RetrogeneDB ID: retro_cfam_35

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 13:13580883..13581342(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000000798
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MGST3
• Ensembl ID: ENSCAFG00000013353
• Aliases: None
• Description: Canis lupus familiaris microsomal glutathione S-transferase 3 (MGST3), mRNA. [Source:RefSeq mRNA;Acc:NM_001252410]

Sequence

>retro_cfam_35
ATGGCTGTCCTCTCGAAGGAATATGGTTTCGTGGTTCTAACCGGTGCTGCTAGCTTCATAATGGTAGCTCATCTAGCCAT
CAATGTTTCCAAGGCCCGAAAGAAGTACAAAGTGGAGTATCCCACCATGTACAGCACGGACCCCGAAAACGGGCACCTGT
TCAACTGCATTCAGCGCGCCCACCAGAACACGTTGGAAGTGTATCCTCCGTTCTTATTTTTCCTAGCGGTTGGAGGTGTT
TACCACCCGCGTATAGCTTCTGGCCTGGGCTTGGCCTGGATTGTTGGACGAGTTCTTTATGCCTATGGTTATTACACAGG
AGAGCCCAGCAAGCGGAGTCGGGGAGCCCTGGGCTCCTTAGCCCTCATCGGCCTGATGGGCACCACGGTGTTCTCTGCCT
TCCAGCATCTTGGTTGGGTTAAAACTGGCTTGGGCGGTGGATCCAAATGCTGCCATTGA

Alignment

ORF - retro_cfam_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAVLSKEYGFVVLTGAASFIMVAHLAINVSKARKKYKVEYPTMYSTDPENGHLFNCIQRAHQNTLEVYPP
          MAVLSKEYGFVVLTGAASFIMVAHLAINVSKARKKYKVEYPTMYSTDPENGHLFNCIQRAHQNTLEVYPP
Retrocopy MAVLSKEYGFVVLTGAASFIMVAHLAINVSKARKKYKVEYPTMYSTDPENGHLFNCIQRAHQNTLEVYPP

Parental  FLFFLAVGGVYHPRIASGLGLAWIVGRVLYAYGYYTGEPSKRSRGALGSLALIGLMGTTVFSAFQHLGWV
          FLFFLAVGGVYHPRIASGLGLAWIVGRVLYAYGYYTGEPSKRSRGALGSLALIGLMGTTVFSAFQHLGWV
Retrocopy FLFFLAVGGVYHPRIASGLGLAWIVGRVLYAYGYYTGEPSKRSRGALGSLALIGLMGTTVFSAFQHLGWV

Parental  KTGLGGGSKCCH
          KTGLGGGSKCCH
Retrocopy KTGLGGGSKCCH

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Expression validation based on RNA-Seq data:

Library	Retrocopy expression	Parental gene expression
SRP012049_cerebellum	11.76 RPM	18.73 RPM
SRP017611_brain	6.75 RPM	23.26 RPM
SRP017611_kidney	59.63 RPM	130.03 RPM
SRP017611_liver	1.31 RPM	4.50 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_35 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_35 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_35 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006658	1 retrocopy	retro_amel_1210,
Canis familiaris	ENSCAFG00000013353	1 retrocopy	retro_cfam_35 ,
Choloepus hoffmanni	ENSCHOG00000012723	2 retrocopies	retro_chof_1872, retro_chof_356,
Echinops telfairi	ENSETEG00000003507	3 retrocopies	retro_etel_1328, retro_etel_1527, retro_etel_1544,
Mustela putorius furo	ENSMPUG00000003817	1 retrocopy	retro_mputfur_1251,
Mus musculus	ENSMUSG00000026688	1 retrocopy	retro_mmus_2709,
Oryctolagus cuniculus	ENSOCUG00000010376	1 retrocopy	retro_ocun_270,
Procavia capensis	ENSPCAG00000015774	2 retrocopies	retro_pcap_385, retro_pcap_393,
Rattus norvegicus	ENSRNOG00000004245	1 retrocopy	retro_rnor_195,
Tupaia belangeri	ENSTBEG00000005299	2 retrocopies	retro_tbel_2989, retro_tbel_752,