RetrogeneDB ID: retro_hsap_19

Retrocopy location

• Organism: Human (Homo sapiens)
• Coordinates: 9:38395745..38397299(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSG00000137124
• Aliases: ALDH1B1, ALDH5, ALDHX
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ALDH2
• Ensembl ID: ENSG00000111275
• Aliases: ALDH2, ALDH-E2, ALDHI, ALDM
• Description: aldehyde dehydrogenase 2 family (mitochondrial) [Source:HGNC Symbol;Acc:404]

Sequence

>retro_hsap_19
ATGCTGCGCTTCCTGGCACCCCGGCTGCTTAGCCTCCAGGGCAGGACCGCCCGCTACTCCTCGGCAGCAGCCCTCCCAAG
CCCCATTCTGAACCCAGACATCCCCTACAACCAGCTGTTCATCAACAATGAATGGCAAGATGCAGTCAGCAAGAAGACCT
TCCCGACGGTCAACCCTACCACCGGGGAGGTCATTGGGCACGTGGCTGAAGGTGACCGGGCTGATGTGGATCGGGCCGTG
AAAGCAGCCCGGGAAGCCTTCCGCCTGGGGTCCCCATGGCGCCGGATGGATGCCTCTGAGCGGGGCCGGCTGCTGAACCG
CCTGGCAGACCTAGTGGAGCGGGATCGAGTCTACTTGGCCTCACTCGAGACCTTGGACAATGGGAAGCCTTTCCAAGAGT
CTTACGCCTTGGACTTGGATGAGGTCATCAAGGTGTATCGGTACTTTGCTGGCTGGGCTGACAAGTGGCATGGCAAGACC
ATCCCCATGGATGGCCAGCATTTCTGCTTCACCCGGCATGAGCCCGTTGGTGTCTGTGGCCAGATCATCCCGTGGAACTT
CCCCTTGGTCATGCAGGGTTGGAAACTTGCCCCGGCACTCGCCACAGGCAACACTGTGGTTATGAAGGTGGCAGAGCAGA
CCCCCCTCTCTGCCCTGTATTTGGCCTCCCTCATCAAGGAGGCAGGCTTTCCCCCTGGGGTGGTGAACATCATCACGGGG
TATGGCCCAACAGCAGGTGCGGCCATCGCCCAGCACGTGGATGTTGACAAAGTTGCCTTCACCGGTTCCACCGAGGTGGG
CCACCTGATCCAGAAAGCAGCTGGCGATTCCAACCTCAAGAGAGTCACCCTGGAGCTGGGTGGTAAGAGCCCCAGCATCG
TGCTGGCCGATGCTGACATGGAGCATGCCGTGGAGCAGTGCCACGAAGCCCTGTTCTTCAACATGGGCCAGTGCTGCTGT
GCTGGCTCCCGGACCTTCGTGGAAGAATCCATCTACAATGAGTTTCTCGAGAGAACCGTGGAGAAAGCAAAGCAGAGGAA
AGTGGGGAACCCCTTTGAGCTGGACACCCAGCAGGGGCCTCAGGTGGACAAGGAGCAGTTTGAACGAGTCCTAGGCTACA
TCCAGCTTGGCCAGAAGGAGGGCGCAAAACTCCTCTGTGGCGGAGAGCGTTTCGGGGAGCGTGGTTTCTTCATCAAGCCT
ACTGTCTTTGGTGGCGTGCAGGATGACATGAGAATTGCCAAAGAGGAGATCTTTGGGCCTGTGCAGCCCCTGTTCAAGTT
CAAGAAGATTGAGGAGGTGGTTGAGAGGGCCAACAACACCAGGTATGGCCTGGCTGCGGCTGTGTTCACCCGGGATCTGG
ACAAGGCCATGTACTTCACCCAGGCACTCCAGGCCGGGACCGTGTGGGTAAACACCTACAACATCGTCACCTGCCACACG
CCATTTGGAGGGTTTAAGGAATCTGGAAACGGGAGGGAGCTGGGTGAGGATGGGCTTAAGGCCTACACAGAGGTAAAGAC
GGTCACCATCAAGGTTCCTCAGAAGAACTCGTAA

Alignment

ORF - retro_hsap_19 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.73 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MLRAAARFGPRLGRRLLSAAATQAVPAPNQQPEVFCNQIFINNEWHDAVSRKTFPTVNPSTGEVICQVAE
          MLR..A.....L..R........A.P.P...P....NQ.FINNEW.DAVS.KTFPTVNP.TGEVI..VAE
Retrocopy MLRFLAPRLLSLQGRTARYSSAAALPSPILNPDIPYNQLFINNEWQDAVSKKTFPTVNPTTGEVIGHVAE

Parental  GDKEDVDKAVKAARAAFQLGSPWRRMDASHRGRLLNRLADLIERDRTYLAALETLDNGKPYVISYLVDLD
          GD..DVD.AVKAAR.AF.LGSPWRRMDAS.RGRLLNRLADL.ERDR.YLA.LETLDNGKP...SY..DLD
Retrocopy GDRADVDRAVKAAREAFRLGSPWRRMDASERGRLLNRLADLVERDRVYLASLETLDNGKPFQESYALDLD

Parental  MVLKCLRYYAGWADKYHGKTIPIDGDFFSYTRHEPVGVCGQIIPWNFPLLMQAWKLGPALATGNVVVMKV
          .V.K..RY.AGWADK.HGKTIP.DG..F..TRHEPVGVCGQIIPWNFPL.MQ.WKL.PALATGN.VVMKV
Retrocopy EVIKVYRYFAGWADKWHGKTIPMDGQHFCFTRHEPVGVCGQIIPWNFPLVMQGWKLAPALATGNTVVMKV

