IKMC Project Report - KOMP-CSD (ID: 35055)

Gnpda2 MGI:1915230 ENSMUSG00000029209 OTTMUSG00000027748
Pre-pipeline Designs Vectors ES Cells Mice
ES Cells - Targeting Confirmed

Mice no data available

Mutagenesis Predictions

This gene has 10 wild type transcripts, of which 5 are protein-coding. Following removal of the floxed region, 5 transcripts are predicted to produce a truncated protein product of which 0 may be subject to non-sense mediated decay (NMD). This mutation is of type 'Deletion' (more information on IKMC alleles can be found here). The table below shows the predicted structure of the gene transcripts. Click the 'view' button for each transcript to see the full prediction for that transcript.

Ensembl transcript id Ensembl Biotype Floxed transcript description Details
ENSMUST00000031117 protein_coding Residual N-terminal, novel C-terminal product view

Predicted translation: 

MRLVILDNYDLASEWAAKYICNRIIKFKPGQDRYFSLGLPTGDDPHNRCAQGLRAVQSHGRRSQSHVDGVRFPATSTHYF
CM*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000844539 UTR UTR
ENSMUSE00001007244 Glc/Gal-6P_isomerase (27/236 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001019446 Glc/Gal-6P_isomerase (35/236 aa) CDS Deleted
ENSMUSE00001057361 Glc/Gal-6P_isomerase (62/236 aa) CDS Deleted
ENSMUSE00000505341 Glc/Gal-6P_isomerase (62/236 aa) CDS Deleted
ENSMUSE00001037502 Glc/Gal-6P_isomerase (53/236 aa) CDS CDS + stop codon + UTR
ENSMUSE00000504387 CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000166298 protein_coding Residual N-terminal, novel C-terminal product view

Predicted translation: 

MRLVILDNYDLASEWAAKYICNRIIKFKPGQDRYFSLGLPTGDDPHNRCAQGLRAVQSHGRRSQSHVDGVRFPATSTHYF
CM*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000899986 UTR UTR
ENSMUSE00001007244 Glc/Gal-6P_isomerase (27/234 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001019446 Glc/Gal-6P_isomerase (35/234 aa) CDS Deleted
ENSMUSE00001057361 Glc/Gal-6P_isomerase (62/234 aa) CDS Deleted
ENSMUSE00001062244 Glc/Gal-6P_isomerase (60/234 aa) CDS Deleted
ENSMUSE00001037502 Glc/Gal-6P_isomerase (53/234 aa) CDS CDS + stop codon + UTR
ENSMUSE00000900477 CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000173927 protein_coding Residual N-terminal, novel C-terminal product view

Predicted translation: 

MRLVILDNYDLASEWAAKYICNRIIKFKPGQDRYFSLGLPTGDDPHNRCAQGLRAVQSHGRRSQSHVDGVRFPATSTHYF
CM*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000936511 UTR UTR
ENSMUSE00001007244 Glc/Gal-6P_isomerase (27/234 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001019446 Glc/Gal-6P_isomerase (35/234 aa) CDS Deleted
ENSMUSE00001057361 Glc/Gal-6P_isomerase (62/234 aa) CDS Deleted
ENSMUSE00001062244 Glc/Gal-6P_isomerase (60/234 aa) CDS Deleted
ENSMUSE00001037502 Glc/Gal-6P_isomerase (53/234 aa) CDS CDS + stop codon + UTR
ENSMUSE00000927434 CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000120789 protein_coding Residual N-terminal, novel C-terminal product view

Predicted translation: 

