RetrogeneDB ID: retro_cfam_182

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 15:33618051..33619038(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSCAFG00000006166
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: MDH2
• Ensembl ID: ENSCAFG00000013515
• Aliases: None
• Description: Malate dehydrogenase [Source:UniProtKB/TrEMBL;Acc:F1PYG8]

Sequence

>retro_cfam_182
ATGCTCTCCGCCCTTGCCCGCCCTGCCGGTGCCTCTCTCCGCCGCAGCGTCAGCACCTCGGCCCAGAACAATGCTAAAGT
AGCTGTGCTTGGGGCTTCCGGAGGAATCAGGCAGATAGTGAGCTGCCTGACCCTCTACGATATTGCTCATACACCCAGAG
TGGCCGCAGATCTGAGCCACATCGAGACCAGAGCAACCGTGAAAGGCTACCTTGGACCTGAGCAGCTGCCGGATTGCCTC
AAAGGCTGCGATGTGGTGGTTATTCCAGCCGGAGTCCCAAGAAAACCAGGCATGACACGGGATGACCTGTTCAACATCAA
TGCCTCAATTGTGGACACCCTGACTGCTGCCTGCGCCCAGCATTGCCCCGAAGCCGTGATCTGCGTCATTTCAAATCCGG
TCAACTCCACCATCCCAATTGCAACGGAGGTTTTCAAGAAACACGGAGCTTACGACTCCAATAAAATCTTCGGGGTGACG
ACCCTGGACATTGTCAGGGCCAACACTTTCACTGCAGAACTAAAGGGTTTGGATCCCGCGCGAGCCAATGTTCCTGTCAT
TGGTGGTCATGCCGGGAAGACCATTATCCCTCTGATCTCTCAGTGCACTCCCAAGGTGGACCTTCCCCAGGACCAGCTGA
CAGCCGTCACTGGGCAGATTCAGGAGGCCGGCACGGAGGTGGTGAAGGCCAAAGCTGGAGCAGGCTCTGCCACCCTGTCC
ATGGCATACGCTGGAGCCCGGTTTGTCTTCTCCCTTGTGGATGCAGTGAATGGGAAGGAAGGAATTGTCGAATGTTCCTT
TGTTAAATCCCAGGACACAGACAGTGACTATTTCTCCACACCATTACTGCTGGAGAAAAAGGGCATCGAGAAGAATCTAG
GCATTGGCAAGATCTCCCCTTTTGAAGAGAAGATGATAGCAGAAGCCATCCCTGAGCTGAAGGCCTCCATCAAAAAGGGA
GAGGAGTTTGTGAAGAACATGAAATGA

Alignment

ORF - retro_cfam_182 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.14 %
• Parental protein coverage: 85.8 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVSRLTLYDIAHTPGVAADLSHIETRATVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNA
          .VS.LTLYDIAHTP.VAADLSHIETRATVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFN.NA
Retrocopy IVSCLTLYDIAHTPRVAADLSHIETRATVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNINA

Parental  SIVATLTAACAQHCPEAMICVISNPVNSTIPIATEVFKKHGAYDPNKIFGVTTLDIVRANTFIAELKGLD
          SIV.TLTAACAQHCPEA.ICVISNPVNSTIPIATEVFKKHGAYD.NKIFGVTTLDIVRANTF.AELKGLD
Retrocopy SIVDTLTAACAQHCPEAVICVISNPVNSTIPIATEVFKKHGAYDSNKIFGVTTLDIVRANTFTAELKGLD

Parental  PARVNVPVIGGHAGKTIIPLISQCTPKVDLPQDQLTAVTGRIQEAGTEVVKAKAGAGSATLSMAYAGARF
          PAR.NVPVIGGHAGKTIIPLISQCTPKVDLPQDQLTAVTG.IQEAGTEVVKAKAGAGSATLSMAYAGARF
Retrocopy PARANVPVIGGHAGKTIIPLISQCTPKVDLPQDQLTAVTGQIQEAGTEVVKAKAGAGSATLSMAYAGARF

Parental  VFSLVDAMNGKEGVVECSFVKSQEADCAYFSTPLLLGKKGIEKNLGIGKISPFEEKMIAEAIPELKASIK
          VFSLVDA.NGKEG.VECSFVKSQ..D..YFSTPLLL.KKGIEKNLGIGKISPFEEKMIAEAIPELKASIK
Retrocopy VFSLVDAVNGKEGIVECSFVKSQDTDSDYFSTPLLLEKKGIEKNLGIGKISPFEEKMIAEAIPELKASIK

Parental  KGEEFVKNMK
          KGEEFVKNMK
Retrocopy KGEEFVKNMK

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	0.21 RPM	50.69 RPM
SRP017611_brain	0.40 RPM	64.31 RPM
SRP017611_kidney	0.53 RPM	107.84 RPM
SRP017611_liver	0.07 RPM	37.42 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_182 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_182 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_182 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010846	1 retrocopy	retro_amel_361,
Canis familiaris	ENSCAFG00000013515	2 retrocopies	retro_cfam_182 , retro_cfam_41,
Myotis lucifugus	ENSMLUG00000017795	1 retrocopy	retro_mluc_1948,
Monodelphis domestica	ENSMODG00000013680	1 retrocopy	retro_mdom_1711,
Mustela putorius furo	ENSMPUG00000016000	2 retrocopies	retro_mputfur_1607, retro_mputfur_478,
Mus musculus	ENSMUSG00000019179	1 retrocopy	retro_mmus_2451,
Otolemur garnettii	ENSOGAG00000009705	1 retrocopy	retro_ogar_3068,
Pteropus vampyrus	ENSPVAG00000003397	1 retrocopy	retro_pvam_981,
Tupaia belangeri	ENSTBEG00000003190	1 retrocopy	retro_tbel_440,
Tursiops truncatus	ENSTTRG00000014834	1 retrocopy	retro_ttru_1550,
Drosophila melanogaster	FBgn0262559	2 retrocopies	retro_dmel_54, retro_dmel_76,