RetrogeneDB ID: retro_rnor_307

Retrocopy location

• Organism: Rat (Rattus norvegicus)
• Coordinates: 5:65901494..65903054(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSRNOG00000011497
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Aldh2
• Ensembl ID: ENSRNOG00000001344
• Aliases: None
• Description: aldehyde dehydrogenase, mitochondrial precursor [Source:RefSeq peptide;Acc:NP_115792]

Sequence

>retro_rnor_307
ATGCTGAACGCCCGATTCTTGGTGCCCCGGCTCCTCTGCCTCCAGGGCAGGACCACCTCATATTCTACAGCGGCTGCTCT
CCCAAACCCAATCCCAAACCCAGAGATTCGCTACAACCAGCTGTTCATCAACAACGAGTGGCATGATGCGGTCAGCAAAA
AGACCTTCCCCACGGTGAACCCCACGACAGGCGAGGTCATTGGGCATGTGGCTGAAGGTGACCGGGCAGATGTGGATCTG
GCTGTGAGAGCAGCCCGAGAAGCCTTCCGCCTGGGGTCCCCGTGGCGCAGGATGGATGCCTCAGAGCGGGGCCGGCTGCT
GAACCGCCTAGCTGATCTCGTGGAACGGGATCGAGTGTACTTGGCCTCACTGGAGACCCTGGATAATGGGAAACCTTTTC
AGGAGTCTTATGTCTTGGACCTGGATGAAGTCATCAAGGTATACCGTTACTTTGCTGGCTGGGCTGACAAATGGCATGGT
AAGACCATCCCAATGGACGGCGAACATTTCTGCTTCACCCGCCATGAGCCAGTGGGTGTCTGTGGCCAGATAATCCCTTG
GAACTTCCCATTGGTCATGCAGGGTTGGAAGCTGGCCCCAGCACTCGCCACAGGCAACACCGTGGTCATGAAGGTGGCAG
AGCAAACCCCACTTTCTGCTCTGTACTTGGCCTCCCTCATCAAGGAAGCGGGGTTTCCCCCAGGAGTGGTGAATATCATC
ACCGGCTACGGCCCCACTGCAGGAGCAGCCATTGCCCAGCACATGGATGTGGATAAAGTCGCCTTCACCGGCTCTACCGA
GGTGGGCCACCTGATTCAGAAGGCCGCCGGTGATTCCAACCTCAAGAGAGTCACCCTGGAGCTGGGTGGGAAAAGCCCCA
GCATCGTGCTGGCAGACGCTGACATGGATCACGCCGTAGACCAGTGTCACGAAGCCCTCTTTTTCAACATGGGTCAGTGC
TGCTGTGCAGGATCCCGGACATTCGTGGAAGAGTCCATCTATCATGAGTTTCTCGAGAGAACTGTGGAGAAGGCCAAGAA
GAGGAAAGTGGGGAACCCCTTTGAGTTGGACACTCAACAGGGACCTCAGGTGGACAAGGAGCAATTTGAAAAGATCCTGG
GCTACATCCGGCTTGGACAGAAGGAAGGGGCAAAGCTTCTCTGTGGTGGGGAGCGTTTCGGGGAACGCGGCTTCTTCATC
AAGCCCACAGTCTTTGGGAATGTTCAGGATGACATGAGGATCGCCAGGGAGGAGATCTTTGGGCCTGTGCAGCCTCTGTT
CAAGTTCAAGAAGATCGAGGAAGTAATCCAGAGAGCCAACAATACCAGGTACGGCTTGGCTGCGGCTGTATTCACCCGAG
ACCTGGACAAGGCCTTATACTTTTCCCAGGCCCTGCAAGCCGGGACCGTGTGGGTGAACACCTACAATATCGTCACCTGC
CACACGCCATTCGGAGGCTTTAAGGAATCCGGCAATGGCAGAGAGCTGGGGGAAGATGGGCTTAAAGCCTACACGGAGGT
GAAGACTGTCACCATCAAGGTTTCTGAGAAGAATTCCTGA

Alignment

ORF - retro_rnor_307 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.45 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRAALSTARRGPRLSRLLSAAATSAVPAPNQQPEVFCNQIFINNEWHDAVSKKTFPTVNPSTGEVICQV
          ML.A.....R......R..S.....A.P.P...PE...NQ.FINNEWHDAVSKKTFPTVNP.TGEVI..V
Retrocopy MLNARFLVPRLLCLQGRTTSYSTAAALPNPIPNPEIRYNQLFINNEWHDAVSKKTFPTVNPTTGEVIGHV

Parental  AEGNKEDVDKAVKAARAAFQLGSPWRRMDASDRGRLLYRLADLIERDRTYLAALETLDNGKPYVISYLVD
          AEG...DVD.AV.AAR.AF.LGSPWRRMDAS.RGRLL.RLADL.ERDR.YLA.LETLDNGKP...SY..D
Retrocopy AEGDRADVDLAVRAAREAFRLGSPWRRMDASERGRLLNRLADLVERDRVYLASLETLDNGKPFQESYVLD

