RetrogeneDB ID: retro_cfam_41

Retrocopy location

• Organism: Dog (Canis familiaris)
• Coordinates: 22:50363194..50364211(-)
• Located in intron of: ENSCAFG00000005838

Retrocopy information

• Ensembl ID: ENSCAFG00000005851
• 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_41
ACGCTCTCCGCCCTCGCCCGCCCTGCCGGCGCCGCTCTCCACCGCAGCTTCAGCACCTCGGCCCAGAACAATGCTAAAGT
AGCTGTGCTTGGGGCTTCCGGAGGAATTGGGCAGCCCCTTGCACTGCTTCTCAAGAACAGCCCCTTAGTGAGCCGCCTGA
CCCTCTACGATATTGCTCATACACCCGGAGTGGCCGCAGATCTGAGCCACATCGAGACCAGAGCAACCGTGAAAGGCTAC
CTTGGACCTGAGCAGCTGCCGGATTGCCTCAAAGGCTGCGATGTGGTGGTTATTCCAGCTGGAGTCCCAAGAAAACCAGG
CATGACACGGAATGACCTGTTCAACACCAATGCCTCAATTGTGGCCACCCTGACTGCTGCCTGCGCCCAGCATTGCCCCG
AGGCCATGATCTGCGTCATTTCAAATCCGGTCAACTCCACCATCCCAATTGCAACAGAGGTTTTCAAGAAACACGGAGCT
TACGACCCCAATAAAATCTTCGGGGTGACGACCCTGGACATTGTCAGGGCCAACACTTTCATTGCAGAACTAAAGGGTTT
GGATCCCGCGCGAGTCAATGTTCCTGTCATTGGCGGTCATGCCGGGAAGACCATCATCCCCCTGATATCTCAGTGCACTC
CCAAGGTGGACCTTCCCCAGGACCAGCTGACAGCCGTCACTGGGCGGATTCAGGAGGCCGGCACGGAGGTGGTGAAGGCC
AAAGCTGGAGCAGGCTCTGCCACCCTGTCCATGGCATACGCTGGAGCTCGGTTTGTCTTCTCCCTTGTGGATGCAATGAA
TGGGAAGGAAGGAGTTGTCGAATGTTCCTTTGTTAAATCCCAGGAAGCAGACTGTGCCTATTTCTCCACACCATTACTGC
TGGGGAAAAAGGGCATCGAGAAGAATCTAGGCATTGGCAAGATCTCCCCTTCTGAAGAGAAGATGATAGCAGAAGCCATC
CCCGAGCTGAAGGCCTCCATCAAAAAGGGAGAGGAGTTTGTGAAGAACATGAAATGA

Alignment

ORF - retro_cfam_41 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.11 %
• Parental protein coverage: 99.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LSALARPAGAALRRSFSTSAQNNAKVAVLGASGGIGQPLALLLKNSPLVSRLTLYDIAHTPGVAADLSHI
          LSALARPAGAAL.RSFSTSAQNNAKVAVLGASGGIGQPLALLLKNSPLVSRLTLYDIAHTPGVAADLSHI
Retrocopy LSALARPAGAALHRSFSTSAQNNAKVAVLGASGGIGQPLALLLKNSPLVSRLTLYDIAHTPGVAADLSHI

Parental  ETRATVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRDDLFNTNASIVATLTAACAQHCPEAMICVIS
          ETRATVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTR.DLFNTNASIVATLTAACAQHCPEAMICVIS
Retrocopy ETRATVKGYLGPEQLPDCLKGCDVVVIPAGVPRKPGMTRNDLFNTNASIVATLTAACAQHCPEAMICVIS

Parental  NPVNSTIPIATEVFKKHGAYDPNKIFGVTTLDIVRANTFIAELKGLDPARVNVPVIGGHAGKTIIPLISQ
          NPVNSTIPIATEVFKKHGAYDPNKIFGVTTLDIVRANTFIAELKGLDPARVNVPVIGGHAGKTIIPLISQ
Retrocopy NPVNSTIPIATEVFKKHGAYDPNKIFGVTTLDIVRANTFIAELKGLDPARVNVPVIGGHAGKTIIPLISQ

Parental  CTPKVDLPQDQLTAVTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQ
          CTPKVDLPQDQLTAVTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQ
Retrocopy CTPKVDLPQDQLTAVTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMNGKEGVVECSFVKSQ

Parental  EADCAYFSTPLLLGKKGIEKNLGIGKISPFEEKMIAEAIPELKASIKKGEEFVKNMK
          EADCAYFSTPLLLGKKGIEKNLGIGKISP.EEKMIAEAIPELKASIKKGEEFVKNMK
Retrocopy EADCAYFSTPLLLGKKGIEKNLGIGKISPSEEKMIAEAIPELKASIKKGEEFVKNMK

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	2.69 RPM	50.69 RPM
SRP017611_brain	0.08 RPM	64.31 RPM
SRP017611_kidney	0.13 RPM	107.84 RPM
SRP017611_liver	1.16 RPM	37.42 RPM

ChIP-Seq

Canis familiaris was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_cfam_41 retrocopy.

TSS

Canis familiaris was not studied using FANTOM5 data.

Lab

retro_cfam_41 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_cfam_41 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,