IKMC Project Report - EUCOMM (ID: 36258)

Gpc6 MGI:1346322 ENSMUSG00000058571 OTTMUSG00000018004
Pre-pipeline Designs Vectors ES Cells Mice
ES Cells - Targeting Confirmed

Mice no data available

Mutagenesis Predictions

This gene has 4 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 3 may be subject to non-sense mediated decay (NMD). The original allele for this mutation is of type 'Knockout-First - Reporter Tagged Insertion'. 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
ENSMUST00000125435 protein_coding No protein product (NMD) view

Predicted translation: 

MPSWIRAVILPLSGLLLTLPAAADVKARSCSEVRQAYGAKGFSLADIPYQEIAGEHLRICPQEYTCCTTEMEDKLSQQSK
LEFENLVEETSHFVRTTFVSRHKKFDGEPHPWLHPGSHEDAVLPILPRLAHCETLQQLLPQRHEGLPGQSGRFGH*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000728908 Glypican (32/541 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001031378 Glypican (54/541 aa) CDS CDS
ENSMUSE00001005739 Glypican (131/541 aa) CDS Deleted
ENSMUSE00000514241 Glypican (56/541 aa) CDS CDS + stop codon + UTR
ENSMUSE00000513638 Glypican (44/541 aa) CDS
ENSMUSE00000511522 Glypican (48/541 aa) CDS
ENSMUSE00000552697 Glypican (10/541 aa) CDS
ENSMUSE00000508988 Glypican (46/541 aa) CDS
ENSMUSE00000506968 Glypican (60/541 aa) CDS
ENSMUSE00000761070 Glypican (65/541 aa) CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000078849 protein_coding No protein product (NMD) view

Predicted translation: 

MPSWIRAVILPLSGLLLTLPAAADVKARSCSEVRQAYGAKGFSLADIPYQEIAGEHLRICPQEYTCCTTEMEDKLSQQSK
LEFENLVEETSHFVRTTFVSRHKKFDGEPHPWLHPGSHEDAVLPILPRLAHCETLQQLLPQRHEGLPGQSGRFGH*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000787225 Glypican (32/531 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001031378 Glypican (54/531 aa) CDS CDS
ENSMUSE00001005739 Glypican (131/531 aa) CDS Deleted
ENSMUSE00000514241 Glypican (56/531 aa) CDS CDS + stop codon + UTR
ENSMUSE00000513638 Glypican (44/531 aa) CDS
ENSMUSE00000511522 Glypican (48/531 aa) CDS
ENSMUSE00000508988 Glypican (46/531 aa) CDS
ENSMUSE00000506968 Glypican (60/531 aa) CDS
ENSMUSE00000507755 Glypican (65/531 aa) CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000088483 protein_coding No protein product (NMD) view

Predicted translation: 

MPSWIRAVILPLSGLLLTLPAAADVKARSCSEVRQAYGAKGFSLADIPYQEIAGEHLRICPQEYTCCTTEMEDKLSQQSK
LEFENLVEETSHFVRTTFVSRHKKFDGEPHPWLHPGSHEDAVLPILPRLAHCETLQQLLPQRHEGLPGQSGRFGH*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000731631 UTR UTR
ENSMUSE00000519575 Glypican (32/531 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001031378 Glypican (54/531 aa) CDS CDS
ENSMUSE00001005739 Glypican (131/531 aa) CDS Deleted
ENSMUSE00000514241 Glypican (56/531 aa) CDS CDS + stop codon + UTR
ENSMUSE00000513638 Glypican (44/531 aa) CDS
ENSMUSE00000511522 Glypican (48/531 aa) CDS
ENSMUSE00000508988 Glypican (46/531 aa) CDS
ENSMUSE00000506968 Glypican (60/531 aa) CDS
ENSMUSE00000833203 Glypican (65/531 aa) CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000123239 retained_intron No analysis available: incomplete transcript
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ES Cell Clones 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 HEPD0549_4_D04 PRPGS00112_A_B04 Gpc6tm1a(EUCOMM)Hmgu Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) JM8A1.N3 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 pass 3' SR-PCR pass
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 HEPD0549_4_G03 PRPGS00112_A_B04 Gpc6tm1a(EUCOMM)Hmgu Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen pass LoxP Screen pass 3' Screen not confirmed
Loss of WT Allele (LOA) - Vector Integrity -
Distribution Centre
Karyotype - Copy Number - Cells Thawed Correctly -
5' LR-PCR - 5' SR-PCR fail 3' SR-PCR pass
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 HEPD0549_4_H01 PRPGS00112_A_B04 Gpc6tm1a(EUCOMM)Hmgu Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) JM8A1.N3 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 pass 5' SR-PCR pass 3' SR-PCR pass
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 HEPD0549_4_F01 PRPGS00112_A_B04 Gpc6tm1e(EUCOMM)Hmgu Targeted Non-Conditional (Promotor Driven Cassette) JM8A1.N3 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 106267 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) PG00112_Y_1_B04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 106267 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) PG00112_Z_1_B04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 106267 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) PRPGS00112_B_B04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 106267 Knockout-First - Reporter Tagged Insertion (Promotor Driven Cassette) PRPGS00112_A_B04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
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Intermediate Vectors

Design ID Vector Type Intermediate Vector
106267 Knockout-First - Reporter Tagged Insertion PCS00112_B_B04
106267 Knockout-First - Reporter Tagged Insertion PCS00112_A_B04