RetrogeneDB ID: retro_btau_1832

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:86174532..86175120(-)
• Located in intron of: ENSBTAG00000011310

Retrocopy information

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

Parental gene information

• Parental gene symbol: BT.30256
• Ensembl ID: ENSBTAG00000004659
• Aliases: None
• Description: coenzyme Q-binding protein COQ10 homolog B, mitochondrial [Source:RefSeq peptide;Acc:NP_001069122]

Sequence

>retro_btau_1832
ATACTGATGAGCAGAACTCTTCCACTACACTCTTCAGTTTTGCCTAAGGAGATATATGCAAGAACTTTCTTCAGAATCAC
TGCACCATTAATAAACAGAAGAAAAAAATATTCAGAGAGGAGAATTATAGGATGTTCTATGCAGGAAATGTATGATGTGG
TATTAGGAACGGAGGATTACAAGCATTTTGCTCCTTGGTGCAAAAAAAAAGATGAAATATCAAGGAGATCTGAATACTGC
AAAACATGATTAGAAATTGGGTTTCTACCTGCAGTGGAGCACTATATATCAGTAGTAACCTTAGTGTAACCACATTTGGT
AAAGGCATACTGTGCTGATGGGAAGCTCTTCAATCATTTGGAGACTGTTTGGCATTTTAGCCCAGGTCTTCCTGGCTACC
CAAGAACTTCTACTTTGGATTTTTTCAATTTCTCTTGAATTTTGCAAACTTCTACCACAGCTTGCCACATGGTTTTTCAA
TGAAGTTGTAAAGCAGATGGTGTCTGCCTTTGAAAGAAGAGCGTGTAAGTGTATGGTCCAGAAACAAATATGCTTCAGGA
ATTAGTGCTTCATGAAGTTCATTGCACA

Alignment

ORF - retro_btau_1832 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.89 %
• Parental protein coverage: 80.74 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ILMSRTLPLHTSVFPKKIHARTFFRIAAPLINKRKEYSERRIIGYSMQEMYDVVSGMEDYKHFVPWCKKS
          ILMSRTLPLH.SV.PK.I.ARTFFRI.APLIN.RK.YSERRIIG.SMQEMYDVV.G.EDYKHF.PWC...
Retrocopy ILMSRTLPLHSSVLPKEIYARTFFRITAPLINRRKKYSERRIIGCSMQEMYDVVLGTEDYKHFAPWCXXX

Parental  DIISRRSGYCKTRLEIGFPPVLERYTSVVTLVKPHLVKASCTDGKLFNHLETVWRFSPGLPGYPRTCTLD
          D.ISRRS.YCKT.LEIGF.P..E.Y.SVVTLV.PHLVKA.C.DGKLFNHLETVW.FSPGLPGYPRT.TLD
Retrocopy DEISRRSEYCKT*LEIGFLPAVEHYISVVTLV*PHLVKAYCADGKLFNHLETVWHFSPGLPGYPRTSTLD

Parental  -FSISFEFRSLLHSQLAMLFFDEVVKQMVTAFERRACK-LYGPETNIPRELMLHEVHHT
          .FSIS.EF..LL..QLA..FF.EVVKQMV.AFERRACK..YGPETN...EL.LHEVH.T
Retrocopy >FSISLEFCKLL-PQLATWFFNEVVKQMVSAFERRACK<VYGPETNMLQELVLHEVHCT

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
ERP005899_liver	0.00 RPM	49.24 RPM
ERP005899_muscle	0.05 RPM	6.86 RPM
SRP017611_brain	0.05 RPM	12.61 RPM
SRP017611_kidney	0.12 RPM	29.52 RPM
SRP017611_liver	0.00 RPM	13.52 RPM
SRP030211_testis	0.00 RPM	24.96 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1832 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1832 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1832 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004659	2 retrocopies	retro_btau_1595, retro_btau_1832 ,
Choloepus hoffmanni	ENSCHOG00000005807	1 retrocopy	retro_chof_1504,
Callithrix jacchus	ENSCJAG00000003971	1 retrocopy	retro_cjac_1836,
Dasypus novemcinctus	ENSDNOG00000003229	2 retrocopies	retro_dnov_1571, retro_dnov_2203,
Dipodomys ordii	ENSDORG00000004090	1 retrocopy	retro_dord_508,
Erinaceus europaeus	ENSEEUG00000001626	1 retrocopy	retro_eeur_401,
Felis catus	ENSFCAG00000022385	1 retrocopy	retro_fcat_1487,
Homo sapiens	ENSG00000115520	1 retrocopy	retro_hsap_3349,
Gorilla gorilla	ENSGGOG00000023373	2 retrocopies	retro_ggor_2270, retro_ggor_569,
Myotis lucifugus	ENSMLUG00000000865	1 retrocopy	retro_mluc_1236,
Macaca mulatta	ENSMMUG00000010488	1 retrocopy	retro_mmul_2434,
Monodelphis domestica	ENSMODG00000012281	1 retrocopy	retro_mdom_600,
Mus musculus	ENSMUSG00000025981	1 retrocopy	retro_mmus_3224,
Nomascus leucogenys	ENSNLEG00000006871	1 retrocopy	retro_nleu_1172,
Ochotona princeps	ENSOPRG00000010091	3 retrocopies	retro_opri_1020, retro_opri_173, retro_opri_664,
Pongo abelii	ENSPPYG00000013045	2 retrocopies	retro_pabe_2758, retro_pabe_576,
Pan troglodytes	ENSPTRG00000012772	1 retrocopy	retro_ptro_2137,
Rattus norvegicus	ENSRNOG00000014456	1 retrocopy	retro_rnor_1620,
Tarsius syrichta	ENSTSYG00000012642	2 retrocopies	retro_tsyr_1213, retro_tsyr_1666,