IKMC Project Report - KOMP-CSD (ID: 30605)

Ydjc MGI:1916351 ENSMUSG00000041774 OTTMUSG00000024793
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 Ydjctm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) EPD0408_2_C01 C57BL/6NTac;C57BL/6N-Atm1Brd/a view
( about ) 		WTSI
Southern Blot na TV Backbone Assay pass 5' LR-PCR na
Loss of WT Allele (LOA) qPCR pass 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 na 3' LR-PCR
Genotyping Comment -

Mutagenesis Predictions

This gene has 6 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). This mutation is of type 'Deletion' (more information on IKMC alleles can be found here). The table below shows the predicted structure of the gene transcripts. Click the 'view' button for each transcript to see the full prediction for that transcript.

Ensembl transcript id Ensembl Biotype Floxed transcript description Details
ENSMUST00000069064 protein_coding Residual N-terminal, unknown C-terminal view

Predicted translation: 

MAFPRVRLVVTADDFGYCPRRDEGIVEAFLAGTVTSVSLLVNGTAAESAAELAR

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000428046 Uncharacterised_UPF0249/HpnK (48/283 aa) UTR + start codon + CDS
ENSMUSE00001056515 Uncharacterised_UPF0249/HpnK (54/283 aa) CDS Deleted
ENSMUSE00001091811 Uncharacterised_UPF0249/HpnK (34/283 aa) CDS Deleted
ENSMUSE00000988842 Uncharacterised_UPF0249/HpnK (60/283 aa) CDS Deleted
ENSMUSE00000278084 Uncharacterised_UPF0249/HpnK (90/283 aa) CDS + stop codon + UTR Deleted
Legend: in frame deleted frameshifted
ENSMUST00000115706 protein_coding Residual N-terminal, novel C-terminal product view

Predicted translation: 

MAFPRVRLVVTADDFGYCPRRDEGIVEAFLAGTVTSVSLLVNGTAAESAAELARRNACSGKEVESWKLSHRKKA*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000703915 Uncharacterised_UPF0249/HpnK (48/200 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001056515 Uncharacterised_UPF0249/HpnK (54/200 aa) CDS Deleted
ENSMUSE00001091811 Uncharacterised_UPF0249/HpnK (34/200 aa) CDS Deleted
ENSMUSE00000988842 Uncharacterised_UPF0249/HpnK (60/200 aa) CDS Deleted
ENSMUSE00000703914 Uncharacterised_UPF0249/HpnK (7/200 aa) CDS Deleted
ENSMUSE00000703913 CDS CDS + stop codon + UTR
ENSMUSE00000513877 Uncharacterised_UPF0249/HpnK (1/200 aa) CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000115702 protein_coding Residual N-terminal, unknown C-terminal view

Predicted translation: 

MAFPRVRLVVTADDFGYCPRRDEGIVEAFLAGTVTSVSLLVNGTAAESAAELAR

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000703909 UTR UTR
ENSMUSE00000703908 UTR UTR
ENSMUSE00000703906 UTR UTR
ENSMUSE00000703905 Uncharacterised_UPF0249/HpnK (48/200 aa) UTR + start codon + CDS
ENSMUSE00001056515 Uncharacterised_UPF0249/HpnK (54/200 aa) CDS Deleted
ENSMUSE00001091811 Uncharacterised_UPF0249/HpnK (34/200 aa) CDS Deleted
ENSMUSE00000988842 Uncharacterised_UPF0249/HpnK (60/200 aa) CDS Deleted
ENSMUSE00000703904 Uncharacterised_UPF0249/HpnK (7/200 aa) CDS + stop codon + UTR Deleted
Legend: in frame deleted frameshifted
ENSMUST00000145198 retained_intron No analysis available: incomplete transcript
ENSMUST00000142576 retained_intron No analysis available: incomplete transcript
ENSMUST00000137267 retained_intron No analysis available: incomplete transcript
show/hide more transcripts

ES Cell Clones Without Conditional Potential (Deletions)

Note: Mutations of type "Deletion" are correctly targeted clones that have had the target exon removed. 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 EPD0408_2_C01 DPGS00168_A_F05 Ydjctm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A3.N1 view yes 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 pass LOXP - LACZ pass
Chromosome 1 pass Chromosome 8a pass Chromosome 8b -
Chromosome 11a pass Chromosome 11b pass Chromosome Y pass
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 EPD0408_2_F03 DPGS00168_A_F05 Ydjctm1(KOMP)Wtsi Deletion (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) - Vector Integrity -
Distribution Centre
Karyotype - Copy Number - Cells Thawed Correctly -
5' LR-PCR - 5' SR-PCR - 3' SR-PCR -
LOA pass LOXP - LACZ pass
Chromosome 1 pass Chromosome 8a pass Chromosome 8b -
Chromosome 11a pass Chromosome 11b pass Chromosome Y pass
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 EPD0408_2_C04 DPGS00168_A_F05 Ydjctm1(KOMP)Wtsi Deletion (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) - Vector Integrity -
Distribution Centre
Karyotype - Copy Number - Cells Thawed Correctly -
5' LR-PCR - 5' SR-PCR - 3' SR-PCR -
LOA fail LOXP - LACZ pass
Chromosome 1 pass Chromosome 8a pass Chromosome 8b -
Chromosome 11a - Chromosome 11b pass Chromosome Y pass
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 EPD0408_2_A03 DPGS00168_A_F05 Ydjctm1(KOMP)Wtsi Deletion (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) - 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 EPD0408_2_B01 DPGS00168_A_F05 Ydjctm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A3.N1 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 EPD0408_2_B03 DPGS00168_A_F05 Ydjctm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A3.N1 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 EPD0408_2_D04 DPGS00168_A_F05 Ydjctm1(KOMP)Wtsi Deletion (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) - 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 EPD0408_2_E02 DPGS00168_A_F05 Ydjctm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A3.N1 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 EPD0408_2_F04 DPGS00168_A_F05 Ydjctm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A3.N1 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 EPD0408_2_G02 DPGS00168_A_F05 Ydjctm1(KOMP)Wtsi Deletion (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) - 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 231413 Deletion (Promotor Driven Cassette) PG00168_Z_8_F05 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 231413 Deletion (Promotor Driven Cassette) PG00168_Z_3_F05 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 231413 Deletion (Promotor Driven Cassette) PG00168_Z_5_F05 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 231413 Deletion (Promotor Driven Cassette) PG00168_Z_7_F06 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 231413 Deletion (Promotor Driven Cassette) PG00168_Z_7_F05 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 231413 Deletion (Promotor Driven Cassette) PG00168_Z_4_F05 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 231413 Deletion (Promotor Driven Cassette) PG00168_Z_6_F05 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 231413 Deletion (Promotor Driven Cassette) PG00168_Z_1_F05 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 231413 Deletion (Promotor Driven Cassette) PG00168_Z_2_F05 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 231413 Deletion (Promotor Driven Cassette) DPGS00168_A_F05 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
show/hide more targeting vectors

Intermediate Vectors

Design ID Vector Type Intermediate Vector
231413 Deletion PCS00168_A_F05