RetrogeneDB ID: retro_mmus_631

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 10:28922733..28923507(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000090126
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: Pdha1
• Ensembl ID: ENSMUSG00000031299
• Aliases: Pdha1, Pdha-1
• Description: pyruvate dehydrogenase E1 alpha 1 [Source:MGI Symbol;Acc:MGI:97532]

Sequence

>retro_mmus_631
GCAAGCAGAGTGCTGGTAGCTTCCCGTAATTTTTCAAATGATGCTACATTTGAGATTAAGAAATTTGACCTTCATCTGTT
AGAAGAGAGCCCTCCAGTCACCACAGTGCTCACCAGAGAGGATGGGCTCAAGTACTACACAAGATGATGCACACTGTGCG
CCAGATGGAGCTAAAGGCAGATCAACTGTATAAGCAGAAAATTATTCGTGTTTTTTGTCACTTGTGCAATGGTCAGGAAG
CCTGCTGTATGGGCCTGGAGGCTGGCATAAACCCCACGGACCATCTCATCACCGCCCATTGTGCGTATGGCTTCACCTTC
ACTCGGAGCCTGCCTGTCTGTGCAGTTCTTGCGAAGCTAACCACACGAAGAGAAGGTTGTGCTAAAGGGAAAGGCGAACC
AATGCACATGTATGCCAAGAACTTCTATGGGGGCAATGCCATTGTTGGAAGTCAGATGCCTCTGGGAGCAGGAATTGCTC
TGGCCTGCAAGTACAATGGAAAAGATGAGATCTGTTTGACAGTATATGGCGATGGTGCGGCTAACCAGGGTCAGATATTT
GAACCTTAAAATATGGCAGCATTGTGGAAATTACCTTGTATTTTCATCTGTGAGAATAACTGCTATGGCATGGGAATATC
GGTTGACAGCGCAGCAGCCATAACAGACTACTATAAAAGAGGAGATTTTATTCCTGGACTGAGGGTAGATGGAATGGATA
CTTGTGTATCCAAAGGAAACAAAGTTTGCAGCTGCCTATTGCAGGTTTGGTAAG

Alignment

ORF - retro_mmus_631 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.63 %
• Parental protein coverage: 66.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ASRVLVASRNFANDATFEIKKCDLHRLEEG-PPVTTVLTREDGLKY-YRMMQTVRRMELKADQLYKQKII
          ASRVLVASRNF.NDATFEIKK.DLH.LEE..P..T..........Y...MM.TVR.MELKADQLYKQKII
Retrocopy ASRVLVASRNFSNDATFEIKKFDLHLLEESPPVTTVLTREDGLKYY<HKMMHTVRQMELKADQLYKQKII

Parental  RGFCHLCDGQEACCVGLEAGINPTDHLITAYRAHGFTFTRGLPVRAILAELTGRRGGCAKGKGGSMHMYA
          R.FCHLC.GQEACC.GLEAGINPTDHLITA..A.GFTFTR.LPV.A.LA.LT.RR.GCAKGKG..MHMYA
Retrocopy RVFCHLCNGQEACCMGLEAGINPTDHLITAHCAYGFTFTRSLPVCAVLAKLTTRREGCAKGKGEPMHMYA

Parental  KNFYGGNGIVGAQVPLGAGIALACKYNGKDEVCLTLYGDGAANQGQIFEAYNMAALWKLPCIFICENNRY
          KNFYGGN.IVG.Q.PLGAGIALACKYNGKDE.CLT.YGDGAANQGQIFE..NMAALWKLPCIFICENN.Y
Retrocopy KNFYGGNAIVGSQMPLGAGIALACKYNGKDEICLTVYGDGAANQGQIFEP*NMAALWKLPCIFICENNCY

Parental  GMGTSVERAAASTDYYKRGDFIPGLRVDGMD-ILCVR-EATKFAAAYCRSGK
          GMG.SV..AAA.TDYYKRGDFIPGLRVDGMD..LC.....TKFAAAYCR.GK
Retrocopy GMGISVDSAAAITDYYKRGDFIPGLRVDGMD<YLCIQ<KETKFAAAYCRFGK

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	136.25 RPM
SRP007412_cerebellum	0.00 RPM	111.85 RPM
SRP007412_heart	0.03 RPM	816.64 RPM
SRP007412_kidney	0.04 RPM	506.84 RPM
SRP007412_liver	0.00 RPM	102.02 RPM
SRP007412_testis	0.00 RPM	4.25 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_631 was not detected

EST

No EST(s) were mapped for retro_mmus_631 retrocopy.

TSS

No TSS is located nearby retro_mmus_631 retrocopy 5' end.

Lab

retro_mmus_631 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_631 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000016730	1 retrocopy	retro_amel_400,
Bos taurus	ENSBTAG00000019852	2 retrocopies	retro_btau_100, retro_btau_1807,
Callithrix jacchus	ENSCJAG00000005496	2 retrocopies	retro_cjac_2414, retro_cjac_27,
Dipodomys ordii	ENSDORG00000011848	1 retrocopy	retro_dord_35,
Equus caballus	ENSECAG00000001964	1 retrocopy	retro_ecab_21,
Erinaceus europaeus	ENSEEUG00000005485	1 retrocopy	retro_eeur_580,
Homo sapiens	ENSG00000131828	1 retrocopy	retro_hsap_41,
Gorilla gorilla	ENSGGOG00000013574	1 retrocopy	retro_ggor_59,
Myotis lucifugus	ENSMLUG00000012932	2 retrocopies	retro_mluc_2363, retro_mluc_323,
Macaca mulatta	ENSMMUG00000017336	1 retrocopy	retro_mmul_123,
Mustela putorius furo	ENSMPUG00000003269	1 retrocopy	retro_mputfur_812,
Mus musculus	ENSMUSG00000031299	2 retrocopies	retro_mmus_63, retro_mmus_631 ,
Nomascus leucogenys	ENSNLEG00000009805	1 retrocopy	retro_nleu_74,
Oryctolagus cuniculus	ENSOCUG00000014748	1 retrocopy	retro_ocun_264,
Pongo abelii	ENSPPYG00000020171	1 retrocopy	retro_pabe_129,
Pan troglodytes	ENSPTRG00000021717	1 retrocopy	retro_ptro_79,
Pteropus vampyrus	ENSPVAG00000005420	1 retrocopy	retro_pvam_1306,
Sarcophilus harrisii	ENSSHAG00000015375	1 retrocopy	retro_shar_84,
Sus scrofa	ENSSSCG00000023643	2 retrocopies	retro_sscr_1015, retro_sscr_281,
Ictidomys tridecemlineatus	ENSSTOG00000015433	1 retrocopy	retro_itri_1529,
Tupaia belangeri	ENSTBEG00000014313	1 retrocopy	retro_tbel_3327,
Tursiops truncatus	ENSTTRG00000000660	1 retrocopy	retro_ttru_1427,