IKMC Project Report - KOMP-CSD (ID: 69138)

Cd6 MGI:103566 ENSMUSG00000024670 OTTMUSG00000036965
Pre-pipeline Designs Vectors ES Cells Mice
ES Cells - Targeting Confirmed

Mice no data available

Mutagenesis Predictions

This gene has 5 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 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
ENSMUST00000080292 protein_coding Residual N-terminal, residual C-terminal product view

Predicted translation: 

MWLFLGIAGLLTAVLSGLPSPAPSGQHKNGTIPNMTLDLESSVPVSVKDKDSQGLTLLILCIVLGILLLVSTIFIVILLL
RAKGQYALPASVNHQQLSTANQAGINNYHPVPITIAKEAPMLFIQPRVPADSDSSSDSDYEHYDFSSQPPVALTTFYNSQ
RHRVTEEEAQQNRFQMPPLEEGLEELHVSHIPAADPRPCVADVPSRGSQYHVRNNSDSSTSSEEGYCNDPSSKPPPWNSQ
AFYSEKSPLTEQPPNLELAGSPAVFSGPSADDSSSTSSGEWYQNFQPPPQHPPAEQFECPGPPGPQTDSIDDDEEDYDDI
GAA*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000901955 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000643064 CDS CDS
ENSMUSE00000643061 Srcr_rcpt (107/107 aa) CDS Deleted
ENSMUSE00000643059 Srcr_rcpt (97/97 aa) CDS Deleted
ENSMUSE00000643056 Srcr_rcpt (1/97 aa) | Srcr_rcpt (93/93 aa) CDS Deleted
ENSMUSE00001002376 Srcr_rcpt (1/93 aa) CDS Deleted
ENSMUSE00000996014 CDS CDS
ENSMUSE00000963587 CDS CDS
ENSMUSE00001041280 CDS CDS
ENSMUSE00001048533 CDS CDS
ENSMUSE00001023889 CDS CDS
ENSMUSE00001071164 CDS CDS
ENSMUSE00000931896 CDS + stop codon + UTR CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000039043 protein_coding Residual N-terminal, residual C-terminal product view

Predicted translation: 

MWLFLGIAGLLTAVLSGLPSPAPSGQHKNGTIPNMTLDLESSVPVSVKDKDSQGLTLLILCIVLGILLLVSTIFIVILLL
RAKGQYALPASVNHQQLSTANQAGINNYHPVPITIAKEDSQRHRVTEEEAQQNRFQMPPLEEGLEELHVSHIPAADPRPC
VADVPSRGSQYHVRNNSDSSTSSEEGYCNDPSSKPPPWNSQAFYSEKSPLTEQPPNLELAGSPAVFSGPSADDSSSTSSG
EWYQNFQPPPQHPPAEQFECPGPPGPQTDSIDDDEEDYDDIGAA*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000935715 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000643064 CDS CDS
ENSMUSE00000643061 Srcr_rcpt (107/107 aa) CDS Deleted
ENSMUSE00000643059 Srcr_rcpt (97/97 aa) CDS Deleted
ENSMUSE00000643056 Srcr_rcpt (1/97 aa) | Srcr_rcpt (93/93 aa) CDS Deleted
ENSMUSE00001002376 Srcr_rcpt (1/93 aa) CDS Deleted
ENSMUSE00000996014 CDS CDS
ENSMUSE00000963587 CDS CDS
ENSMUSE00001048533 CDS CDS
ENSMUSE00001023889 CDS CDS
ENSMUSE00001071164 CDS CDS
ENSMUSE00000928140 CDS + stop codon + UTR CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000174176 protein_coding No analysis available: incomplete transcript
ENSMUST00000025572 retained_intron No analysis available: incomplete transcript
ENSMUST00000173613 retained_intron Target region does not overlap 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 EPD0323_3_G04 DPGS00142_B_G12 Cd6tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen not confirmed 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 EPD0323_3_D02 DPGS00142_B_G12 Cd6tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen not confirmed 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 EPD0323_3_B03 DPGS00142_B_G12 Cd6tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen not confirmed 3' Screen pass
Loss of WT Allele (LOA) - Vector Integrity -
Distribution Centre
Karyotype 0.4 - 0.31 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 EPD0323_3_E02 DPGS00142_B_G12 Cd6tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen not confirmed LoxP Screen not confirmed 3' Screen pass
Loss of WT Allele (LOA) - Vector Integrity -
Distribution Centre
Karyotype 0.4 - 0.31 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 EPD0323_3_D01 DPGS00142_B_G12 Cd6tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen not confirmed 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 EPD0323_3_H04 DPGS00142_B_G12 Cd6tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A1.N3 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 0.6 - 0.51 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 EPD0323_3_B01 DPGS00142_B_G12 Cd6tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A1.N3 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 0.6 - 0.51 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 EPD0323_3_F04 DPGS00142_B_G12 Cd6tm1(KOMP)Wtsi Deletion (Promotor Driven Cassette) JM8A1.N3 view no view    ( about )
Production Centre
5' Screen not confirmed 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 210898 Deletion (Promotor Driven Cassette) DPGS00142_B_G12 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 210898 Deletion (Promotor Driven Cassette) PG00142_Y_4_G12 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 210898 Deletion (Promotor Driven Cassette) PG00142_Y_1_F12 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 210898 Deletion (Promotor Driven Cassette) PG00142_Y_2_G12 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
order 210898 Deletion (Promotor Driven Cassette) PG00142_Y_1_G12 L1L2_Bact_P R3R4_pBR_DTA+_Bsd_amp view
show/hide more targeting vectors

Intermediate Vectors

Design ID Vector Type Intermediate Vector
210898 Deletion PCS00142_A_G12