IKMC Project Report - KOMP-CSD (ID: 47646)

H1foo MGI:2176207 ENSMUSG00000042279 OTTMUSG00000033828
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 H1footm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) EPD0228_7_B01 C57BL/6N;C57BL/6N;C57BL/6N view
( about ) 		TCP/UCD
Southern Blot na TV Backbone Assay na 5' LR-PCR pass
Loss of WT Allele (LOA) qPCR na Homozygous Loss of WT Allele (LOA) SR-PCR na Neo Count (qPCR) na
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 3 are protein-coding. Following removal of the floxed region, 3 transcripts are predicted to produce a truncated protein product of which 3 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
ENSMUST00000037831 protein_coding No protein product (NMD) view

Predicted translation: 

MAPGSVSSVSSSSFPSRDTSPSGSCGLPGADKPASSKAQDKESLCPQSRQGSCRCQGDRLQEIWIAEERPSWQGHDGERA
EEEGLPLQGSHTGDGT*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000307154 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001079661 Histone_H1/H5 (74/76 aa) CDS Deleted
ENSMUSE00000979132 Histone_H1/H5 (2/76 aa) CDS CDS + stop codon + UTR
ENSMUSE00001068296 CDS
ENSMUSE00001024717 CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000161617 protein_coding No protein product (NMD) view

Predicted translation: 

MAPGSVSSVSSSSFPSRDTSPSGSCGLPGADKPASSKAQDKESLCPQSRQGSCRCQGDRLQEIWIAEERPSWQGHDGERA
EEEGLPLQGSHTGDGT*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000307154 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001079661 Histone_H1/H5 (74/76 aa) CDS Deleted
ENSMUSE00000979132 Histone_H1/H5 (2/76 aa) CDS CDS + stop codon + UTR
ENSMUSE00000857695 CDS
ENSMUSE00001024717 CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000161969 protein_coding No protein product (NMD) view

Predicted translation: 

MAPGSVSSVSSSSFPSRDTSPSGSCGLPGADKPASSKAQDKESLCPQSRQGSCRCQGDRLQEIWIAEERPSWQGHDGERA
EEEGLPLQGSHTGDGT*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000307154 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001079661 Histone_H1/H5 (74/76 aa) CDS Deleted
ENSMUSE00000979132 Histone_H1/H5 (2/76 aa) CDS CDS + stop codon + UTR
ENSMUSE00000849924 CDS
ENSMUSE00000858804 CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000162084 nonsense_mediated_decay No protein product (NMD) view

Predicted translation: 

MAPGSVSSVSSSSFPSRDTSPSGSCGLPGADKPGTTSFCSPRLIWK*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000307154 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000869415 CDS + stop codon + UTR CDS + stop codon + UTR
ENSMUSE00000989990 UTR Deleted
ENSMUSE00001072519 UTR UTR
ENSMUSE00001005544 UTR UTR
ENSMUSE00001031179 UTR UTR
Legend: in frame deleted frameshifted
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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 EPD0228_7_B01 PRPGS00093_A_C03 H1footm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8.N4 view yes view    ( about )
Production Centre
5' Screen not attempted LoxP Screen pass 3' Screen pass
Loss of WT Allele (LOA) fail Vector Integrity -
Distribution Centre
Karyotype 0.8 - 0.71 Copy Number pass 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 EPD0228_7_F02 PRPGS00093_A_C03 H1footm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8.N4 view no view    ( about )
Production Centre
5' Screen not attempted LoxP Screen pass 3' Screen pass
Loss of WT Allele (LOA) fail Vector Integrity -
Distribution Centre
Karyotype 0.8 - 0.71 Copy Number pass 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 EPD0873_5_B02 PG00093_Z_1_C03 H1footm2a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen pass 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 EPD0873_5_E02 PG00093_Z_1_C03 H1footm2a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen pass 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 EPD0873_5_G03 PG00093_Z_1_C03 H1footm2a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen pass 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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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 EPD0873_5_A03 PG00093_Z_1_C03 H1footm2e(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 EPD0873_5_E03 PG00093_Z_1_C03 H1footm2e(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 EPD0873_5_E04 PG00093_Z_1_C03 H1footm2e(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 -
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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 89538 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00093_Z_2_C03 L1L2_Bact_P L4L3_pD223_DTA_spec view
order 89538 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00093_Z_3_C03 L1L2_Bact_P L4L3_pD223_DTA_spec view
order 89538 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PRPGS00093_A_C03 L1L2_Bact_P L4L3_pD223_DTA_spec view
order 89538 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00093_Z_1_C03 L1L2_Bact_P L4L3_pD223_DTA_spec view
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Intermediate Vectors

Design ID Vector Type Intermediate Vector
89538 Knockout First, Reporter-tagged insertion with conditional potential PCS00093_A_C03
89538 Knockout First, Reporter-tagged insertion with conditional potential PCS00093_B_C03