RetrogeneDB ID: retro_btau_1794

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: X:10114749..10116022(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSBTAG00000022399
• Aliases: None
• Status: KNOWN_PSEUDOGENE

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_1794
AAGAAGCCCAAGCGGCCGGCGGCGCCGCGCTCGCTGGTGAACTACCTGAAGGGGCGCGAGGTGGGCGCGCGGGGCCGCGC
CAGGCTCCCGGGCTTCGATGGCGAGCTGCGCGGCTTCGCGGTGCGGAAGCTCCCCGAGCTGCTACGGGAGCGCGAGCTGC
CCCTGGGCACCCTCAACAAGGTGTTCGCGTCACAGTGGCTGAACGCCAGGCAGGTGGTGTGCGGTACCAAGTGCAACACG
CTCTTCGTGGTGGACGTGCAGTCGGGCCAGATAACGCGCATCCCCCTTATGCGGGATCGCGGGCCTCCGCCGGCCCGCGC
CCAGCCGGGCTGCGGCATCCATGCCATCCAGCTGAATCCCTCCAAGACCCTGCTGGCCACCGGGGGCGAGAACCCCAACA
GCCTTGCCATCTACCAGTTGCCAACGCTGGACCCCATGTGCCTGGGCGACCGCCACGGCCACAAGGACTGGATCTTCGCC
ATCGCCTGGATGAGCGACACCGTGGCCGTGAGCGGCTCCCGTGACGGTACCTTGGCGCTCTGGAAGATAGACCCCGACAT
ATTCCAGGGCAGCATTGCCTGGCACAGCGATGCAGGGCTCCCCGTGTACGCCCACATCCGTCCCCGGGATGTGGAGAACA
TCCCCAGGGCCAGCACCAACCCCAGTAACCGCAAGGTGCGGGCCCTGGCCTTCAGCGCCAAGAACCAGGAGCTGGGAGCC
GTGTCCCTGGACGGCTACTTCCACCTGTGGAAAGCCCGGAGCACCCTGTCCAGGCTGCTGTCCATCAGGCTGCCCTACTG
CCGAGAGAACGTGTGCCTGACCTACTGCGATGAGTTGTCCCTCTACGCGGTGGGCTCCCAGTCCCATGTCTCTTTCCTGG
ATCCGCGGCAGCGCCAGCAGAACATTCGGCCCCTGTGCTCCCGCGAGGGCGGCACGGGTGTGCGCTCCCTCAGCTTCTAT
GAGCACATCGTCACCGTGGGCACCGGCCACGGCTCTCTGCTCTTCTATGACGTCCGCGCGCAGAAGTTCCTGGAGGAGAG
GGCCTCGGCCAGCCCGTACTCCTCTCCAGGGCATGCAGGGAGGAAGCTCAAGCTGACCTGTGGCAGAGGCTGGCTCAACC
ATGATGACCTGTGGGTGAACTATTTTCGGTGGCATCGGCGAGTTCCCCAACGCGCTCTACACCCACTGCTACAACTGGCC
GGAGATGAAGCTCTTTGTCGCTGGCGGCCCTCTCCCTTCAGGCCTCCATGGGAACTATGCAGGCCTCTGGAGC

Alignment

ORF - retro_btau_1794 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.12 %
• Parental protein coverage: 92.49 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KRKRLPPVKRSLVYYLKNREVRLQNET---SYSRVLHGYAAQQLPSLLKEREFHLGTLNKVFASQWLNHR
          K....P...RSLV.YLK.REV..............L.G.A...LP.LL.ERE..LGTLNKVFASQWLN.R
Retrocopy KKPKRPAAPRSLVNYLKGREVGARGRARLPGFDGELRGFAVRKLPELLRERELPLGTLNKVFASQWLNAR

Parental  QVVCGTKCNTLFVVDVQTSQITKIPILKDR-EPGCVTQQGCGIHAIELNPSRTLLATGGDNPNSLAIYRL
          QVVCGTKCNTLFVVDVQ..QIT.IP...DR..P....Q.GCGIHAI.LNPS.TLLATGG.NPNSLAIY.L
Retrocopy QVVCGTKCNTLFVVDVQSGQITRIPLMRDRGPPPARAQPGCGIHAIQLNPSKTLLATGGENPNSLAIYQL

Parental  PTLDPVCVGD-DGHKDWIFSIAWISDTMAVSGSRDGSMGLWEVTDDVLTKSDARHNVSRVPVYSHITHKA
          PTLDP.C.GD..GHKDWIF.IAW.SDT.AVSGSRDG...LW....D....S.A.H.....PVY.HI....
Retrocopy PTLDPMCLGDRHGHKDWIFAIAWMSDTVAVSGSRDGTLALWKIDPDIFQGSIAWHSDAGLPVYAHIRPRD

Parental  LKDIPKEDTNPDNCKVRALAFNNKNKELGAVSLDGYFHLWKTENTLSKLLSTKLPYCRENVCLAYGNEWS
          ...IP...TNP.N.KVRALAF..KN.ELGAVSLDGYFHLWK...TLS.LLS..LPYCRENVCL.Y..E.S
Retrocopy VENIPRASTNPSNRKVRALAFSAKNQELGAVSLDGYFHLWKARSTLSRLLSIRLPYCRENVCLTYCDELS

Parental  VYAVGSQAHVSFLDPRQPSYNVKSVCSRERGSGIRSVSFYEHIITVGTGQGSLLFYDIRAQRFLEEKLSA
          .YAVGSQ.HVSFLDPRQ...N....CSRE.G.G.RS.SFYEHI.TVGTG.GSLLFYD.RAQ.FLEE..SA
Retrocopy LYAVGSQSHVSFLDPRQRQQNIRPLCSREGGTGVRSLSFYEHIVTVGTGHGSLLFYDVRAQKFLEERASA

Parental  CYGSKPKLAGENLKLTTGKGWLNHDETWRNY-FSDIDFFPNAVYTHCYDSSGTKLFVAGGPLPSGLHGNY
          ...S.P..AG..LKLT.G.GWLNHD..W.NY.F..I..FPNA.YTHCY.....KLFVAGGPLPSGLHGNY
Retrocopy SPYSSPGHAGRKLKLTCGRGWLNHDDLWVNY>FGGIGEFPNALYTHCYNWPEMKLFVAGGPLPSGLHGNY

Parental  AGLWS
          AGLWS
Retrocopy AGLWS

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	0.11 RPM	58.97 RPM
SRP017611_brain	0.41 RPM	40.29 RPM
SRP017611_kidney	0.24 RPM	69.64 RPM
SRP017611_liver	0.08 RPM	41.08 RPM
SRP030211_testis	0.97 RPM	172.39 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1794 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1794 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1794 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Sus scrofa	retro_sscr_17
Equus caballus	retro_ecab_1128

---

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,