RetrogeneDB ID: retro_mmus_222

Retrocopy location

• Organism: Mouse (Mus musculus)
• Coordinates: 4:45802463..45804023(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSMUSG00000035561
• Aliases: Aldh1b1, 2700007F14Rik
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Aldh2
• Ensembl ID: ENSMUSG00000029455
• Aliases: None
• Description: aldehyde dehydrogenase 2, mitochondrial [Source:MGI Symbol;Acc:MGI:99600]

Sequence

>retro_mmus_222
ATGCTGACTGCCCGACTCTTGCTGCCCCGGCTCCTCTGCCTCCAGGGCAGGACTACCTCTTACTCTACAGCAGCTGCTCT
CCCGAACCCAATCCCAAACCCAGAGATTTGCTACAACAAGCTGTTCATCAACAACGAGTGGCATGATGCGGTCAGCAAAA
AGACCTTCCCCACAGTGAACCCCACTACAGGTGAGGTCATTGGGCATGTGGCCGAAGGTGACCGGGCAGATGTGGATCTG
GCTGTAAAAGCAGCCCGAGAAGCCTTCCGCCTGGGGTCCCCATGGCGCAGGATGGATGCCTCAGAGCGGGGCCGGCTGCT
GAACCGCCTAGCTGATCTTGTGGAACGAGATCGAGTGTACTTGGCCTCACTGGAGACGCTAGATAACGGGAAACCTTTCC
AGGAGTCTTATGTCTTGGATCTGGATGAAGTCATCAAGGTGTACCGTTACTTCGCTGGCTGGGCTGACAAGTGGCATGGT
AAGACCATCCCTATGGATGGTGAGCATTTCTGCTTCACCCGACATGAGCCAGTGGGTGTCTGTGGCCAGATAATCCCTTG
GAACTTCCCACTGGTCATGCAGGGCTGGAAGCTGGCCCCGGCACTCGCCACGGGCAACACTGTGGTCATGAAGGTGGCAG
AGCAGACCCCACTCTCTGCTCTGTACTTGGCCTCCCTCATCAAAGAGGCGGGGTTTCCCCCAGGAGTGGTGAACATCATC
ACTGGCTACGGCCCCACGGCGGGAGCTGCCATCGCTCAGCACATGGATGTGGATAAAGTCGCCTTCACGGGCTCCACTGA
GGTAGGCCACCTGATTCAGAAGGCAGCTGGCGAGTCTAACCTCAAGAGAGTCACCCTGGAGCTGGGTGGGAAGAGCCCCA
GCATTGTGCTGGCAGACGCTGACATGGAGCATGCCGTAGATCAGTGTCACGAAGCCCTTTTCTTCAACATGGGCCAGTGC
TGCTGTGCAGGCTCCCGGACATTCGTGGAAGAGTCCATCTACCGTGAGTTTCTCGAGAGAACTGTGGAGAAGGCCAAGCA
GAGGAAAGTGGGGAACCCCTTTGAGTTGGACACCCAGCAGGGACCTCAGGTGGACAAGGAGCAGTTTGAACGAATCCTGG
GCTACATCCGGCTGGGACAGAAGGAAGGGGCAAAGCTTCTCTGTGGCGGGGAGCGTTTGGGGGAGCGCGGCTTCTTCATC
AAACCCACAGTCTTCGGGGACGTTCAGGATGGCATGAGGATCGCCAAGGAGGAGATCTTTGGGCCCGTGCAGCCTCTGTT
CAAGTTCAAGAAGATCGAGGAAGTAATCCAGAGAGCCAACAACACCAGGTATGGCCTGGCTGCGGCTGTGTTCACCCGAG
ACCTGGACAAGGCCATCTACTTCACGCAGGCCCTGCAAGCTGGGACGGTGTGGGTGAACACCTATAACATTGTCACCTGC
CACACGCCATTCGGAGGCTTTAAGGAATCTGGCAATGGCAGGGAGCTGGGGGAGGACGGGCTCAGAGCCTACACGGAGGT
GAAGACTGTCACCATCAAGGTTCCCGAGAAGAATTCCTGA

Alignment

ORF - retro_mmus_222 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.25 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRAALTTVRRGPRLSRLLSAAATSAVPAPNHQPEVFCNQIFINNEWHDAVSRKTFPTVNPSTGEVICQV
          ML.A.L...R......R..S.....A.P.P...PE...N..FINNEWHDAVS.KTFPTVNP.TGEVI..V
Retrocopy MLTARLLLPRLLCLQGRTTSYSTAAALPNPIPNPEICYNKLFINNEWHDAVSKKTFPTVNPTTGEVIGHV