Parental  AEQTPLTALYVANLIKEAGFPPGVVNIVPGFGPTAGAAIASHEDVDKVAFTGSTEIGRVIQVAAGSSNLK
          AEQTPL.ALY.A.LIKEAGFPPGVVNI..G.GPTAGAAIA.H.DVDKVAFTGSTE.G..IQ.AAG.SNLK
Retrocopy AEQTPLSALYLASLIKEAGFPPGVVNIITGYGPTAGAAIAQHVDVDKVAFTGSTEVGHLIQKAAGDSNLK

Parental  RVTLELGGKSPNIIMSDADMDWAVEQAHFALFFNQGQCCCAGSRTFVQEDIYDEFVERSVARAKSRVVGN
          RVTLELGGKSP.I...DADM..AVEQ.H.ALFFN.GQCCCAGSRTFV.E.IY.EF.ER.V..AK.R.VGN
Retrocopy RVTLELGGKSPSIVLADADMEHAVEQCHEALFFNMGQCCCAGSRTFVEESIYNEFLERTVEKAKQRKVGN

Parental  PFDSKTEQGPQVDETQFKKILGYINTGKQEGAKLLCGGGIAADRGYFIQPTVFGDVQDGMTIAKEEIFGP
          PF...T.QGPQVD..QF...LGYI..G..EGAKLLCGG.....RG.FI.PTVFG.VQD.M.IAKEEIFGP
Retrocopy PFELDTQQGPQVDKEQFERVLGYIQLGQKEGAKLLCGGERFGERGFFIKPTVFGGVQDDMRIAKEEIFGP

Parental  VMQILKFKTIEEVVGRANNSTYGLAAAVFTKDLDKANYLSQALQAGTVWVNCYDVFGAQSPFGGYKMSGS
          V....KFK.IEEVV.RANN..YGLAAAVFT.DLDKA.Y..QALQAGTVWVN.Y.......PFGG.K.SG.
Retrocopy VQPLFKFKKIEEVVERANNTRYGLAAAVFTRDLDKAMYFTQALQAGTVWVNTYNIVTCHTPFGGFKESGN

Parental  GRELGEYGLQAYTEVKTVTVKVPQKNS
          GRELGE.GL.AYTEVKTVT.KVPQKNS
Retrocopy GRELGEDGLKAYTEVKTVTIKVPQKNS

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
bodymap2_adipose	15.66 RPM	333.89 RPM
bodymap2_adrenal	56.15 RPM	64.99 RPM
bodymap2_brain	4.73 RPM	197.93 RPM
bodymap2_breast	13.37 RPM	664.35 RPM
bodymap2_colon	18.91 RPM	256.66 RPM
bodymap2_heart	5.54 RPM	150.37 RPM
bodymap2_kidney	25.40 RPM	145.61 RPM
bodymap2_liver	30.54 RPM	513.35 RPM
bodymap2_lung	9.32 RPM	231.14 RPM
bodymap2_lymph_node	8.15 RPM	81.85 RPM
bodymap2_ovary	30.50 RPM	122.29 RPM
bodymap2_prostate	100.73 RPM	188.89 RPM
bodymap2_skeletal_muscle	24.10 RPM	84.12 RPM
bodymap2_testis	22.53 RPM	89.14 RPM
bodymap2_thyroid	25.40 RPM	145.32 RPM
bodymap2_white_blood_cells	3.80 RPM	124.13 RPM

ChIP-Seq

RNA Polymerase II activity near the 5' end of retro_hsap_19 was not detected

EST

30 EST(s) were mapped to retro_hsap_19 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA102706	38396031	38396192	96.9	159	2	156
AA313769	38396353	38396825	99.6	468	2	465
BE886318	38395867	38396529	97.2	646	11	631
BE889631	38395889	38396605	99	689	6	675
BE890488	38395733	38396385	99.4	648	2	642
BG402530	38396032	38396721	98.2	659	7	637
BI752803	38395733	38396534	97	792	8	774
BI762845	38395733	38396468	99.1	727	4	716
BM749166	38395798	38396281	99.4	480	3	477
BP282430	38396210	38396793	99.9	582	1	581
BQ229478	38395838	38396482	96.7	632	3	617
BQ302635	38395888	38396460	99.2	565	5	558
BQ318064	38396487	38396878	96.7	385	6	376
BQ322648	38395970	38396375	99.6	402	2	399
BQ349201	38396930	38397093	100	163	0	163
BQ362402	38396013	38396236	97.8	218	5	213
BQ362472	38396578	38396833	98.5	254	1	252
BQ362545	38396578	38396812	98.8	231	3	228
BQ953419	38395851	38396599	98.8	739	8	729
CN255157	38396228	38396426	98.5	198	0	197
CN255158	38395745	38396218	99.6	471	2	469
CN255159	38395745	38396359	99.9	613	1	612
CV025636	38395745	38396358	99.2	610	2	607
CV317139	38396247	38396472	98.7	222	3	219
DA485658	38395884	38396451	99.9	566	1	565
DA518874	38396041	38396586	98.9	542	3	538
DA762256	38396038	38396594	99.9	554	1	553
DR006146	38395758	38395890	100	131	0	131
HY001477	38395733	38396218	99.6	483	2	481
HY116078	38396003	38396479	99.8	475	1	474

TSS

No TSS is located nearby retro_hsap_19 retrocopy 5' end.

Lab

retro_hsap_19 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_hsap_19 has 8 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
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
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 22 parental genes, and 23 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 ,
Homo sapiens	ENSG00000164904	1 retrocopy	retro_hsap_3196,
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,