RetrogeneDB ID: retro_sscr_86

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: JH118515.1:66149..66662(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000028206
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSSSCG00000022362
• Aliases: None
• Description: None

Sequence

>retro_sscr_86
ATGGGAAATGAGCCCAGTAACCCAATGGAGATGTGCTCCCAGTTTGACCAAAACGAAATTAAACAGCTGAGCAAGCGGTT
TAAGAAGGTGGACTTGGACAGTTCGGGCACTCTGACTATGAAGGAGCTCATGTCCCTGCCGGGGCTGCAGGTGAACCCGT
TGGTGCAGCGAGTGTTCGACATTTTCGACACAGACGGCAACGGAGAAGTGGACTTCAAGGAATTCCTCGTGGGGACCTCC
CAGTTCAGTGTCAAGGGCGACAAGGAGCAGAAGCTGAGGTTTGCTTTCAGCATCTATGACATGGACAAAGACGGCTACAT
TTCCAACGGGGAGCTCTTCCAGGTGCTAAACATGATGGTGGGAGACAACCTGAAAGACTGGCAGTTACAGCAGCTGGTGG
ACAAAACCATCATCGCCCTGGACAAGGATGGAGATGGGAAAATATCCTTCCACGAATTCTGCGCTGTGGCCAGAAACCTG
AAGGTCCACGAGAAATTGGGGGTAATTGTGTGA

Alignment

ORF - retro_sscr_86 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.5 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MCSHFDADEIKRLGKRFKKLDLDNSGSLSVEEFMSLPELQQNPLVQRVIDIFDTDGNGEVDFKEFIEGVS
          MCS.FD..EIK.L.KRFKK.DLD.SG.L...E.MSLP.LQ.NPLVQRV.DIFDTDGNGEVDFKEF..G.S
Retrocopy MCSQFDQNEIKQLSKRFKKVDLDSSGTLTMKELMSLPGLQVNPLVQRVFDIFDTDGNGEVDFKEFLVGTS

Parental  QFSVKGDKEQKLRFAFRIYDMDKDGYISNGELFQVLKMMVGNNLKDTQLQQIVDKTIINADKDGDGRISF
          QFSVKGDKEQKLRFAF.IYDMDKDGYISNGELFQVL.MMVG.NLKD.QLQQ.VDKTII..DKDGDG.ISF
Retrocopy QFSVKGDKEQKLRFAFSIYDMDKDGYISNGELFQVLNMMVGDNLKDWQLQQLVDKTIIALDKDGDGKISF

Parental  EEFCAVVGGLDIHKKMVVDV
          .EFCAV...L..H.K..V.V
Retrocopy HEFCAVARNLKVHEKLGVIV

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
SRP014902_placenta	0.00 RPM	2.12 RPM
SRP014902_testis	0.00 RPM	7.36 RPM
SRP018288_heart	0.00 RPM	11.81 RPM
SRP018288_kidney	0.00 RPM	12.02 RPM
SRP018288_liver	0.00 RPM	12.31 RPM
SRP018288_lung	0.00 RPM	16.70 RPM
SRP018856_adipose	0.00 RPM	6.11 RPM
SRP035408_brain	0.00 RPM	54.63 RPM
SRP035408_liver	0.00 RPM	14.33 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_86 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_86 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_86 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
Bos taurus	retro_btau_1660
Equus caballus	retro_ecab_651

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Parental genes homology:

Parental genes homology involve 20 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000010619	1 retrocopy	retro_btau_1660,
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,
Tursiops truncatus	ENSTTRG00000021395	1 retrocopy	retro_ttru_382,
Vicugna pacos	ENSVPAG00000015522	1 retrocopy	retro_vpac_3,
Drosophila melanogaster	FBgn0015614	1 retrocopy	retro_dmel_53,