HGPS+Results

DNA Alignment


 * Using Blastn (Blast setting that searches nucleotides only) the human nucleotide sequence was one of the first items obtained during initial stages of research:

ORIGIN 1 gtgggaccat ccagttgcag gaaaacaagc ttaacacgcc cactgattct acattatgct 61 cctacctccc agcagcctct ccaggcccag aactttctcc agtcagcctc tacagaccaa 121 gctcatgact cacaatggcc tatttaggcc cataccctac ctcacggcag tctccgcaga 181 tgagcctact gcctcacaac agcctccaca ggcacagctc catcgttaca atggcctctt 241 tagacccagc tcctgcctcc cagccttctc tccaggccct gaactttctc aagtcgacct 301 caccaggccc agctcatgct tctttgcagc ctctccaggc ccagctcctg catcttggtg 361 gcacctccag gcccagcctc tgcctcccgt cggcctctac aatcccaaca tctgcctcac 421 agcagattct tcaggcccag catctgcctc actgtggacc ccccaagcca agctcccaac 481 ctttcagcag cttctacaca cccaactcct gccacccagt ggcctcttta ggccaagctc 541 atgcttcaca agggcctttc caggctcaac ttttgtctca tggcaacctt tcctggccag 601 attcctgcct gtctcccagc agcctagaca ggcccaggtc ttgcctcaca ctggcctctc 661 tacatccagc tcatgcctca cggtggcctc tccaggccca actcctgtcc caggacgtca 721 tctccgggcc caaaacttac tcaagtcaga ctctctagtc ccaactgctg cctcctggtg 781 gcctatgaag gcccaaaatc tcctcaagtg gacctctcca ggcccagctc ctgcctcctg <span style="display: block; font-family: Verdana,Geneva,sans-serif; text-align: justify;">841 tcagcgtcta caggcccaac ctctgcctca tgggggcttc tccaggccca cctcttcctc <span style="display: block; font-family: Verdana,Geneva,sans-serif; text-align: justify;">901 ttggctgggt ctacaggcac aactgctgcc tcacaacagc cttttttggc ccagttcctg <span style="display: block; font-family: Verdana,Geneva,sans-serif; text-align: justify;">961 tccagctcat ggcggccaat gtaggcccaa aacttcctca agtcaaactc tccaggccca <span style="display: block; font-family: Verdana,Geneva,sans-serif; text-align: justify;">1021 ccttctgctt cccggtggca tgaacaggcc cagctttgac ttgagaacag cctctgcagg <span style="display: block; font-family: Verdana,Geneva,sans-serif; text-align: justify;">1081 ccctgctctt gcctcccagg ggctttttcc agacccagct cctgcctcat ggcagctgcc

<span style="font-family: Verdana,Geneva,sans-serif;">1141 ccaggccaaa tttctgcctg cctgccagca gcctcaacag gcacagctcc tccctcacag

<span style="font-family: Verdana,Geneva,sans-serif;">1201 tggcccattt aggcccaact catga


 * <span style="font-family: Verdana,Geneva,sans-serif; line-height: 1.5;">In order to compare the human sequence, nucleotide sequences of eight different species LMNA gene were then aligned and compared in MEGA6:
 * 1) <span style="font-family: Verdana,Geneva,sans-serif;">Synthetic construct homo sapien
 * 2) <span style="font-family: Verdana,Geneva,sans-serif;">Homo sapiens
 * 3) <span style="font-family: Verdana,Geneva,sans-serif;">Common chimpanzee
 * 4) <span style="font-family: Verdana,Geneva,sans-serif;">Water buffalo
 * 5) <span style="font-family: Verdana,Geneva,sans-serif;">Pig
 * 6) <span style="font-family: Verdana,Geneva,sans-serif;">Minke whale
 * 7) <span style="font-family: Verdana,Geneva,sans-serif;">Cattle
 * 8) <span style="font-family: Verdana,Geneva,sans-serif;">Crab-eating macaque

<span style="font-family: Verdana,Geneva,sans-serif;">Species were selected and aligned:

<span style="font-family: Verdana,Geneva,sans-serif;">A phylogenetic analysis was performed:

<span style="color: #ea7017; font-family: Verdana,Geneva,sans-serif; font-size: 130%;">Protein Alignment


 * <span style="font-family: Verdana,Geneva,sans-serif; line-height: 1.5;">Protein sequences of seven species were aligned and compared using MEGA6:
 * 1) <span style="font-family: Verdana,Geneva,sans-serif;">Norwegian rat
 * 2) <span style="font-family: Verdana,Geneva,sans-serif;">African clawed frog
 * 3) <span style="font-family: Verdana,Geneva,sans-serif;">Humans
 * 4) <span style="font-family: Verdana,Geneva,sans-serif;">House mouse
 * 5) <span style="font-family: Verdana,Geneva,sans-serif;">Pig
 * 6) <span style="font-family: Verdana,Geneva,sans-serif;">Zebrafish
 * 7) <span style="font-family: Verdana,Geneva,sans-serif;">Chicken

<span style="font-family: Verdana,Geneva,sans-serif;">Phylogenetic analysis was performed:

<span style="color: #ea7118; font-family: Verdana,Geneva,sans-serif; font-size: 120%;">Cn3D Results



Another view of the C-terminus of LMNA:

<span style="color: #ea7017; font-family: Verdana,Geneva,sans-serif; font-size: 120%;">STRING Results



<span style="font-family: Verdana,Geneva,sans-serif;"> The associated proteins and their functions according to the STRING (Fig. 7) results are shown below:
 * <span style="font-family: Verdana,Geneva,sans-serif;">EMD (emerin): stabilize and promote formation of nuclear actin cortical network
 * <span style="font-family: Verdana,Geneva,sans-serif;">LMNB1 (lamin B1): nuclear lamina component
 * <span style="font-family: Verdana,Geneva,sans-serif;">LMNB2 (lamin B2): nuclear lamina component
 * <span style="font-family: Verdana,Geneva,sans-serif;">CASP6 (caspase 6): apoptosis-related cysteine peptidase
 * <span style="font-family: Verdana,Geneva,sans-serif;">FOS (FBJ murine osteosarcoma viral oncogene homolog) nuclear phosphoprotein
 * <span style="font-family: Verdana,Geneva,sans-serif;">TMPO (thymopoietin) may help direct assembly of nuclear lamina
 * <span style="font-family: Verdana,Geneva,sans-serif;">UBE21 (ubiquitin-conjugating enzyme) accepts ubiquitin-like proteins
 * <span style="font-family: Verdana,Geneva,sans-serif;">SYNE1 (spectrin repeat) maintain nuclear organization
 * <span style="font-family: Verdana,Geneva,sans-serif;">CD83 (CD83 molecule) role in antigen presentation
 * <span style="font-family: Verdana,Geneva,sans-serif;">NARF: nuclear prelmain A recognition factor

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