RetrogeneDB ID: retro_mmus_2451

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:36003322..36003845(-)
• Located in intron of: ENSMUSG00000045083

Retrocopy information

• Ensembl ID: ENSMUSG00000082169
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Mdh2
• Ensembl ID: ENSMUSG00000019179
• Aliases: Mdh2, MDH, Mdh-2, Mor-1, Mor1
• Description: malate dehydrogenase 2, NAD (mitochondrial) [Source:MGI Symbol;Acc:MGI:97050]

Sequence

>retro_mmus_2451
CAGCACTGACCTGAAGCCAATGTTTGCACCATTGCCAATCTAGTTAACTCAACCATCCCTGTCACAGCAGAAGTTTTCAA
GAAGCATGGCGTGTACAACCTCAACAAGATCTTTGGTGTGACAACCCTTGACATCATGAGAACGAACGTTTGTGGCAGAG
CTAAAGGGTCAATCCAGCTCAAGACAACATGCCATCATTGGTGGTCACACCGGGAAGAAGATCATGCCCCTGATCTCTCA
GTGTACTTTCAAGGTTGACTTTCCCCAAGACCAGCTAGCCTCTGGGAGGATCCAGGAGGCTGGCACAGATGTAGTAAAGG
CCAAGGCTGCTCTTTCTATGGCTTATAATGGGGTCTGCTTTGTCCTCTTCATCATGGATGCCATGAATAGGAAGGAAGGA
AGGAGTTGCTGAGTGTTCTTCTGTTCAGTCCAAAGAGACAGAGTGTACGTATTTCTCTACACCATTTCGATTAGGGGCAA
AAAGGACCCGGAGAAGAAGAACCTGGGTATTGGCAACATCTCT

Alignment

ORF - retro_mmus_2451 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.28 %
• Parental protein coverage: 53.25 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QHCPEAMVCIIANPVNSTIPITAEVFKKHGVYNPNKIFGVTTLDIVRANTFVAELKG-LDPARVNVP-VI
          QH.PEA.VC.IAN.VNSTIP.TAEVFKKHGVYN.NKIFGVTTLDI.R.N......KG...PA..N.P..I
Retrocopy QH*PEANVCTIANLVNSTIPVTAEVFKKHGVYNLNKIFGVTTLDIMRTNV-CGRAKG<VNPAQDNMP<II

Parental  GGHAGKTIIPLISQCTPKVDFPQDQLATLTGRIQEAGTEVVKAKAGAGSATLSMAYAGARFVFSLVDAMN
          GGH.GK.I.PLISQCT.KVDFPQDQLA...GRIQEAGT.VVKAKA....A..........F.........
Retrocopy GGHTGKKIMPLISQCTFKVDFPQDQLA--SGRIQEAGTDVVKAKAALSMAYNGVCF--VLFIMDAMNRKE

Parental  GKEGVVECSFVQSKETECTYFSTPLLLGKKGLE-KNLGIGKIT
          G....V....VQ..........T....GKK..E.KNLGIG.I.
Retrocopy GRSC*VFFCSVQ-RDRVYVFLYTISIRGKKDPEKKNLGIGNIS

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
SRP007412_brain	0.02 RPM	210.13 RPM
SRP007412_cerebellum	0.00 RPM	243.77 RPM
SRP007412_heart	0.00 RPM	1255.51 RPM
SRP007412_kidney	0.00 RPM	584.59 RPM
SRP007412_liver	0.00 RPM	199.16 RPM
SRP007412_testis	0.00 RPM	33.53 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_2451 was not detected

EST

No EST(s) were mapped for retro_mmus_2451 retrocopy.

TSS

No TSS is located nearby retro_mmus_2451 retrocopy 5' end.

Lab

retro_mmus_2451 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2451 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,