IKMC Project Report - KOMP-CSD (ID: 30314)

Pabpn1 MGI:1859158 ENSMUSG00000022194 OTTMUSG00000037620
Pre-pipeline Designs Vectors ES Cells Mice
ES Cells - Targeting Confirmed

Mice no data available

Mutagenesis Predictions

This gene has 9 wild type transcripts, of which 8 are protein-coding. Following removal of the floxed region, 8 transcripts are predicted to produce a truncated protein product of which 1 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
ENSMUST00000022808 protein_coding No protein product (NMD) view

Predicted translation: 

MAAAAAAAAAAGAAGGRGSGPGRRRHLVPGAGGEAGEGDPGGAGDYGNGLESEELEPGELLPEPEPEEEPPRPRAPPGAP
GPGPGSGAPGSQEEEEEPGLVEADPGDGAIEDPVCIYRVLGQRVSEDVPGLR*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000389586 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000978943 CDS Deleted
ENSMUSE00000996549 RRM_dom (4/70 aa) CDS Deleted
ENSMUSE00000975831 RRM_dom (36/70 aa) CDS Deleted
ENSMUSE00001068923 RRM_dom (30/70 aa) CDS CDS + stop codon + UTR
ENSMUSE00001018074 RRM_dom (1/70 aa) CDS
ENSMUSE00000780517 CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000150975 protein_coding Residual N-terminal, novel C-terminal product view

Predicted translation: 

MAAAAAAAAAAGAAGGRGSGPGRRRHLVPGAGGEAGEGDPGGAGDYGNGLESEELEPGELLPEPEPEEEPPRPRAPPGAP
GPGPGSGAPGSQEEEEEPGLVEADPGDGAIEDPVCIYRVLGQRVSEDVPGLR*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000821995 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000978943 CDS Deleted
ENSMUSE00000996549 RRM_dom (4/70 aa) CDS Deleted
ENSMUSE00000975831 RRM_dom (36/70 aa) CDS Deleted
ENSMUSE00000802790 RRM_dom (31/70 aa) CDS + stop codon + UTR CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000116476 protein_coding Residual N-terminal, novel C-terminal product view

Predicted translation: 

MAAAAAAAAAAGAAGGRGSGPGRRRHLVPGAGGEAGEGDPGGAGDYGNGLESEELEPGELLPEPEPEEEPPRPRAPPGAP
GPGPGSGAPGSQEEEEEPGLVEADPGDGAIEDPVCIYRVLGQRVSEDVPGLR*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000389586 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000978943 CDS Deleted
ENSMUSE00000996549 RRM_dom (4/70 aa) CDS Deleted
ENSMUSE00000975831 RRM_dom (36/70 aa) CDS Deleted
ENSMUSE00001068923 RRM_dom (30/70 aa) CDS CDS + stop codon + UTR
ENSMUSE00000706548 RRM_dom (1/70 aa) CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000172557 protein_coding No protein product
ENSMUST00000141446 protein_coding No protein product
ENSMUST00000139985 protein_coding Novel (out of frame) product view

Predicted translation: 

MAEHGCGRAQTKCTAQPLRLVNCMPCSFIVVCIYRVLGQRVSEDVPGLR*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000792785 UTR UTR + start codon + CDS
ENSMUSE00000792785 UTR + start codon + CDS Deleted
ENSMUSE00000996549 RRM_dom (4/70 aa) CDS Deleted
ENSMUSE00000975831 RRM_dom (36/70 aa) CDS Deleted
ENSMUSE00001068923 RRM_dom (30/70 aa) CDS CDS + stop codon + UTR
ENSMUSE00000821737 RRM_dom (1/70 aa) CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000140691 protein_coding No analysis available: incomplete transcript
ENSMUST00000146271 protein_coding No analysis available: incomplete transcript
ENSMUST00000172695 nonsense_mediated_decay No protein product (NMD) view

Predicted translation: 

MAAAAAAAAAAGAAGGRGSGPGRRRHLVPGAGGEAGEGDPGGAGDYGNGLDSGSWARLGSPRQSGGGGRAGTG*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000939115 CDS CDS
ENSMUSE00000940993 CDS + stop codon + UTR CDS + stop codon + UTR
ENSMUSE00000988820 UTR Deleted
ENSMUSE00001061868 UTR Deleted
ENSMUSE00001090196 UTR Deleted
ENSMUSE00001072521 UTR UTR
ENSMUSE00001088439 UTR UTR
ENSMUSE00000939118 UTR UTR
Legend: in frame deleted frameshifted
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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 EPD0400_4_E09 DPGS00166_A_B03 Pabpn1tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen not confirmed 3' Screen pass
Loss of WT Allele (LOA) - Vector Integrity fail
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 EPD0400_4_H11 DPGS00166_A_B03 Pabpn1tm1(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 0.9 - 0.81 Copy Number pass Cells Thawed Correctly -
5' LR-PCR fail 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 EPD0400_4_D12 DPGS00166_A_B03 Pabpn1tm1(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 fail
Distribution Centre
Karyotype 0.7 - 0.61 Copy Number pass Cells Thawed Correctly -
5' LR-PCR fail 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 EPD0400_4_F10 DPGS00166_A_B03 Pabpn1tm1(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 fail 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 EPD0400_4_E11 DPGS00166_A_B03 Pabpn1tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen not confirmed 3' Screen pass
Loss of WT Allele (LOA) - Vector Integrity pass
Distribution Centre
Karyotype 0.1 - 0 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 pass 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 EPD0400_4_F09 DPGS00166_A_B03 Pabpn1tm1(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 0.5 - 0.41 Copy Number pass Cells Thawed Correctly -
5' LR-PCR fail 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 230604 Deletion (Promotor Driven Cassette) DPGS00166_A_B03 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 230604 Deletion (Promotor Driven Cassette) PG00166_Z_8_B03 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 230604 Deletion (Promotor Driven Cassette) PG00166_Z_7_B03 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 230604 Deletion (Promotor Driven Cassette) PG00166_Z_2_B03 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 230604 Deletion (Promotor Driven Cassette) PG00166_Z_6_B03 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 230604 Deletion (Promotor Driven Cassette) PG00166_Z_1_B03 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 230604 Deletion (Promotor Driven Cassette) PG00166_Z_4_B03 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 230604 Deletion (Promotor Driven Cassette) PG00166_Z_5_B03 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 230604 Deletion (Promotor Driven Cassette) PG00166_Z_3_B03 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
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Intermediate Vectors

Design ID Vector Type Intermediate Vector
230604 Deletion PCS00166_A_B03