Tools for the biologist enabling optimized use of gene trap clones

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UniTrap UNI26827
Trapped Gene
Dctn2 (ENSMUSG00000025410)
Vector Insertion
Chr 10: 126704539 - 126711769
Public Clones (sanger) (sanger) (sanger) (sanger) P138A08 (ggtc) P138A08 (ggtc)
D088H03 (ggtc) CMHD-GT_485G4-3 (cmhd) PST20694-NL (escells) IST14055H2 (tigm)
IST14055H2 (tigm)
Private Clones OST92617 (lexicon) OST42595 (lexicon) OST16308 (lexicon)
Severity of mutation (?) Insertion after 9% of polypeptide chain

Suggested RT-PCR (?)
Control PCR for the trapped allele
Upstream Exon
ENSMUSE00000278783 (Chr10:126704470..126704538 +)
Vector Sequence
Forward Primer Location Tm %GC LacZrt Reverse Primer Location
AGCGACCTACCTGAGGATGA Chr10:126704500..126704519 59.83 55 TGGCGAAAGGGGGATGTG Gene trap vector
Control PCR for the wild-type allele
Upstream Exon
ENSMUSE00000278783 (Chr10:126704470..126704538 +)
Downstram Exon
ENSMUSE00000278774 (Chr10:126711770..126711866 +)
Forward Primer Location Tm %GC Reverse Primer Location Tm %GC
AGCGACCTACCTGAGGATGA Chr10:126704500..126704519 59.83 55 TTGGGGTTGACAATGATGTG Chr10:126711819..126711838 60.22 45

Other possible Exon-Primers for RT-PCR (?)
  Exon ID Exon location Forward Primer Primer location Tm %GC
upstream ENSMUSE00000455534 Chr10:126703455..126703590 CCCTAAATACGCCGATCTCC Chr10:126703563..126703582 60.78 55
upstream ENSMUSE00000278783 Chr10:126704470..126704538 AGCGACCTACCTGAGGATGA Chr10:126704500..126704519 59.83 55

*** Putative Vector Insertion (Chr 10: 126704539 - 126711769) ***

  Exon ID Exon location Reverse Primer Primer location Tm %GC
downstream ENSMUSE00000278774 Chr10:126711770..126711866 TTGGGGTTGACAATGATGTG Chr10:126711819..126711838 60.22 45
downstream ENSMUSE00000150579 Chr10:126712050..126712111 TGGTCTTTCCAATGCGATCT Chr10:126712079..126712098 60.6 45
downstream ENSMUSE00000150581 Chr10:126712880..126712978 CCTTCACTCCCAGACCCTCT Chr10:126712907..126712926 60.64 60
downstream ENSMUSE00000150584 Chr10:126713440..126713600 No primer for this exon
downstream ENSMUSE00000150587 Chr10:126713758..126713905 TGGCAGCTTGAGAGAACTTG Chr10:126713906..126713925 59.31 50
downstream ENSMUSE00000150575 Chr10:126714311..126714376 AGACGCTTCTCGAGTTCTGC Chr10:126714336..126714355 59.9 55
downstream ENSMUSE00000150580 Chr10:126714543..126714581 TAAGGCAGGCTCCCTGTAGA Chr10:126714582..126714601 59.97 55
downstream ENSMUSE00000150573 Chr10:126714751..126714828 AAGCCGAGCCTCTACTTGGT Chr10:126714828..126714847 60.4 55
downstream ENSMUSE00000150578 Chr10:126714923..126714994 TCATTCACCTTTCCCAGGAC Chr10:126714948..126714967 59.9 50
downstream ENSMUSE00000150589 Chr10:126715176..126715278 GGTGACAAGTCGCTGTACCA Chr10:126715259..126715278 59.75 55
downstream ENSMUSE00000150586 Chr10:126715373..126715464 CTTAAGGGAACTGGCCATCA Chr10:126715443..126715462 60.07 50
downstream ENSMUSE00000361731 Chr10:126718457..126718862 GTACCCCACATGCAAGAACC Chr10:126718668..126718687 60.24 55

Suggested Genomic-PCR (?)
  Forward Forward location Tm %GC Reverse name Reverse Reverse Location
PCR 1 TCCTCGCCTTCTCTCTTGTC Chr10:126704542..126704562 59.68 55 L232 GATGTGCTGCAAGGCGATTA Gene trap vector
PCR 2 TCCTCGCCTTCTCTCTTGTC Chr10:126704542..126704562 59.68 55 LacZ CCAGGGTTTTCCCAGTCACG Gene trap vector

Come back to gene ENSMUSG00000025410