RetrogeneDB ID: retro_btau_1796

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:10453572..10454265(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF12
• Ensembl ID: ENSBTAG00000021573
• Aliases: DCAF12, WDR40A
• Description: DDB1- and CUL4-associated factor 12 [Source:UniProtKB/Swiss-Prot;Acc:Q3MHH0]

Sequence

>retro_btau_1796
CGGCGCAATGCTGAAGGGCTCTCCGTGTATGCCCACATCCGTCCCGCGGAAGTGGAGGATGTCCCCAGGGCCTCCACCAA
CCGACGTAACTCCAAGGTGCGGGCTATGGCCTTCAGCGCCACGAGGCAGGAGCTGGGAGCCGTGACCATGGATGGCTACT
TCCACCTGTGGAAAGCCCAGAATACCTTGTCCAAGCTGTTGTCCATCAGGCTGCCTTACTGCAGAGAGAACGTGTGCCTG
ACCTTCTGCGGTGAGTTGTCCCTGTACGCGGTAGGCTCCCAGTCCCATGTCTCTTTCCTGGACCTGCGCCAGGGTCACCA
GAGCATCCGGTACCTGTGCTCCCACGAGGGCAGCACGGGTGTGCGCTCCCTCAGCTTCTATGAGCACATGGTCACCGTGG
GCACCGGCCACGGCTCTCTGCTGTTCTATGACATCCGCGCGCAGAAGTTCCTGGAGGAGAAGGTCTCGGACAGCCAGCAC
TCCTCTCCGCGGCCCACAGGGCGGAGGTTCAGGCTGATTTGTGGCAGAGGCTGGCTCAACCAAGATGACCTGCAGATGAA
CGACCTCAGTGCCTTGGGCGAGTTGCCCAATGCTCTCTACACCCATTGCTACAACTGGCCGGAGATGAAGCTCTTCGTCG
CTGGCGGCCCTCTTCCTTCAATCCTCCGTGGGAACTATGCAGGCCTCTGGAGC

Alignment

ORF - retro_btau_1796 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.31 %
• Parental protein coverage: 50.99 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RHNVSRVPVYSHITHKALKDIPKEDTNPDNCKVRALAFNNKNKELGAVSLDGYFHLWKTENTLSKLLSTK
          R.N.....VY.HI......D.P...TN..N.KVRA.AF.....ELGAV..DGYFHLWK..NTLSKLLS..
Retrocopy RRNAEGLSVYAHIRPAEVEDVPRASTNRRNSKVRAMAFSATRQELGAVTMDGYFHLWKAQNTLSKLLSIR

Parental  LPYCRENVCLAYGNEWSVYAVGSQAHVSFLDPRQPSYNVKSVCSRERGSGIRSVSFYEHIITVGTGQGSL
          LPYCRENVCL....E.S.YAVGSQ.HVSFLD.RQ........CS.E...G.RS.SFYEH..TVGTG.GSL
Retrocopy LPYCRENVCLTFCGELSLYAVGSQSHVSFLDLRQGHQSIRYLCSHEGSTGVRSLSFYEHMVTVGTGHGSL

Parental  LFYDIRAQRFLEEKLSACYGSKPKLAGENLKLTTGKGWLNHDETWRNYFSDIDFFPNAVYTHCYDSSGTK
          LFYDIRAQ.FLEEK.S....S.P...G....L..G.GWLN.D....N..S.....PNA.YTHCY.....K
Retrocopy LFYDIRAQKFLEEKVSDSQHSSPRPTGRRFRLICGRGWLNQDDLQMNDLSALGELPNALYTHCYNWPEMK

Parental  LFVAGGPLPSGLHGNYAGLWS
          LFVAGGPLPS.L.GNYAGLWS
Retrocopy LFVAGGPLPSILRGNYAGLWS

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	39.94 RPM
ERP005899_muscle	0.00 RPM	58.97 RPM
SRP017611_brain	0.00 RPM	40.29 RPM
SRP017611_kidney	0.00 RPM	69.64 RPM
SRP017611_liver	0.00 RPM	41.08 RPM
SRP030211_testis	1.16 RPM	172.39 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1796 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1796 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1796 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 15 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000309	1 retrocopy	retro_amel_73,
Bos taurus	ENSBTAG00000021573	3 retrocopies	retro_btau_1794, retro_btau_1795, retro_btau_1796 ,
Equus caballus	ENSECAG00000023064	2 retrocopies	retro_ecab_1128, retro_ecab_1129,
Erinaceus europaeus	ENSEEUG00000013279	1 retrocopy	retro_eeur_403,
Microcebus murinus	ENSMICG00000005881	1 retrocopy	retro_mmur_14,
Macaca mulatta	ENSMMUG00000017458	1 retrocopy	retro_mmul_202,
Nomascus leucogenys	ENSNLEG00000004996	1 retrocopy	retro_nleu_6,
Otolemur garnettii	ENSOGAG00000015799	1 retrocopy	retro_ogar_237,
Ochotona princeps	ENSOPRG00000001281	2 retrocopies	retro_opri_1178, retro_opri_470,
Pongo abelii	ENSPPYG00000019127	1 retrocopy	retro_pabe_64,
Pteropus vampyrus	ENSPVAG00000008654	1 retrocopy	retro_pvam_16,
Sus scrofa	ENSSSCG00000010986	1 retrocopy	retro_sscr_17,
Ictidomys tridecemlineatus	ENSSTOG00000006904	1 retrocopy	retro_itri_168,
Tarsius syrichta	ENSTSYG00000014394	1 retrocopy	retro_tsyr_1965,
Tursiops truncatus	ENSTTRG00000010591	1 retrocopy	retro_ttru_8,