Parental  LDMVLKCLRYYAGWADKYHGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVM
          LD.V.K..RY.AGWADK.HGKTIP.DG..F..TRHEPVGVCGQIIPWNFPL.MQ.WKL.PALATGN.VVM
Retrocopy LDEVIKVYRYFAGWADKWHGKTIPMDGEHFCFTRHEPVGVCGQIIPWNFPLVMQGWKLAPALATGNTVVM

Parental  KVAEQTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEVGHLIQVAAGSSN
          KVAEQTPL.ALY.A.LIKEAGFPPGVVNI..G.GPTAGAAIA.H.DVDKVAFTGSTEVGHLIQ.AAG.SN
Retrocopy KVAEQTPLSALYLASLIKEAGFPPGVVNIITGYGPTAGAAIAQHMDVDKVAFTGSTEVGHLIQKAAGDSN

Parental  LKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDVYDEFVERSVARAKSRVV
          LKRVTLELGGKSP.I...DADMD.AV.Q.H.ALFFN.GQCCCAGSRTFV.E..Y.EF.ER.V..AK.R.V
Retrocopy LKRVTLELGGKSPSIVLADADMDHAVDQCHEALFFNMGQCCCAGSRTFVEESIYHEFLERTVEKAKKRKV

Parental  GNPFDSRTEQGPQVDETQFKKILGYIKSGQQEGAKLLCGGGAAADRGYFIQPTVFGDVKDGMTIAKEEIF
          GNPF...T.QGPQVD..QF.KILGYI..GQ.EGAKLLCGG.....RG.FI.PTVFG.V.D.M.IA.EEIF
Retrocopy GNPFELDTQQGPQVDKEQFEKILGYIRLGQKEGAKLLCGGERFGERGFFIKPTVFGNVQDDMRIAREEIF

Parental  GPVMQILKFKTIEEVVGRANNSKYGLAAAVFTKDLDKANYLSQALQAGTVWINCYDVFGAQSPFGGYKMS
          GPV....KFK.IEEV..RANN..YGLAAAVFT.DLDKA.Y.SQALQAGTVW.N.Y.......PFGG.K.S
Retrocopy GPVQPLFKFKKIEEVIQRANNTRYGLAAAVFTRDLDKALYFSQALQAGTVWVNTYNIVTCHTPFGGFKES

Parental  GSGRELGEYGLQAYTEVKTVTVKVPQKNS
          G.GRELGE.GL.AYTEVKTVT.KV..KNS
Retrocopy GNGRELGEDGLKAYTEVKTVTIKVSEKNS

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
SRP017611_brain	8.99 RPM	59.17 RPM
SRP017611_kidney	22.68 RPM	600.76 RPM
SRP017611_liver	14.25 RPM	1119.30 RPM

ChIP-Seq

Rattus norvegicus was not studied using ChIP-Seq data.

EST

1 EST(s) were mapped to retro_rnor_307 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
DY560872	65901648	65902363	99.9	709	0	707

TSS

Rattus norvegicus was not studied using FANTOM5 data.

Lab

retro_rnor_307 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_rnor_307 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_19
Pan troglodytes	retro_ptro_118
Gorilla gorilla	retro_ggor_33
Pongo abelii	retro_pabe_32
Macaca mulatta	retro_mmul_247
Mus musculus	retro_mmus_222
Bos taurus	retro_btau_48
Sus scrofa	retro_sscr_9

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Parental genes homology:

Parental genes homology involve 21 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013664	1 retrocopy	retro_amel_51,
Bos taurus	ENSBTAG00000008743	1 retrocopy	retro_btau_48,
Canis familiaris	ENSCAFG00000008683	1 retrocopy	retro_cfam_1493,
Equus caballus	ENSECAG00000017673	2 retrocopies	retro_ecab_1054, retro_ecab_1061,
Felis catus	ENSFCAG00000022000	1 retrocopy	retro_fcat_1590,
Homo sapiens	ENSG00000111275	1 retrocopy	retro_hsap_19,
Gorilla gorilla	ENSGGOG00000007108	1 retrocopy	retro_ggor_33,
Latimeria chalumnae	ENSLACG00000011798	1 retrocopy	retro_lcha_108,
Microcebus murinus	ENSMICG00000003487	1 retrocopy	retro_mmur_19,
Myotis lucifugus	ENSMLUG00000017084	1 retrocopy	retro_mluc_1918,
Macaca mulatta	ENSMMUG00000008336	1 retrocopy	retro_mmul_247,
Mustela putorius furo	ENSMPUG00000002282	1 retrocopy	retro_mputfur_27,
Mus musculus	ENSMUSG00000029455	1 retrocopy	retro_mmus_222,
Nomascus leucogenys	ENSNLEG00000000016	1 retrocopy	retro_nleu_22,
Otolemur garnettii	ENSOGAG00000033093	1 retrocopy	retro_ogar_203,
Pongo abelii	ENSPPYG00000004966	1 retrocopy	retro_pabe_32,
Pteropus vampyrus	ENSPVAG00000013189	1 retrocopy	retro_pvam_163,
Rattus norvegicus	ENSRNOG00000001344	1 retrocopy	retro_rnor_307 ,
Sus scrofa	ENSSSCG00000009889	1 retrocopy	retro_sscr_9,
Ictidomys tridecemlineatus	ENSSTOG00000015009	1 retrocopy	retro_itri_33,
Xenopus tropicalis	ENSXETG00000020930	1 retrocopy	retro_xtro_12,