Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI23397
Trapped Gene
Syn1 (ENSMUSG00000037217)
Vector Insertion
Chr X: 20443035 - 20484202
Public Clones CMHD-GT_453B8-3 (cmhd) (cmhd) IST14108D10 (tigm) IST11531G10 (tigm)
IST14108D10 (tigm)
Private Clones OST261123 (lexicon) OST191587 (lexicon)
Severity of mutation (?) Insertion after 38% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000378197 (ChrX:20484203..20484292 -)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
GCCCAGATGGTTCGACTACA ChrX:20484270..20484289 61.07 55 TGGCGAAAGGGGGATGTG Gene trap vector
 
 
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000378197 (ChrX:20484203..20484292 -)
Downstram Exon
ENSMUSE00000324360 (ChrX:20442972..20443034 -)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
GCCCAGATGGTTCGACTACA ChrX:20484270..20484289 61.07 55 CCACAGGGTATGTTGTGCTG ChrX:20442988..20443007 60.03 55

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000468803 ChrX:20497539..20498022 GCTTCTTCTCGTCGCTGTCT ChrX:20497673..20497692 59.9 55
upstream ENSMUSE00000702543 ChrX:20497539..20498130 GCTTCTTCTCGTCGCTGTCT ChrX:20497673..20497692 59.9 55
upstream ENSMUSE00000324391 ChrX:20486651..20486708 GGGAAGAAGATCCATGGAGAA ChrX:20486672..20486692 60.4 47.62
upstream ENSMUSE00000324386 ChrX:20486463..20486554 TGGAAGTTCTTCGGAATGGA ChrX:20486477..20486496 60.57 45
upstream ENSMUSE00000624562 ChrX:20485077..20485233 CTTCAGCATGGCACGTAATG ChrX:20485175..20485194 60.28 50
upstream ENSMUSE00000378197 ChrX:20484203..20484292 GCCCAGATGGTTCGACTACA ChrX:20484270..20484289 61.07 55

*** Putative Vector Insertion (Chr X: 20443035 - 20484202) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000324360 ChrX:20442972..20443034 CCACAGGGTATGTTGTGCTG ChrX:20442988..20443007 60.03 55
downstream ENSMUSE00000624561 ChrX:20442245..20442387 GTTCTGCCCAATCTTCTGGA ChrX:20442237..20442256 60.19 50
downstream ENSMUSE00000324341 ChrX:20442081..20442155 GGTCTTCCAGTTACCCGACA ChrX:20442103..20442122 59.97 55
downstream ENSMUSE00000324329 ChrX:20441887..20441989 GATGTCAAGTCCCCCAAAAA ChrX:20441916..20441935 59.77 45
downstream ENSMUSE00000324320 ChrX:20440710..20440856 AGTTCCACGATGAGCTGCTT ChrX:20440767..20440786 60.02 50
downstream ENSMUSE00000324312 ChrX:20440309..20440396 No primer for this exon
downstream ENSMUSE00000495548 ChrX:20439899..20440216 AAAGATGTTGCTGGCCTTGT ChrX:20440108..20440127 59.74 45
downstream ENSMUSE00000556820 ChrX:20439625..20439814 No primer for this exon
downstream ENSMUSE00000624560 ChrX:20439625..20440216 AAAGATGTTGCTGGCCTTGT ChrX:20440108..20440127 59.74 45
downstream ENSMUSE00000702557 ChrX:20437641..20438735 GGGCTGTCTAGGGGTTTAGG ChrX:20438540..20438559 59.96 60
downstream ENSMUSE00000702539 ChrX:20437637..20438697 GGGCTGTCTAGGGGTTTAGG ChrX:20438540..20438559 59.96 60

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 AGATGCCAGAGATGCAAAGG ChrX:20454173..20454193 60.36 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 AGATGCCAGAGATGCAAAGG ChrX:20454173..20454193 60.36 50 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector
PCR 3 ATCCAAGCCACATCCATACG ChrX:20454300..20454320 60.74 50 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 4 CAAGAAGCTTGGAACAGAGGA ChrX:20454247..20454268 59.6 47.62 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000037217