IKMC Project Report - KOMP-CSD (ID: 38198)

Arhgef4 MGI:2442507 ENSMUSG00000037509 OTTMUSG00000033276
Pre-pipeline Designs Vectors ES Cells Mice
Mice - Phenotype Data Available

Mice

Microinjection Status Allele Allele Type ES Cell Clone Genetic Background QC Data MI/Distribution Centre
contact distributor Genotype confirmed Arhgef4tm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) EPD0135_1_A05 C57BL/6NTac;C57BL/6N view
( about ) 		WTSI/UCD
Southern Blot na TV Backbone Assay pass 5' LR-PCR pass
Loss of WT Allele (LOA) qPCR na Homozygous Loss of WT Allele (LOA) SR-PCR pass Neo Count (qPCR) pass
LacZ SR-PCR pass 5' Cassette Integrity Neo SR-PCR na
Mutant Specific SR-PCR pass LoxP Confirmation pass 3' LR-PCR
Genotyping Comment -

Mutagenesis Predictions

This gene has 7 wild type transcripts, of which 4 are protein-coding. Following removal of the floxed region, 4 transcripts are predicted to produce a truncated protein product of which 0 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
ENSMUST00000047664 protein_coding Residual N-terminal, residual C-terminal product view

Predicted translation: 

MDDQELGFKAGDVIEVMDATNREWWWGRVADGEGWFPASFVRGEDLLVRSSELIHSGELTRVTQPQARSQQRMFFLFDRQ
LIYCKKDLLRRDVLYYKGRLDMDDLEVVDVEDGKDRDLHVSVKNAFRLYCGTTGDSHLLCARKPEQKQRWLKAFAREREQ
VRLDQETGFSITELQRKQAMLNASKQQATGKPKAVGRPGYLTRHKHPSLPASRPQQQVLVLAEPRRKPSNFWHSISRLAP
FRK*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000857141 UTR UTR
ENSMUSE00001057030 SH3_domain (37/37 aa) | SH3_2 (39/40 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001057754 DH-domain (20/180 aa) | SH3_2 (1/40 aa) CDS Deleted
ENSMUSE00001051137 DH-domain (60/180 aa) CDS Deleted
ENSMUSE00000233682 DH-domain (78/180 aa) CDS Deleted
ENSMUSE00000233675 DH-domain (23/180 aa) CDS Deleted
ENSMUSE00000233666 Pleckstrin_homology (32/101 aa) CDS CDS
ENSMUSE00000233661 Pleckstrin_homology (69/101 aa) CDS CDS
ENSMUSE00000233653 CDS CDS
ENSMUSE00000859384 CDS + stop codon + UTR CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000159747 protein_coding Residual N-terminal, residual C-terminal product view

Predicted translation: 

