Codon differences in chromosome M

Chromosome M has its own genome that is different in 4 codons from the other chromosomes.

Ion Reporter™ Software uses the Homo sapiens mitochondrion, complete genome NCBI Reference Sequence: NC_012920.1.

The new rCRS chrM assembly has 16569 bases. The previous version had 16571 bases.

The 2 coding tables, one for standard chromosomes and one for chromosome M, are listed below. These tables are from the following NCBI site:

http://www.ncbi.nlm.nih.gov/Taxonomy/Utils/wprintgc.cgi#SG2

The Standard Code (transl_table=1) for chromosomes 1-22, X and Y (NUCLEAR)

By default all transl_table in GenBank flatfiles are equal to id 1, and this is not shown. When transl_table is not equal to id 1, it is shown as a qualifier on the CDS feature.

Note: In these tables, an asterisk represents a STOP codon.

TTT F Phe      TCT S Ser      TAT Y Tyr      TGT C Cys  
TTC F Phe      TCC S Ser      TAC Y Tyr      TGC C Cys  
TTA L Leu      TCA S Ser      TAA * Ter      TGA * Ter  
TTG L Leu i    TCG S Ser      TAG * Ter      TGG W Trp  
CTT L Leu      CCT P Pro      CAT H His      CGT R Arg  
CTC L Leu      CCC P Pro      CAC H His      CGC R Arg  
CTA L Leu      CCA P Pro      CAA Q Gln      CGA R Arg  
CTG L Leu i    CCG P Pro      CAG Q Gln      CGG R Arg  
ATT I Ile      ACT T Thr      AAT N Asn      AGT S Ser  
ATC I Ile      ACC T Thr      AAC N Asn      AGC S Ser  
ATA I Ile      ACA T Thr      AAA K Lys      AGA R Arg  
ATG M Met i    ACG T Thr      AAG K Lys      AGG R Arg  
GTT V Val      GCT A Ala      GAT D Asp      GGT G Gly  
GTC V Val      GCC A Ala      GAC D Asp      GGC G Gly  
GTA V Val      GCA A Ala      GAA E Glu      GGA G Gly  
GTG V Val      GCG A Ala      GAG E Glu      GGG G Gly 

The Vertebrate Mitochondrial Code (transl_table=2) for chromosome M.

TTT F Phe      TCT S Ser      TAT Y Tyr      TGT C Cys  
TTC F Phe      TCC S Ser      TAC Y Tyr      TGC C Cys  
TTA L Leu      TCA S Ser      TAA * Ter      TGA W Trp  
TTG L Leu      TCG S Ser      TAG * Ter      TGG W Trp  
CTT L Leu      CCT P Pro      CAT H His      CGT R Arg  
CTC L Leu      CCC P Pro      CAC H His      CGC R Arg  
CTA L Leu      CCA P Pro      CAA Q Gln      CGA R Arg  
CTG L Leu      CCG P Pro      CAG Q Gln      CGG R Arg  
ATT I Ile i    ACT T  Thr      AAT N Asn      AGT S  Ser  
ATC I Ile i    ACC T Thr      AAC N Asn      AGC S Ser  
ATA M Met i    ACA T Thr      AAA K Lys      AGA * Ter  
ATG M Met i    ACG T Thr      AAG K Lys      AGG * Ter  
GTT V Val      GCT A Ala      GAT D Asp      GGT G Gly  
GTC V Val      GCC A Ala      GAC D Asp      GGC G Gly  
GTA V Val      GCA A Ala      GAA E Glu      GGA G Gly  
GTG V Val i    GCG A Ala      GAG E Glu      GGG G Gly  

The differences from the Standard Code are:

Code 2

Standard

AGA

Ter *

Arg R

AGG

Ter *

Arg R

AUA

Met M

Ile I

UGA

Trp W

Ter *