https://www.youtube.com/watch?v=5o1foQX8wvg /mnt/1T-5e7/mycodehtml/Biology/SangSooKim/Bioinformatics_basic/005/001_Nucleotide_RefSeq_and_translation/main.html ================================================================================ Click search ================================================================================ Click advanced ================================================================================ X chromosome ================================================================================ Configure "Base position" ================================================================================ Put the "Base position" Click Search ================================================================================ rs387... reference SNP's ID ================================================================================ ================================================================================ ================================================================================ Click rs387... reference SNP's ID ================================================================================ ================================================================================ RefSeq accession numbers ================================================================================ To represent sequence of genomic molecules, use NC ================================================================================ To represent mRNA sequence, use NM ================================================================================ To represent protein sequence, use NP ================================================================================ To represent non-coding RNA sequence (which doesn't code the protein), use NR ================================================================================ To represent mRNA and protein sequence, but when it starts with "X", it's a model ================================================================================ NC: chromosome ================================================================================ Search NC_000023 ================================================================================ GRCh38: RefSeq version 38 ================================================================================ Click ================================================================================ Database becomes Nucleotide ================================================================================ /home/young/Pictures/2019_07_01_08:50:13.png Total size of this DNA: 156040895 bp Linear DNA 12-MAR-2015: updated date Version: 11 ================================================================================ /home/young/Pictures/2019_07_01_08:55:00.png - Split X chromosome into 9 pieces - Sequence and analyze them in individual teams ================================================================================ /home/young/Pictures/2019_07_01_08:57:15.png Let's search the data with NM_001167 /home/young/Pictures/2019_07_01_08:57:43.png ================================================================================ /home/young/Pictures/2019_07_01_08:58:13.png 8460 bp mRNA Version: 3 ================================================================================ /home/young/Pictures/2019_07_01_09:00:31.png CDS: coding sequence /home/young/Pictures/2019_07_01_09:01:09.png 1...159: non coding sequence ATG: starting codon ================================================================================ Translate "3 base pairs" into protein /home/young/Pictures/2019_07_01_09:02:26.png ================================================================================ 1...159: 5' UTR 1654...: 3' UTR UTR: untranslated region ================================================================================ /home/young/Pictures/2019_07_01_09:06:28.png In this mRNA, 608th base pair has potential variant (G ---> A) c608: in coding sequence, 608th base pair 160th base pair: start base - Calculation 160th bp, 1th coding base xth bp, 608th bp has potential SNP x=160th_bp+608th_bp-1 x=767th_bp ================================================================================ /home/young/Pictures/2019_07_01_09:11:53.png This G is converted into A in SNP ================================================================================ Find "amino acid position" of this SNP (608th_bp-1)/3=203.333 This SNP occurs in 203th codon Cys is converted into Tyr ================================================================================