RetrogeneDB ID: retro_btau_393

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 11:18248437..18248980(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SCO1
• Ensembl ID: ENSBTAG00000021780
• Aliases: None
• Description: Protein SCO1 homolog, mitochondrial [Source:UniProtKB/Swiss-Prot;Acc:A1A4J8]

Sequence

>retro_btau_393
ATGGCAGGGCTGTCACTCGTGCTGGCTGGATAATGCGGCTTCCGGCAGCCAACTTTGGCGTCTCTTGCCTCACGGATTCT
GGGTTTGGTGCCCAGGGAAGGAGACCATGAGGGTCTTGCTGGGGCAGCTCTGCACGAAGCCAGAGGAGGCATGACGAGCC
TCCGGGCAGGCTGGCTGCTGCCTGGGGAGCCGCCCCCTTGACACTGTGATGCCGCCCCCTCCCAGGTCGTCAGGACCCCA
GAACGGAAGGGCAGCAGAGACCCCACGTGCCCCCTTGAAGCCCGGGCCTGTTTCCTGGAAGTCTTTAGCCATCACATTTG
CTATTTGGGGAGCTTTATTGGCTGGAGTGAAGTACTTCAAGAAAGAAAAGACAGAGAAACTGGAGAAGGAATGGCAGCGA
AGCATTGGAAAGCCTTTATTGGGGGCCCGTTTTCCCTCACAACTCATACTGGCAAGTCCAAAACTGATAAGGACTACCTG
GGTCAATGGGTATTGATTTATTTTGGTTTTACTGATTGTCCTGATGAACTAGAAGAACTAGTT

Alignment

ORF - retro_btau_393 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.6 %
• Parental protein coverage: 60.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAGLLLA-PGRIMRLP-GSQLWRLFPRGFGVWGPGKETASVLLGRLCARPEEAWRASGLAACCLGSRPLS
          MAGL.L...G.IMRLP.GSQLWRL.P.GF.VW.PGKET..VLLG.LC..PEEA.RASG.A.CCLGSRPL.
Retrocopy MAGLSLV<AGWIMRLP<GSQLWRLLPHGFWVWCPGKETMRVLLGQLCTKPEEA*RASGQAGCCLGSRPLD

Parental  TAMPPPPGSSGPE-WKGSGDPMRPSKPGPVSWKSLAVTFAIGGALLAGMKYFKKEKTEKLEKERHRSIGK
          T.MPPPP.SSGP........P..P.KPGPVSWKSLA.TFAI.GALLAG.KYFKKEKTEKLEKE..RSIGK
Retrocopy TVMPPPPRSSGPQNGRAAETPRAPLKPGPVSWKSLAITFAIWGALLAGVKYFKKEKTEKLEKEWQRSIGK

Parental  PLL-GGPFSLTTHTGEPKTDKDYLGQWVLIYFGFTHCPDICPEELEKMI
          PLL.GGPFSLTTHTG..KTDKDYLGQWVLIYFGFT.CPD....ELE...
Retrocopy PLL<GGPFSLTTHTGKSKTDKDYLGQWVLIYFGFTDCPD----ELEELV

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	27.68 RPM
ERP005899_muscle	0.00 RPM	58.28 RPM
SRP017611_brain	0.00 RPM	18.82 RPM
SRP017611_kidney	0.00 RPM	82.09 RPM
SRP017611_liver	0.00 RPM	25.07 RPM
SRP030211_testis	0.00 RPM	24.86 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_393 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_393 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_393 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000325	1 retrocopy	retro_amel_67,
Bos taurus	ENSBTAG00000021780	1 retrocopy	retro_btau_393 ,
Choloepus hoffmanni	ENSCHOG00000007572	7 retrocopies	retro_chof_2118, retro_chof_2547, retro_chof_2648, retro_chof_447, retro_chof_516, retro_chof_68, retro_chof_827,
Danio rerio	ENSDARG00000067593	1 retrocopy	retro_drer_14,
Equus caballus	ENSECAG00000025151	1 retrocopy	retro_ecab_50,
Erinaceus europaeus	ENSEEUG00000011060	1 retrocopy	retro_eeur_4,
Felis catus	ENSFCAG00000003959	1 retrocopy	retro_fcat_36,
Homo sapiens	ENSG00000133028	1 retrocopy	retro_hsap_1112,
Gallus gallus	ENSGALG00000013382	1 retrocopy	retro_ggal_14,
Loxodonta africana	ENSLAFG00000005056	1 retrocopy	retro_lafr_567,
Oreochromis niloticus	ENSONIG00000009584	1 retrocopy	retro_onil_50,
Oryzias latipes	ENSORLG00000001047	1 retrocopy	retro_olat_14,