IKMC Project Report - EUCOMM (ID: 40038)

Ddx52 MGI:1925644 ENSMUSG00000020677 OTTMUSG00000000973
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 Ddx52tm1a(EUCOMM)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotorless Cassette) EPD0102_1_B10 C57BL/6NTac;C57BL/6NTac;C57BL/6N view
( about ) 		ICS
Southern Blot na TV Backbone Assay na 5' LR-PCR na
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 2 wild type transcripts, of which 1 are protein-coding. Following removal of the floxed region, 1 transcript is predicted to produce a truncated protein product of which 1 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
ENSMUST00000049257 protein_coding No protein product (NMD) view

Predicted translation: 

MDSYDLFRRLGAGAKFDVKRFSADATRFQVGKRKFDSESLEVLKGLDFFGNKKSVSDECGALQIHQEPPNEEKTQGVLLE
RSKEPKKKKRKKMTSEVPAQEDFDGGIQWTSSVEAKLQDEKVSGEKKLTSGKLEHLRKEKVNFFRNKHKIHVQGTDLPDP
IATFQQLDQEYKINSRLLQNILDAGFQVPTPIQMQAIPVMLHGRELLASAPTGSGKTLAFSIPILMQLKQPTNKGFRALV
ISPTRELASQISL*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000400934 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000383108 CDS CDS
ENSMUSE00000337347 CDS CDS
ENSMUSE00000276146 DNA/RNA_helicase_DEAD/DEAH_N (12/174 aa) CDS CDS
ENSMUSE00001080009 DNA/RNA_helicase_DEAD/DEAH_N (48/174 aa) | Helicase/UvrB_dom (47/126 aa) CDS CDS
ENSMUSE00001007900 DNA/RNA_helicase_DEAD/DEAH_N (38/174 aa) | Helicase/UvrB_dom (38/126 aa) CDS Deleted
ENSMUSE00000276119 DNA/RNA_helicase_DEAD/DEAH_N (25/174 aa) | Helicase/UvrB_dom (25/126 aa) CDS CDS + stop codon + UTR
ENSMUSE00000107783 DNA/RNA_helicase_DEAD/DEAH_N (53/174 aa) | Helicase/UvrB_dom (18/126 aa) CDS
ENSMUSE00000107789 CDS
ENSMUSE00000107786 Helicase_C (18/76 aa) CDS
ENSMUSE00000107785 Helicase_C (51/76 aa) CDS
ENSMUSE00000107787 Helicase_C (8/76 aa) CDS
ENSMUSE00000276183 CDS
ENSMUSE00000276109 CDS
ENSMUSE00000359935 CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000130982 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 EPD0102_1_B10 PGS00040_A_E01 Ddx52tm1a(EUCOMM)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotorless Cassette) JM8.F6 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 pass 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 EPD0102_1_A10 PGS00040_A_E01 Ddx52tm1a(EUCOMM)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotorless Cassette) JM8.F6 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 EPD0102_1_A12 PGS00040_A_E01 Ddx52tm1a(EUCOMM)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotorless Cassette) JM8.F6 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 EPD0102_1_C12 PGS00040_A_E01 Ddx52tm1a(EUCOMM)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotorless Cassette) JM8.F6 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 EPD0102_1_E10 PGS00040_A_E01 Ddx52tm1e(EUCOMM)Wtsi Targeted Non-Conditional (Promotorless Cassette) JM8.F6 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 EPD0102_1_E11 PGS00040_A_E01 Ddx52tm1e(EUCOMM)Wtsi Targeted Non-Conditional (Promotorless Cassette) JM8.F6 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 33659 Knockout First, Reporter-tagged insertion with conditional potential (Promotorless Cassette) PG00040_A_4_E01 L1L2_gt0 L3L4_pZero_DTA_kan view
order 33659 Knockout First, Reporter-tagged insertion with conditional potential (Promotorless Cassette) PG00040_A_2_E01 L1L2_gt0 L3L4_pZero_DTA_kan view
order 33659 Knockout First, Reporter-tagged insertion with conditional potential (Promotorless Cassette) PG00040_A_3_E01 L1L2_gt0 L3L4_pZero_DTA_kan view
order 33659 Knockout First, Reporter-tagged insertion with conditional potential (Promotorless Cassette) PGS00040_A_E01 L1L2_gt0 L3L4_pZero_DTA_kan view
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Intermediate Vectors

Design ID Vector Type Intermediate Vector
33659 Knockout First, Reporter-tagged insertion with conditional potential PCS00040_A_E01