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 flat files 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 *

Background information

The UCSC website has this note about chrM:

“Note on chrM:

Since the release of the UCSC hg19 assembly, the Homo sapiens mitochondrion sequence (represented as "chrM" in the Genome Browser) has been replaced in GenBank with the record NC_012920. We have not replaced the original sequence, NC_001807, in the hg19 Genome Browser. We plan to use the Revised Cambridge Reference Sequence (rCRS) in the next human assembly release.”

The IGSR: The International Genome Sample Resource has this entry:

Which reference assembly do you use?

The reference assembly the 1000 genomes project has mapped sequence data that has changed over the course of the project.

For the pilot phase we mapped data to NCBI36. A copy of our reference FASTA file can be found on the ftp site.

For the phase1 and phase 3 analysis we mapped to GRCh37. Our FASTA file which can be found here called human_g1k_v37.fasta.gz, it contains the autosomes, X, Y and MT but no haplotype sequence or EBV.