ENSMUSE00000692690 Bromodomain (49/49 aa) CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000162804 processed_transcript Target region does not overlap transcript
ENSMUST00000161377 processed_transcript Target region does not overlap transcript
show/hide more transcripts

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 EPD0126_2_D06 PRPGS00056_A_C01 Brdttm1a(EUCOMM)Wtsi Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) JM8A1 view yes view    ( about )
Production Centre
5' Screen not attempted 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 EPD0126_2_C08 PRPGS00056_A_C01 Brdttm1a(EUCOMM)Wtsi Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) JM8A1 view no view    ( about )
Production Centre
5' Screen not attempted 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 EPD0126_2_D05 PRPGS00056_A_C01 Brdttm1a(EUCOMM)Wtsi Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) JM8A1 view no view    ( about )
Production Centre
5' Screen not attempted 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 EPD0126_2_G07 PRPGS00056_A_C01 Brdttm1a(EUCOMM)Wtsi Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) JM8A1 view no view    ( about )
Production Centre
5' Screen not attempted 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 EPD0126_2_G08 PRPGS00056_A_C01 Brdttm1a(EUCOMM)Wtsi Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) JM8A1 view no view    ( about )
Production Centre
5' Screen not attempted 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 -
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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 EPD0126_2_E05 PRPGS00056_A_C01 Brdttm1e(EUCOMM)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A1 view no view    ( about )
Production Centre
5' Screen not attempted 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 EPD0126_2_E07 PRPGS00056_A_C01 Brdttm1e(EUCOMM)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8A1 view no view    ( about )
Production Centre
5' Screen not attempted 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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Targeting Vectors

Genome Browsers: Ensembl (mouse) - UCSC (mouse)
Tools: LRPCR Genotyping Primers
Design ID Vector Type Targeting Vector Cassette Backbone Genbank File
order 44475 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) PG00056_Z_4_C01 L1L2_Bact_P L3L4_pD223_DTA_spec view
order 44475 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) PG00056_Z_3_C01 L1L2_Bact_P L3L4_pD223_DTA_spec view
order 44475 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) PG00056_Z_2_C01 L1L2_Bact_P L3L4_pD223_DTA_spec view
order 44475 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) PG00056_Z_1_C01 L1L2_Bact_P L3L4_pD223_DTA_spec view
order 44475 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) PRPGS00056_A_C01 L1L2_Bact_P L3L4_pD223_DTA_spec view
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Intermediate Vectors

Design ID Vector Type Intermediate Vector
44475 Knockout-First - Reporter Tagged Insertion PCS00056_A_C01