MLTAGRRDEACPCSRVASFVQESVPASVCFSKHASSNSSPHLQQARSRGYLDAPVVCPCFRRHCELGQSWPQIHIRTAAA
KIPPTGSQHNDFPLWIRTKKGPAPRSTVGTDLFWVHPFLDIACQPRLGTPYLLDTKCHQSTPENLGANAKPPQGYLCWQV
KTLVRAHSIASFPLGCPKEPLKQKGTNWPYLREGTEIEPDHPILHKTQSPGPTQLSRLLPTSQSRAPPLQGECKLSDCSF
KRASPDTPCVGLPLENQVEQASRSCPAPSHLTSELLKLNSQEEVPRPAECKPGHSPESRLEEPKGVHPDDVISKQQCLLN
ISGEAGSQTENYPSMSALQEERKPPDRASLFPQHCCHGEVPVCNRMLAGSWEEESDSACAPRTALKSSVIGSLEAAEEGV
VLDLQRNGKALQSLLDFPTLEVSHRNPGSECAQGPGDDPEPSPSGQRQAPGAHGASRHSCKFIMIAVKQEGRQTSTRKAH
CLIEPQCGHLPEKGTSATAYESSRASEMPVFGNECELLGCPGAEVDGGALQLLAQGIEHVRVPVSRTSSDDTLSSEETLE
GELLGERLDLGSECVHTEQNQELPSSDRKRGRCGTGDAENAEICACAGEVEGPLSRVLASSTTTLEFQEPCGGFQQSVLE
SEQHPACLQMTPLRTDMPWSREMPGGDIPYSQALTSEDLNPVCPSPEERVPHSPCQGEPPLHHVHQSVSLETKSGVIQVG
TSGDLSGEGPSPESYNIKRLKTTESKIKARLALAHKTFTNFFEAKVMEKTNTGSVKGEKEKRRRARGSWRAFLRSKDAEG
SKRPALVSGVPEPGFPQLLCSSPPATRGHCEKWTIDTDSHVFGEHWTPLNSPATLSSSHLASPEHRRRSEPTIRRTAAQE
SSTHLSSGVFPKSSWLTSATSPGAAQIDISFALPCSSACHLTYENQGMPCRPTSPKPRSPMAGAQRMDLCLRGRTSAVSM
VSLRSDKDANRSSEVPERPKASKARASLLLSLQTLNQNDQKEDKSQCQCYHGLGTVPFLRDHPGNESYIAQESPPDKKRN
CSHDQKTYTEPPHRPVSATEVTRTLPSMSAEQVPREVPLQFRRAPQHSHFSFDDIWLEKAQRRKLKKQMLLRRQMCAELV
PEDPVQCWRKTTITSPESPHLPRRSHLLSQSAPMGLDHTGWPEPTSDTGMPDGTLDTVCAEETGSEEDLYEELHNSGHHY
SHPRGGGEQLAINELISDGSVVCAEALWDHVTMDDQELGFKAGDVIEVMDATNREWWWGRVADGEGWFPASFVRGEDLLV
RSSELIHSGELTRVTQPQARSQQRMFFLFDRQLIYCKKDLLRRDVLYYKGRLDMDDLEVVDVEDGKDRDLHVSVKNAFRL
YCGTTGDSHLLCARKPEQKQRWLKAFAREREQVRLDQETGFSITELQRKQAMLNASKQQATGKPKAVGRPGYLTRHKHPS
LPASRPQQQVLVLAEPRRKPSNFWHSISRLAPFRK*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000871242 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000861267 CDS CDS
ENSMUSE00000880582 CDS CDS
ENSMUSE00001005944 CDS CDS
ENSMUSE00001053718 SH3_domain (45/45 aa) | SH3_2 (45/46 aa) CDS CDS
ENSMUSE00001057754 DH-domain (20/180 aa) | SH3_2 (1/46 aa) CDS Deleted
ENSMUSE00001051137 DH-domain (60/180 aa) CDS Deleted
ENSMUSE00000233682 DH-domain (78/180 aa) CDS Deleted
ENSMUSE00000233675 DH-domain (23/180 aa) CDS Deleted
ENSMUSE00000233666 Pleckstrin_homology (32/101 aa) CDS CDS
ENSMUSE00000233661 Pleckstrin_homology (69/101 aa) CDS CDS
ENSMUSE00000233653 CDS CDS
ENSMUSE00000412032 CDS + stop codon + UTR CDS + stop codon + UTR
Legend: in frame deleted frameshifted
ENSMUST00000162599 protein_coding Residual N-terminal, residual C-terminal product view

Predicted translation: 

MSAEQVPREVPLQFRRAPQHSHFSFDDIWLEKAQRRKLKKQMLLRRQMCAELVPEDPVQCWRKTTITSPESPHLPRRSHL
LSQSAPMGLDHTGWPEPTSDTGMPDGTLDTVCAEETGSEEDLYEELHNSGHHYSHPRGGGEQLAINELISDGSVVCAEAL
WDHVTMDDQELGFKAGDVIEVMDATNREWWWGRVADGEGWFPASFVRGEDLLVRSSELIHSGELTRVTQPQARSQQRMFF
LFDRQLIYCKKDLLRRDVLYYKGRLDMDDLEVVDVEDGKDRDLHVSVKNAFRLYCGTTGDSHLLCARKPEQKQRWLKAFA
REREQVRLDQETGFSITELQRKQAMLNASKQQATGKPKAVGRPGYLTRHKHPSLPASRPQQQVLVLAEPRRKPSNFWHSI
SRLAPFRK*

