IKMC Project Report - EUCOMM (ID: 101290)

Ptchd4 MGI:1920485 ENSMUSG00000042256
Pre-pipeline Designs Vectors ES Cells Mice
ES Cells - Targeting Confirmed

Mice no data available

Mutagenesis Predictions

This gene has 1 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 0 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
ENSMUST00000048691 protein_coding Residual N-terminal, novel C-terminal product view

Predicted translation: 

MRRPGAPASWIWWRMLRQVLRRGLQSFCHRLGLCVSRHPVFFLTVPAVLTITFGLSALNRFQTEGDLERLVAPSHSLAKI
ERSLASSLFPLDQSKSQLYSDLHTPGRYGRVILLSSPGDNILLQAEGILQTHRAVMEMKVNHKGYNYTFSHLCVLRNQDK
KCVLDDIISVLEDLRQAAVSNKTTARVQVRYPNTKLKVMELKEYLSFCLDGGEPKRIYPSKTG*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000891694 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000317427 Patched (70/739 aa) CDS CDS
ENSMUSE00000877475 Patched (161/739 aa) | (46/152 aa) CDS Deleted
ENSMUSE00000390042 Patched (509/739 aa) | (107/152 aa) CDS + stop codon + UTR CDS + stop codon + UTR
Legend: in frame deleted frameshifted

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 HEPD0816_7_F07 PG00250_Z_2_A03 Ptchd4tm1a(EUCOMM)Hmgu Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8A3.N1.C2 view no view    ( about )
Production Centre
5' Screen pass 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 -

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 HEPD0816_7_D05 PG00250_Z_2_A03 Ptchd4tm1e(EUCOMM)Hmgu Targeted Non-Conditional (Promotor Driven Cassette) JM8A3.N1.C2 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 -

Targeting Vectors

Genome Browsers: Ensembl (mouse) - UCSC (mouse)
Tools: LRPCR Genotyping Primers
Design ID Vector Type Targeting Vector Cassette Backbone Genbank File
order 375501 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00250_Z_2_G01 L1L2_Bact_P L3L4_pD223_DTA_T_spec view
order 375501 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00250_Z_2_F06 L1L2_Bact_P L3L4_pD223_DTA_T_spec view
order 375501 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00250_Z_2_A06 L1L2_Bact_P L3L4_pD223_DTA_T_spec view
order 375501 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00250_Z_2_A03 L1L2_Bact_P L3L4_pD223_DTA_T_spec view
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Intermediate Vectors

Design ID Vector Type Intermediate Vector
375501 Knockout First, Reporter-tagged insertion with conditional potential PCS00250_A_B01