Parental  AEGNKEDVDKAVKAARAAFQLGSPWRRMDASDRGRLLYRLADLIERDRTYLAALETLDNGKPYVISYLVD
          AEG...DVD.AVKAAR.AF.LGSPWRRMDAS.RGRLL.RLADL.ERDR.YLA.LETLDNGKP...SY..D
Retrocopy AEGDRADVDLAVKAAREAFRLGSPWRRMDASERGRLLNRLADLVERDRVYLASLETLDNGKPFQESYVLD

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

Parental  KVAEQTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEGVDKVAFTGSTEVGHLIQVAAGSSN
          KVAEQTPL.ALY.A.LIKEAGFPPGVVNI..G.GPTAGAAIA.H..VDKVAFTGSTEVGHLIQ.AAG.SN
Retrocopy KVAEQTPLSALYLASLIKEAGFPPGVVNIITGYGPTAGAAIAQHMDVDKVAFTGSTEVGHLIQKAAGESN

Parental  LKRVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQENVYDEFVERSVARAKSRVV
          LKRVTLELGGKSP.I...DADM..AV.Q.H.ALFFN.GQCCCAGSRTFV.E..Y.EF.ER.V..AK.R.V
Retrocopy LKRVTLELGGKSPSIVLADADMEHAVDQCHEALFFNMGQCCCAGSRTFVEESIYREFLERTVEKAKQRKV

Parental  GNPFDSRTEQGPQVDETQFKKILGYIKSGQQEGAKLLCGGGAAADRGYFIQPTVFGDVKDGMTIAKEEIF
          GNPF...T.QGPQVD..QF..ILGYI..GQ.EGAKLLCGG.....RG.FI.PTVFGDV.DGM.IAKEEIF
Retrocopy GNPFELDTQQGPQVDKEQFERILGYIRLGQKEGAKLLCGGERLGERGFFIKPTVFGDVQDGMRIAKEEIF

Parental  GPVMQILKFKTIEEVVGRANDSKYGLAAAVFTKDLDKANYLSQALQAGTVWINCYDVFGAQSPFGGYKMS
          GPV....KFK.IEEV..RAN...YGLAAAVFT.DLDKA.Y..QALQAGTVW.N.Y.......PFGG.K.S
Retrocopy GPVQPLFKFKKIEEVIQRANNTRYGLAAAVFTRDLDKAIYFTQALQAGTVWVNTYNIVTCHTPFGGFKES

Parental  GSGRELGEYGLQAYTEVKTVTVKVPQKNS
          G.GRELGE.GL.AYTEVKTVT.KVP.KNS
Retrocopy GNGRELGEDGLRAYTEVKTVTIKVPEKNS

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	4.37 RPM	58.80 RPM
SRP007412_cerebellum	0.83 RPM	66.70 RPM
SRP007412_heart	13.70 RPM	256.64 RPM
SRP007412_kidney	5.18 RPM	495.24 RPM
SRP007412_liver	56.34 RPM	1919.65 RPM
SRP007412_testis	10.29 RPM	81.32 RPM

ChIP-Seq

RNA Polymerase II actvity near the 5' end of retro_mmus_222 was not detected

EST

14 EST(s) were mapped to retro_mmus_222 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA144340	45802983	45803430	100	446	0	445
AA469589	45802928	45803371	99.3	421	1	405
AA655422	45802477	45802626	100	148	0	147
AI526762	45802789	45803177	98.2	380	6	372
AI528239	45802789	45803110	97.8	306	5	294
AI892559	45802983	45803455	100	472	0	472
BG962634	45802613	45803283	95.6	598	4	577
BG967081	45802887	45803484	99.2	595	2	592
BI217017	45802452	45803163	99.2	710	1	707
BI222043	45802457	45803162	99.5	700	1	692
BI414832	45802457	45803135	100	676	0	674
BI901537	45802978	45803528	99.7	548	2	546
BM894719	45803010	45803573	100	563	0	563
BU523348	45802452	45803274	97.7	809	4	794

TSS

No TSS is located nearby retro_mmus_222 retrocopy 5' end.

Lab

retro_mmus_222 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_mmus_222 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
Rattus norvegicus	retro_rnor_307
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,