IKMC Project Report - KOMP-CSD (ID: 35680)

Yars MGI:2147627 ENSMUSG00000028811 OTTMUSG00000009617
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
currently unavailable Genotype confirmed Yarstm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) EPD0170_3_C06 C57BL/6NCrl;B6N-Tyrc/BrdCrCrl;C57BL/6N view
( about ) 		TCP
Southern Blot na TV Backbone Assay na 5' LR-PCR pass
Loss of WT Allele (LOA) qPCR pass Homozygous Loss of WT Allele (LOA) SR-PCR na Neo Count (qPCR) na
LacZ SR-PCR pass 5' Cassette Integrity Neo SR-PCR pass
Mutant Specific SR-PCR pass LoxP Confirmation pass 3' LR-PCR
Genotyping Comment -

Mutagenesis Predictions

This gene has 9 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 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
ENSMUST00000106054 protein_coding No protein product (NMD) view

Predicted translation: 

MQPDGTSVTVPGTRRRRRTRKGRGCRLSAGNRDSGAMGDAPSPEEKLHLITRNLQRVHTGCVPTVLCGHTTRRQESGG*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000668420 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001072442 aa-tRNA-synth_Ic (36/290 aa) CDS Deleted
ENSMUSE00000182408 aa-tRNA-synth_Ic (59/290 aa) CDS Deleted
ENSMUSE00001022922 aa-tRNA-synth_Ic (44/290 aa) CDS CDS + stop codon + UTR
ENSMUSE00001009932 aa-tRNA-synth_Ic (27/290 aa) CDS
ENSMUSE00001039145 aa-tRNA-synth_Ic (31/290 aa) CDS
ENSMUSE00001061844 aa-tRNA-synth_Ic (46/290 aa) CDS
ENSMUSE00001080581 aa-tRNA-synth_Ic (29/290 aa) CDS
ENSMUSE00000988410 aa-tRNA-synth_Ic (20/290 aa) CDS
ENSMUSE00001057986 tRNA-bd_dom (10/96 aa) CDS
ENSMUSE00001089842 tRNA-bd_dom (65/96 aa) CDS
ENSMUSE00000991777 tRNA-bd_dom (22/96 aa) CDS
ENSMUSE00000182400 CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000001365 protein_coding No protein product (NMD) view

Predicted translation: 

MGDAPSPEEKLHLITRNLQRVHTGCVPTVLCGHTTRRQESGG*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000182420 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001072442 aa-tRNA-synth_Ic (36/290 aa) CDS Deleted
ENSMUSE00000182408 aa-tRNA-synth_Ic (59/290 aa) CDS Deleted
ENSMUSE00001022922 aa-tRNA-synth_Ic (44/290 aa) CDS CDS + stop codon + UTR
ENSMUSE00001009932 aa-tRNA-synth_Ic (27/290 aa) CDS
ENSMUSE00001039145 aa-tRNA-synth_Ic (31/290 aa) CDS
ENSMUSE00001061844 aa-tRNA-synth_Ic (46/290 aa) CDS
ENSMUSE00001080581 aa-tRNA-synth_Ic (29/290 aa) CDS
ENSMUSE00000988410 aa-tRNA-synth_Ic (20/290 aa) CDS
ENSMUSE00001057986 tRNA-bd_dom (10/96 aa) CDS
ENSMUSE00001089842 tRNA-bd_dom (65/96 aa) CDS
ENSMUSE00000991777 tRNA-bd_dom (22/96 aa) CDS
ENSMUSE00000182400 CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000133992 nonsense_mediated_decay No analysis available: incomplete transcript
ENSMUST00000148619 retained_intron Target region does not overlap transcript
ENSMUST00000137591 processed_transcript Target region does not overlap transcript
ENSMUST00000128287 processed_transcript No analysis available: incomplete transcript
ENSMUST00000146106 retained_intron Target region does not overlap transcript
ENSMUST00000147248 retained_intron Target region does not overlap transcript
ENSMUST00000140708 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 EPD0170_3_C06 PRPGS00070_A_B01 Yarstm1a(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) - Vector Integrity pass
Distribution Centre
Karyotype 0.9 - 0.81 Copy Number pass Cells Thawed Correctly -
5' LR-PCR pass 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 EPD0170_3_B08 PRPGS00070_A_B01 Yarstm1a(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) - Vector Integrity pass
Distribution Centre
Karyotype 0.3 - 0.21 Copy Number pass Cells Thawed Correctly -
5' LR-PCR pass 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 EPD0170_3_D05 PRPGS00070_A_B01 Yarstm1a(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) - Vector Integrity pass
Distribution Centre
Karyotype 0.8 - 0.71 Copy Number pass Cells Thawed Correctly -
5' LR-PCR pass 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 EPD0170_3_E06 PRPGS00070_A_B01 Yarstm1a(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) - 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 EPD0170_3_F05 PRPGS00070_A_B01 Yarstm1a(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) - 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 EPD0170_3_G06 PRPGS00070_A_B01 Yarstm1a(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) - 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 48610 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00070_Z_4_B01 L1L2_Bact_P L3L4_pD223_DTA_spec view
order 48610 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PRPGS00070_B_B01 L1L2_Bact_P L3L4_pD223_DTA_spec view
order 48610 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PRPGS00070_A_B01 L1L2_Bact_P L3L4_pD223_DTA_spec view
order 48610 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00070_Z_3_B01 L1L2_Bact_P L3L4_pD223_DTA_spec view
order 48610 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00070_X_4_B01 L1L2_Bact_P L3L4_pD223_DTA_spec view
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Intermediate Vectors

Design ID Vector Type Intermediate Vector
48610 Knockout First, Reporter-tagged insertion with conditional potential PCS00070_A_B01