RetrogeneDB ID: retro_btau_1660

Retrocopy location

• Organism: Cow (Bos taurus)
• Coordinates: 8:92969086..92969596(-)
• Located in intron of: ENSBTAG00000018445

Retrocopy information

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

Parental gene information

• Parental gene symbol: PPP3R1
• Ensembl ID: ENSBTAG00000010619
• Aliases: None
• Description: Calcineurin subunit B type 1 [Source:UniProtKB/Swiss-Prot;Acc:P63099]

Sequence

>retro_btau_1660
ATGGGAAATGAGGCCAGTTACCCGGCGGAGATATGCTCGCACTTCGACGAAGATGAAATTAAAAGGCTGCGCAAGCGTTT
TAAGAAGCTGGACTTGGACAGTTCCAGCGCTCTGAGCGTCAAAGAGTTCACGTCCATGCCAGAGCTGCAGGAGAACCCGC
TGGTGCAGCGGGTGATAGACGTCTTCGACACCGACGGCGACGGACAGGTGGACTTCCGGGAATTCATCCTGGGGACCTCC
CAGTTCAGCGTCCGGGGAGATGAGGAGCAGAAGCTGAGGTTTGCTTTCAGCATCTACGACATGGACAAAGACGGCTACAT
TTCCAACGGGGAGCTCTTCCAGGTGCTGAAGATGATGGTAGGCGACAACCTGAAAGACTGGCAGTTACAGCAGCTGGTGG
ACAAAACCATCATCCTCCTGGACAAAGACGGGGACGGGAAAATCTCCTTCCAGGAATTCAGTGCTGTGGTCAGAAGCCTG
GAGATCCACAAGCACTTGGTGACCATTGTG

Alignment

ORF - retro_btau_1660 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.41 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MGNEASYPLEMCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEV
          MGNEASYP.E.CSHFD.DEIKRL.KRFKKLDLD.S..LSV.EF.S.PELQ.NPLVQRVID.FDTDG.G.V
Retrocopy MGNEASYPAEICSHFDEDEIKRLRKRFKKLDLDSSSALSVKEFTSMPELQENPLVQRVIDVFDTDGDGQV

Parental  DFKEFIEGVSQFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINA
          DF.EFI.G.SQFSV.GD.EQKLRFAF.IYDMDKDGYISNGELFQVLKMMVG.NLKD.QLQQ.VDKTII..
Retrocopy DFREFILGTSQFSVRGDEEQKLRFAFSIYDMDKDGYISNGELFQVLKMMVGDNLKDWQLQQLVDKTIILL

Parental  DKDGDGRISFEEFCAVVGGLDIHKKMVVDV
          DKDGDG.ISF.EF.AVV..L.IHK..V..V
Retrocopy DKDGDGKISFQEFSAVVRSLEIHKHLVTIV

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	4.97 RPM
ERP005899_muscle	0.00 RPM	21.22 RPM
SRP017611_brain	0.00 RPM	95.93 RPM
SRP017611_kidney	0.00 RPM	29.81 RPM
SRP017611_liver	0.00 RPM	19.03 RPM
SRP030211_testis	58.38 RPM	14.57 RPM

ChIP-Seq

Bos taurus was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_btau_1660 retrocopy.

TSS

Bos taurus was not studied using FANTOM5 data.

Lab

retro_btau_1660 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_btau_1660 has 7 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Homo sapiens	retro_hsap_3
Pan troglodytes	retro_ptro_2909
Macaca mulatta	retro_mmul_1141
Callithrix jacchus	retro_cjac_624
Oryctolagus cuniculus	retro_ocun_272
Sus scrofa	retro_sscr_86
Equus caballus	retro_ecab_651

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Parental genes homology:

Parental genes homology involve 22 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010619	1 retrocopy	retro_btau_1660 ,
Bos taurus	ENSBTAG00000027173	1 retrocopy	retro_btau_1785,
Choloepus hoffmanni	ENSCHOG00000002893	1 retrocopy	retro_chof_2602,
Callithrix jacchus	ENSCJAG00000006498	1 retrocopy	retro_cjac_624,
Dipodomys ordii	ENSDORG00000019760	1 retrocopy	retro_dord_404,
Equus caballus	ENSECAG00000009627	1 retrocopy	retro_ecab_651,
Felis catus	ENSFCAG00000028482	1 retrocopy	retro_fcat_1639,
Homo sapiens	ENSG00000221823	1 retrocopy	retro_hsap_3,
Loxodonta africana	ENSLAFG00000022682	1 retrocopy	retro_lafr_1014,
Macaca mulatta	ENSMMUG00000017460	1 retrocopy	retro_mmul_1141,
Mustela putorius furo	ENSMPUG00000006250	1 retrocopy	retro_mputfur_537,
Nomascus leucogenys	ENSNLEG00000026538	1 retrocopy	retro_nleu_1049,
Oryctolagus cuniculus	ENSOCUG00000027562	1 retrocopy	retro_ocun_272,
Otolemur garnettii	ENSOGAG00000034876	1 retrocopy	retro_ogar_1011,
Pan troglodytes	ENSPTRG00000041941	1 retrocopy	retro_ptro_2909,
Rattus norvegicus	ENSRNOG00000043210	1 retrocopy	retro_rnor_1932,
Sus scrofa	ENSSSCG00000022362	1 retrocopy	retro_sscr_86,
Ictidomys tridecemlineatus	ENSSTOG00000025985	1 retrocopy	retro_itri_1569,
Tarsius syrichta	ENSTSYG00000019531	2 retrocopies	retro_tsyr_326, retro_tsyr_41,
Tursiops truncatus	ENSTTRG00000021395	1 retrocopy	retro_ttru_382,
Vicugna pacos	ENSVPAG00000015522	1 retrocopy	retro_vpac_3,
Drosophila melanogaster	FBgn0015614	1 retrocopy	retro_dmel_53,