IKMC Project Report - KOMP-CSD (ID: 38773)

Ybx2 MGI:1096372 ENSMUSG00000018554 OTTMUSG00000006029
Pre-pipeline Designs Vectors ES Cells Mice
ES Cells - Targeting Confirmed

Mice no data available

Mutagenesis Predictions

This gene has 5 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 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
ENSMUST00000018698 protein_coding No protein product (NMD) view

Predicted translation: 

MSEAEASVVATAAPAATVPATAAGVVAVVVPVPAGEPQKAGGGAGGGGGAASGPAAGTPSAPGPRTPGNQATAASGTPAP
PARSQADKPVLAIQVLGTVKWFNVRNGYGFINRVQKLLMSLGLGGYQ*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000727608 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001044963 CSP_DNA-bd (18/69 aa) CDS CDS
ENSMUSE00001068032 CSP_DNA-bd (12/69 aa) CDS Deleted
ENSMUSE00001006115 CSP_DNA-bd (30/69 aa) CDS Deleted
ENSMUSE00001046749 CSP_DNA-bd (10/69 aa) CDS CDS + stop codon + UTR
ENSMUSE00001011648 CDS
ENSMUSE00001091761 CDS
ENSMUSE00001039312 CDS + stop codon + UTR
ENSMUSE00000805046 UTR UTR
Legend: in frame deleted frameshifted
ENSMUST00000108601 protein_coding No protein product (NMD) view

Predicted translation: 

MSRRAGQAGSAKALAIQVLGTVKWFNVRNGYGFINRVQKLLMSLGLGGYQ*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000677332 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001044963 CSP_DNA-bd (18/69 aa) CDS CDS
ENSMUSE00001068032 CSP_DNA-bd (12/69 aa) CDS Deleted
ENSMUSE00001006115 CSP_DNA-bd (30/69 aa) CDS Deleted
ENSMUSE00001046749 CSP_DNA-bd (10/69 aa) CDS CDS + stop codon + UTR
ENSMUSE00001011648 CDS
ENSMUSE00001091761 CDS
ENSMUSE00001039312 CDS + stop codon + UTR
ENSMUSE00000770168 UTR UTR
Legend: in frame deleted frameshifted
ENSMUST00000149194 protein_coding Residual C-terminal product view

Predicted translation: 

MVAEAPSGGTEPGSEGERAEDSGQRPRRRRPPPFFYRRRFVRGPRPPNQQQPIEGSDGVEPKETAPLEGDQQQGDERVPP
PRFRPRYRRPFRPRPPQQPTTEGGDGETKPSQGPTDGSRPEPQRPRNRPYFQRRRQQPPGPRQPIAAETSAPINSGDPPT
TILE*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000759918 UTR UTR
ENSMUSE00000975682 UTR UTR
ENSMUSE00001065190 UTR Deleted
ENSMUSE00000986208 UTR Deleted
ENSMUSE00001074253 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001011648 CDS CDS
ENSMUSE00001091761 CDS CDS
ENSMUSE00001039312 CDS + stop codon + UTR CDS + stop codon + UTR
ENSMUSE00000724928 UTR UTR
Legend: in frame deleted frameshifted
ENSMUST00000148395 retained_intron Target region does not overlap transcript
ENSMUST00000130377 retained_intron Target region does not overlap transcript
show/hide more transcripts

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 EPD0134_5_E12 PRPGS00075_A_A08 Ybx2tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8.N4 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 EPD0134_5_G12 PRPGS00075_A_A08 Ybx2tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8.N4 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 EPD0134_5_C11 PRPGS00075_A_A08 Ybx2tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8.N4 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 EPD0134_5_G11 PRPGS00075_A_A08 Ybx2tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8.N4 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 EPD0134_5_D09 PRPGS00075_A_A08 Ybx2tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8.N4 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 EPD0134_5_F10 PRPGS00075_A_A08 Ybx2tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8.N4 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 EPD0134_5_G09 PRPGS00075_A_A08 Ybx2tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8.N4 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 EPD0134_5_C12 PRPGS00075_A_A08 Ybx2tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8.N4 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 EPD0134_5_D11 PRPGS00075_A_A08 Ybx2tm1e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8.N4 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 51168 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00075_Z_4_A07 L1L2_Bact_P L4L3_pD223_DTA_spec view
order 51168 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PRPGS00075_A_A08 L1L2_Bact_P L4L3_pD223_DTA_spec view
show/hide more targeting vectors

Intermediate Vectors

Design ID Vector Type Intermediate Vector
51168 Knockout First, Reporter-tagged insertion with conditional potential PCS00075_A_A08