RetrogeneDB ID: retro_mmus_2196

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 3:110399129..110399774(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: Atp5o
• Ensembl ID: ENSMUSG00000022956
• Aliases: Atp5o, ATPO, D12Wsu28e, OSCP
• Description: ATP synthase, H+ transporting, mitochondrial F1 complex, O subunit [Source:MGI Symbol;Acc:MGI:106341]

Sequence

>retro_mmus_2196
ATGGCCACCCCAGCGGTGTCCAGTCTGTCCCAACAGACGCTGAGCTTCAGTGCATCTGTGGTCAGGCCCTTTGCCAAGCA
TGTGATGCCCCCTGTCTAGATATATGGCATTGAAGGTCACTGTACCACTTCTGTTTTTTCTGCTGCATCTAAAATGAATA
AGCAAGACTGAATGGAAAGGAGTTGCTGCTACTAGGACAACTCCTAAAAGATGCCAAGGTGTCTCTTACTCTTCTGAATT
CTTATATTAAGCACTGCATCAAAGTGAAAACCACGAAAGACATCACAACAAGGGAAATATTTTCCCCACTGATATCTAAC
CTCATCAATTTACTAGCTGAAAATGGTCACCTAAGCAACCAGGGAGTCATCTCTGCTTTTTCCACCACAGTGAGTATTTA
CCCTGGAAAAATGAGTTGCACTGTGACCACAGCATTTCCTTTATACGAAATTGTTCTCTCTGAGCTAATGACAGTGCTTA
TAGAGCATCTCAAGGCAAGGCCAGGTATTGAAATTTGAGGTTAAGACTGCCCCATTAATCATGGGTGAGATGGTTGCTGG
CATTGCTGAGAATTGGTGAGAAGTCATTAATATGTTTGCAAAGACCCCAGTTCAGAAGCTCAGCCAGATCATGAGGGAGA
TGCTT

Alignment

ORF - retro_mmus_2196 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.09 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAPAASGLSRQVRSFSTSVVRPFAKLVRPPVQVYGIEGRYATALYSAASKEKKLDQVE-KELLRVGQLL
          MA.PA.S.LS.Q..SFS.SVVRPFAK.V.PPV..YGIEG...T...SAASK..K.D..E.KELL..GQLL
Retrocopy MATPAVSSLSQQTLSFSASVVRPFAKHVMPPV*IYGIEGHCTTSVFSAASKMNKQD*ME<KELLLLGQLL

Parental  KDPKVSLAVLNPYIKRTVKVKSLNDITKREKFSPLTANLMNLLAENGRLGNTQGIISAFSTIMSVHRGEV
          KD.KVSL..LN.YIK...KVK...DIT.RE.FSPL..NL.NLLAENG.L.N.QG.ISAFST..S...G..
Retrocopy KDAKVSLTLLNSYIKHCIKVKTTKDITTREIFSPLISNLINLLAENGHLSN-QGVISAFSTTVSIYPGKM

Parental  PCTVTTASPLDDAVLSELKTVLKSFLS-PNQILKLEIKTDPSIMGGMIVRIGEKY---VDMSAKSKIQKL
          .CTVTTA.PL...VLSEL.TVL...L....Q.LK.E.KT.P.IMG.M...I.E.......M.AK...QKL
Retrocopy SCTVTTAFPLYEIVLSELMTVLIEHLK>QGQVLKFEVKTAPLIMGEMVAGIAENW*EVINMFAKTPVQKL

Parental  SKAMREML
          S..MREML
Retrocopy SQIMREML

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	0.00 RPM	104.29 RPM
SRP007412_cerebellum	0.00 RPM	95.09 RPM
SRP007412_heart	0.00 RPM	589.05 RPM
SRP007412_kidney	0.00 RPM	266.72 RPM
SRP007412_liver	0.00 RPM	102.49 RPM
SRP007412_testis	0.00 RPM	51.46 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_mmus_2196 was not detected

EST

No EST(s) were mapped for retro_mmus_2196 retrocopy.

TSS

No TSS is located nearby retro_mmus_2196 retrocopy 5' end.

Lab

retro_mmus_2196 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_2196 has 0 orthologous retrocopies within eutheria group .

---

Parental genes homology:

Parental genes homology involve 22 parental genes, and 47 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014708	1 retrocopy	retro_amel_1914,
Canis familiaris	ENSCAFG00000009541	3 retrocopies	retro_cfam_1277, retro_cfam_2198, retro_cfam_235,
Choloepus hoffmanni	ENSCHOG00000011242	1 retrocopy	retro_chof_638,
Callithrix jacchus	ENSCJAG00000002873	1 retrocopy	retro_cjac_1567,
Equus caballus	ENSECAG00000009059	1 retrocopy	retro_ecab_633,
Echinops telfairi	ENSETEG00000000807	5 retrocopies	retro_etel_1412, retro_etel_1906, retro_etel_507, retro_etel_839, retro_etel_841,
Felis catus	ENSFCAG00000028656	1 retrocopy	retro_fcat_1511,
Homo sapiens	ENSG00000241837	1 retrocopy	retro_hsap_2377,
Gorilla gorilla	ENSGGOG00000012611	1 retrocopy	retro_ggor_1803,
Macropus eugenii	ENSMEUG00000006613	4 retrocopies	retro_meug_122, retro_meug_1552, retro_meug_381, retro_meug_805,
Myotis lucifugus	ENSMLUG00000008224	3 retrocopies	retro_mluc_1833, retro_mluc_826, retro_mluc_856,
Macaca mulatta	ENSMMUG00000015504	1 retrocopy	retro_mmul_253,
Monodelphis domestica	ENSMODG00000021057	2 retrocopies	retro_mdom_280, retro_mdom_95,
Mustela putorius furo	ENSMPUG00000001319	5 retrocopies	retro_mputfur_1593, retro_mputfur_1628, retro_mputfur_1639, retro_mputfur_581, retro_mputfur_918,
Mus musculus	ENSMUSG00000022956	2 retrocopies	retro_mmus_2196 , retro_mmus_955,
Otolemur garnettii	ENSOGAG00000015850	4 retrocopies	retro_ogar_3518, retro_ogar_418, retro_ogar_559, retro_ogar_944,
Pongo abelii	ENSPPYG00000011384	1 retrocopy	retro_pabe_2247,
Pan troglodytes	ENSPTRG00000013876	1 retrocopy	retro_ptro_1739,
Rattus norvegicus	ENSRNOG00000001991	1 retrocopy	retro_rnor_2210,
Sarcophilus harrisii	ENSSHAG00000000409	3 retrocopies	retro_shar_369, retro_shar_389, retro_shar_668,
Sus scrofa	ENSSSCG00000012042	2 retrocopies	retro_sscr_226, retro_sscr_566,
Ictidomys tridecemlineatus	ENSSTOG00000008658	3 retrocopies	retro_itri_1030, retro_itri_565, retro_itri_794,