IKMC Project Report - KOMP-CSD (ID: 29470)

Slc6a13 MGI:95629 ENSMUSG00000030108 OTTMUSG00000023510
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 2 are protein-coding. Following removal of the floxed region, 2 transcripts are 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
ENSMUST00000064580 protein_coding No protein product (NMD) view

Predicted translation: 

MENRASGTTSNGETKPVCPAMEKVEEDGTLEREHWNNKMEFVLSVAGEIIGLGNVWRFPYLCYKNGGGAFFIPYLIFLFT
CGIPVFFLETALGQYTNQGGITAWRRICPIFEGIGYASQMIVSLLNVYYIVVLAWALFYLFSSFTTDLPWGSCSHEWNTG
GES*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000764371 UTR UTR
ENSMUSE00001055082 Na/ntran_symport (36/523 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000971353 Na/ntran_symport (46/523 aa) CDS CDS
ENSMUSE00001004751 Na/ntran_symport (48/523 aa) CDS CDS
ENSMUSE00001012883 Na/ntran_symport (29/523 aa) CDS Deleted
ENSMUSE00001018763 Na/ntran_symport (45/523 aa) CDS CDS + stop codon + UTR
ENSMUSE00000978230 Na/ntran_symport (45/523 aa) CDS
ENSMUSE00001028670 Na/ntran_symport (35/523 aa) CDS
ENSMUSE00001064797 Na/ntran_symport (43/523 aa) CDS
ENSMUSE00001058325 Na/ntran_symport (38/523 aa) CDS
ENSMUSE00000195370 Na/ntran_symport (46/523 aa) CDS
ENSMUSE00000986382 Na/ntran_symport (35/523 aa) CDS
ENSMUSE00000195361 Na/ntran_symport (34/523 aa) CDS
ENSMUSE00000195363 Na/ntran_symport (50/523 aa) CDS
ENSMUSE00000482319 CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000142419 protein_coding No analysis available: incomplete transcript
ENSMUST00000142021 processed_transcript No analysis available: incomplete transcript
ENSMUST00000142144 retained_intron Target region does not overlap 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 EPD0213_5_F10 PRPGS00036_B_G10 Slc6a13tm3a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8.N4 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 -

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 EPD0154_1_G05 PRPGS00036_B_G10 Slc6a13tm3e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8.N4 view no view    ( about )
Production Centre
5' Screen pass LoxP Screen not confirmed 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 - 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 EPD0154_1_H02 PRPGS00036_B_G10 Slc6a13tm3e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8.N4 view no view    ( about )
Production Centre
5' Screen pass LoxP Screen not confirmed 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 - 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 EPD0154_1_G06 PRPGS00036_B_G10 Slc6a13tm3e(KOMP)Wtsi Targeted Non-Conditional (Promotor Driven Cassette) JM8.N4 view no view    ( about )
Production Centre
5' Screen pass LoxP Screen not confirmed 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 - 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 42042 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00036_W_3_G10 L1L2_Bact_P R3R4_pBR_amp view
order 42042 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00036_W_2_G10 L1L2_Bact_P R3R4_pBR_amp view
order 42042 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00036_W_4_G10 L1L2_Bact_P R3R4_pBR_amp view
order 42042 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PRPGS00036_B_G10 L1L2_Bact_P R3R4_pBR_amp view
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Intermediate Vectors

Design ID Vector Type Intermediate Vector
42042 Knockout First, Reporter-tagged insertion with conditional potential PCS00036_A_G10