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00001004381 UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00000880582 CDS CDS
ENSMUSE00001005944 CDS CDS
ENSMUSE00001053718 SH3_domain (45/45 aa) | SH3_2 (45/46 aa) CDS CDS
ENSMUSE00001057754 SH3_2 (1/46 aa) CDS Deleted
ENSMUSE00000233682 DH-domain (76/98 aa) CDS Deleted
ENSMUSE00000233675 DH-domain (23/98 aa) CDS Deleted
ENSMUSE00000233666 Pleckstrin_homology (32/101 aa) CDS CDS
ENSMUSE00000233661 Pleckstrin_homology (69/101 aa) CDS CDS
ENSMUSE00000233653 CDS CDS
ENSMUSE00000852707 CDS + stop codon + UTR CDS
Legend: in frame deleted frameshifted
ENSMUST00000159021 protein_coding No analysis available: incomplete transcript
ENSMUST00000160855 nonsense_mediated_decay Residual N-terminal, unknown C-terminal view

Predicted translation: 

MDDQELGFKAGDVIEVMDATNREWWWGRVADGEGWFPASFVR

Ensembl Exon ID Pfam Domains WildType Floxed
ENSMUSE00000451258 UTR UTR
ENSMUSE00001057030 SH3_domain (37/37 aa) | SH3_2 (39/40 aa) UTR + start codon + CDS UTR + start codon + CDS
ENSMUSE00001057754 DH-domain (20/83 aa) | SH3_2 (1/40 aa) CDS Deleted
ENSMUSE00001051137 DH-domain (60/83 aa) CDS Deleted
ENSMUSE00000865347 DH-domain (3/83 aa) CDS + stop codon + UTR Deleted
ENSMUSE00000855946 UTR Deleted
Legend: in frame deleted frameshifted
ENSMUST00000162760 retained_intron No analysis available: incomplete transcript
ENSMUST00000159059 retained_intron No analysis available: incomplete 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 EPD0135_1_A05 PRPGS00075_A_F03 Arhgef4tm1a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8.N4 view yes 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 -
order EPD0135_1_D08 PRPGS00075_A_F03 Arhgef4tm1a(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 -
order EPD0873_4_H10 PG00075_V_1_F03 Arhgef4tm2a(KOMP)Wtsi Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) JM8A3.N1 view no view    ( about )
Production Centre
5' Screen not confirmed 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 -
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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 51087 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00075_V_1_F03 L1L2_Bact_P L4L3_pD223_DTA_spec view
order 51087 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00075_V_2_F03 L1L2_Bact_P L4L3_pD223_DTA_spec view
order 51087 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00075_V_3_F03 L1L2_Bact_P L4L3_pD223_DTA_spec view
order 51087 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00075_Z_3_F03 L1L2_Bact_P L4L3_pD223_DTA_spec view
order 51087 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PRPGS00075_B_F03 L1L2_Bact_P L4L3_pD223_DTA_spec view
order 51087 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00075_Z_4_F03 L1L2_Bact_P L4L3_pD223_DTA_spec view
order 51087 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00075_Z_2_G03 L1L2_Bact_P L4L3_pD223_DTA_spec view
order 51087 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PG00075_Z_1_F03 L1L2_Bact_P L4L3_pD223_DTA_spec view
order 51087 Knockout First, Reporter-tagged insertion with conditional potential (Promotor Driven Cassette) PRPGS00075_A_F03 L1L2_Bact_P L4L3_pD223_DTA_spec view
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Intermediate Vectors

Design ID Vector Type Intermediate Vector
51087 Knockout First, Reporter-tagged insertion with conditional potential PCS00075_A_F03
51087 Knockout First, Reporter-tagged insertion with conditional potential PCS00075_B_F03