RetrogeneDB ID: retro_ecab_1129

Retrocopy location

• Organism: Horse (Equus caballus)
• Coordinates: X:100478965..100480132(-)
• Located in intron of: ENSECAG00000006930

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF12
• Ensembl ID: ENSECAG00000023064
• Aliases: DCAF12, WDR40A
• Description: DDB1 and CUL4 associated factor 12 [Source:HGNC Symbol;Acc:19911]

Sequence

>retro_ecab_1129
CTGCGCGGCTACGCGGTGCAGAAGCTGCCCGAGCTGCTGCGGGAGCGCGAGCTGGCCCTGGGCACCCTCAACAAGGTGTT
CGCGTCGCAGTGGCTGAACGCCAGGCAGGTGGTGTGCGGCACCAAGTGCAACACGCTCTTCGTGGTGGACGTGCAGTCGG
GCCAGATCACGCGCATCCCCCTCATGCGGGACCGGGAACCCGGGCCGGCTCGGGCCCAGCCGAGCTGCGGCATCCACGCC
ATCGAGTTGAATCCCTCCAAGACGCTTCTGGCCACGGGGGGCGAGAACCCCAACAGTCTGGCTGTCTACCAGCTGCCCAC
CCTGGACCCCGTGTGCCTGGGCGACCGCCTCGGCCACAGGGACTGGATCTTCGCCATCGCCTGGATAAGCGACACCGTGG
TCGTGAGCGGTTCCCGCGATGGCACCGTGGCTCTGTGGCGGATGGACCCCGACATATTCAATGGCAGCATCGCCTGGCAC
AATGACGCGGGGCTCCCCGTGTACGCCCACATCCGTCCAAGGGACTTGGAGACCATCCCCAGGGCCAACACCAACCCCAG
TAACCGCAAGGTACGGGCCCTGGCTTTTAATCGCAAGAACCAGGAGCTGGGAGCGGTGTCCCTGGACGGCTACTTCCACC
TGTGGAAAGCCCGGAGCACCCTGTCCAGGCTGCTGTCCATCAGGCTGCCCTACTGCCGAGAGAACGTGTGCCTAACCTAC
TGCGACGAGTTGTCCCTGTACGCGGTGGGCTCCCAATCCCACGTCTCCTTCCTGGATCTGCGCCATGGTCACCAAAACAT
CCGGCCCCTGTGCTCTCGAGAGGGCGGCACGGGCGTGCGCTCGCTGAGCTTCTACCAGCACATCGTCACCGTGGGCACGG
GCCACGGCTCCCTGCTCTTCTATGACGTCAGAGCCCAGAAGTTCCTGGAGGAGAAGGCCTTGGCCAGCCCGGACTCCTCT
CCCGGGCCCGCAGCGAGGAAGCTCAAGCTCACCTGTGGCAGAGGCTGGCTCAACCACGATGACCTGTGGGTGAACTACTT
TGGCGGCGTAGGCGAGTTCCCCAACGCGCTCTACACCCACTGCTACAACTGGCCTGAGATGAAGCTCTTCGTGGCTGGGG
GCCCTCTCCCTTCAGGCCTCCATGGGAACTACGCAGGCCTCTGGAGC

Alignment

ORF - retro_ecab_1129 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.15 %
• Parental protein coverage: 85.43 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LHGYAAQQLPGLLKEREFHLGTLNKVFASQWLNHRQVVCGTKCNTLFVVDVQTSQITKIPILKDREPGCV
          L.GYA.Q.LP.LL.ERE..LGTLNKVFASQWLN.RQVVCGTKCNTLFVVDVQ..QIT.IP...DREPG..
Retrocopy LRGYAVQKLPELLRERELALGTLNKVFASQWLNARQVVCGTKCNTLFVVDVQSGQITRIPLMRDREPGPA

Parental  -TQQGCGIHAIELNPSRTLLATGGDNPNSLAIYRLPTLDPVCVGDD-GHKDWIFSIAWISDSMAVSGSRD
          ..Q..CGIHAIELNPS.TLLATGG.NPNSLA.Y.LPTLDPVC.GD..GH.DWIF.IAWISD...VSGSRD
Retrocopy RAQPSCGIHAIELNPSKTLLATGGENPNSLAVYQLPTLDPVCLGDRLGHRDWIFAIAWISDTVVVSGSRD

Parental  GSMGLWEVTDDVLTKSDARHNVSRVPVYTHITHKALKDIPKEDTNPDNCKVRALAFNNKNKELGAVSLDG
          G...LW....D....S.A.HN....PVY.HI....L..IP...TNP.N.KVRALAFN.KN.ELGAVSLDG
Retrocopy GTVALWRMDPDIFNGSIAWHNDAGLPVYAHIRPRDLETIPRANTNPSNRKVRALAFNRKNQELGAVSLDG

Parental  YFHLWKAENTLSKLLSTKLPYCRENVCLAYGSEWSVYAVGSQAHVSFLDPRQPSYNVKSVCSRERGSGIR
          YFHLWKA..TLS.LLS..LPYCRENVCL.Y..E.S.YAVGSQ.HVSFLD.R....N....CSRE.G.G.R
Retrocopy YFHLWKARSTLSRLLSIRLPYCRENVCLTYCDELSLYAVGSQSHVSFLDLRHGHQNIRPLCSREGGTGVR

Parental  SVSFYEHIITVGTGQGSLLFYDIRAQRFLEERLAACYGSKPKLAGENLKLTTGKGWLNHDETWRNYFSDI
          S.SFY.HI.TVGTG.GSLLFYD.RAQ.FLEE...A...S.P..A...LKLT.G.GWLNHD..W.NYF...
Retrocopy SLSFYQHIVTVGTGHGSLLFYDVRAQKFLEEKALASPDSSPGPAARKLKLTCGRGWLNHDDLWVNYFGGV

Parental  DFFPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNYAGLWS
          ..FPNA.YTHCY.....KLFVAGGPLPSGLHGNYAGLWS
Retrocopy GEFPNALYTHCYNWPEMKLFVAGGPLPSGLHGNYAGLWS

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
SRP021940_articular_cartilage	0.00 RPM	33.71 RPM
SRP021940_cerebellum	1.30 RPM	26.07 RPM
SRP021940_embryo	0.64 RPM	40.79 RPM
SRP021940_placental_villous	0.00 RPM	44.02 RPM
SRP021940_synovial_membrane	0.11 RPM	39.64 RPM
SRP021940_testis	2.37 RPM	189.78 RPM

ChIP-Seq

Equus caballus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_ecab_1129 retrocopy.

TSS

Equus caballus was not studied using FANTOM5 data.

Lab

retro_ecab_1129 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_ecab_1129 has 1 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pongo abelii	retro_pabe_64

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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,