MRLVILDNYDLASEWAAKYICNRIIKFKPGQDRYFSLGLPTGDDPHNRCAQGLRAVQSHGRRSQSHVDGVRFPATSTHYF
CM*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000711749 UTR UTR
ENSMUSE00001007244 Glc/Gal-6P_isomerase (27/236 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001019446 Glc/Gal-6P_isomerase (35/236 aa) CDS Deleted
ENSMUSE00001057361 Glc/Gal-6P_isomerase (62/236 aa) CDS Deleted
ENSMUSE00000505341 Glc/Gal-6P_isomerase (62/236 aa) CDS Deleted
ENSMUSE00001037502 Glc/Gal-6P_isomerase (53/236 aa) CDS CDS + stop codon + UTR
ENSMUSE00000712347 CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000174233 protein_coding Residual N-terminal, unknown C-terminal view

Predicted translation: 

MRLVILDNYDLASEWAAKYICNRIIKFKPGQDRYFSLGLPT

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000929548 UTR UTR
ENSMUSE00001007244 Glc/Gal-6P_isomerase (27/166 aa) UTR + start codon + CDS
ENSMUSE00001019446 Glc/Gal-6P_isomerase (35/166 aa) CDS Deleted
ENSMUSE00001057361 Glc/Gal-6P_isomerase (62/166 aa) CDS Deleted
ENSMUSE00000937302 Glc/Gal-6P_isomerase (44/166 aa) CDS + stop codon + UTR Deleted
Legend: in frame deleted frameshifted
ENSMUST00000139632 nonsense_mediated_decay No protein product (NMD) view

Predicted translation: 

MRLVILDNYDLASEWAAKYICNRIIKFKPGQDRYFSLGLPTGDDPHNRCAQGLRAVQSHGRRSQSHVDGVRFPATSTHYF
CM*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000734304 UTR UTR
ENSMUSE00001007244 Glc/Gal-6P_isomerase (27/236 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001019446 Glc/Gal-6P_isomerase (35/236 aa) CDS Deleted
ENSMUSE00001057361 Glc/Gal-6P_isomerase (62/236 aa) CDS Deleted
ENSMUSE00000505341 Glc/Gal-6P_isomerase (62/236 aa) CDS Deleted
ENSMUSE00001037502 Glc/Gal-6P_isomerase (53/236 aa) CDS CDS + stop codon + UTR
ENSMUSE00000820420 CDS + stop codon + UTR
ENSMUSE00000801503 UTR UTR
Legend: in frame deleted frameshifted
ENSMUST00000153536 nonsense_mediated_decay No analysis available: incomplete transcript
ENSMUST00000154018 retained_intron No analysis available: incomplete transcript
ENSMUST00000145775 processed_transcript No analysis available: incomplete transcript
ENSMUST00000144203 processed_transcript No analysis available: incomplete transcript
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ES Cell Clones Without Conditional Potential (Deletions)

Note: Mutations of type "Deletion" are correctly targeted clones that have had the target exon removed. 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 EPD0388_2_C05 DPGS00165_A_D04 Gnpda2tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A3.N1 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 -
order EPD0388_2_E06 DPGS00165_A_D04 Gnpda2tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A3.N1 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 -
order EPD0388_2_G06 DPGS00165_A_D04 Gnpda2tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen pass LoxP Screen not confirmed 3' Screen not confirmed
Loss of WT Allele (LOA) - Vector Integrity pass
Distribution Centre
Karyotype - 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 EPD0388_2_B08 DPGS00165_A_D04 Gnpda2tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A3.N1 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 pass 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 EPD0388_2_F05 DPGS00165_A_D04 Gnpda2tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A3.N1 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 -
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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 221996 Deletion (Promotor Driven Cassette) PG00165_Z_6_D04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 221996 Deletion (Promotor Driven Cassette) PG00165_Z_7_D04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 221996 Deletion (Promotor Driven Cassette) PG00165_Z_8_D04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 221996 Deletion (Promotor Driven Cassette) PG00165_Z_1_D04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 221996 Deletion (Promotor Driven Cassette) DPGS00165_A_D04 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
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Intermediate Vectors

Design ID Vector Type Intermediate Vector
221996 Deletion PCS00165_A_D04