RetrogeneDB ID: retro_sscr_678

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 2:104252238..104252922(-)
• Located in intron of: ENSSSCG00000027608

Retrocopy information

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

Parental gene information

• Parental gene symbol: POU5F1
• Ensembl ID: ENSSSCG00000001393
• Aliases: POU5F1, OCT3, OCT4, Oct-4
• Description: Sus scrofa POU class 5 homeobox 1 (POU5F1), mRNA. [Source:RefSeq mRNA;Acc:NM_001113060]

Sequence

>retro_sscr_678
CCAAGGCCCGCTCTGCCAGAGGACATCTCTGCGGTAGAGAAGGAGATGGAGCAGCTGGCCAAGGAACTGAGAGAGAGGAG
GATGACCCTGGGGTACTCGCAGGCCGATGTGGGGTTCGCTGTGGGGGCTCTTTTTGGAAAGATGCTTAGCCAGACGACCA
TCTGCCGCTTTGAGGCCCAGCAGCTGAGCCTCGCCAACATGTGGAAGCTGCGACCACTGCTGAAAATGTGGCTGGAGCAA
GTGGACACCAAGAACCTTCTAGGCATATGCAAAATGGAGATGATCCTGCAGCAAGCTCGGAAGCGGAGACGCGCAAGCAG
GGAGAGACGCATCGGAAACAACCTGGAGAAACTCTTCCTGCAGTGCCCAAAGCCCACGCCCCAGCAGATCAGCTGCATCG
CTGGGCAGCTACGGCTACAAAAGGACCTGGTCCAAGTTTGGTTCTATAACAGGAGCAGGCAGGGCGGTCGGCCAAGCAGT
GATTTCTACCCCCTGGCCGAGGTGGGGGCAGCCGGGCCTCCTTTCTCAGGGGGACCAGTGTGCTTTCCCCTGACATCGGG
ATTCCATTTTGGTCCCCCCCACTGTGGGGGACCCTACTTTCCACCTTTGTGCTCCTATGCCCCTGCCGCTTTTCCTGCGG
GAGGAACCCTCCTCTCTGCCCCGGCCACCACTCTGAGCTTTCCA

Alignment

ORF - retro_sscr_678 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.33 %
• Parental protein coverage: 62.78 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PNPEESQDIKALQKDLEQFAKLLKQKRITLGYTQADVGLTLGVLFGKVFSQTTICRFEALQLSFKNMCKL
          P.P....DI.A..K..EQ.AK.L...R.TLGY.QADVG...G.LFGK..SQTTICRFEA.QLS..NM.KL
Retrocopy PRPALPEDISAVEKEMEQLAKELRERRMTLGYSQADVGFAVGALFGKMLSQTTICRFEAQQLSLANMWKL

Parental  RPLLQKWVEEADNNENLQEICKAETLV-QARKRKRTSIENRVRGNLESMFLQCPKPTLQQISHIAQQLGL
          RPLL..W.E..D...NL..ICK.E....QARKR.R.S.E.R...NLE..FLQCPKPT.QQIS.IA.QL.L
Retrocopy RPLLKMWLEQVD-TKNLLGICKMEMILQQARKRRRASRERRIGNNLEKLFLQCPKPTPQQISCIAGQLRL

Parental  EKDVVRVWFCNRRQKGKRSSSDYSQREDFEAAGSPFPGGPVSFPLAPGPHFGTPGYGGPHFTTLYSSVP-
          .KD.V.VWF.NR...G.R.SSD........AAG.PF.GGPV.FPL..G.HFG.P..GGP.F..L.S..P.
Retrocopy QKDLVQVWFYNRSRQGGRPSSDFYPLAEVGAAGPPFSGGPVCFPLTSGFHFGPPHCGGPYFPPLCSYAPA

Parental  -FPEGEAFPSVSVTPLGSP
          .FP.G....S...T.L..P
Retrocopy AFPAGGTLLSAPATTLSFP

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	0.13 RPM	0.27 RPM
SRP014902_testis	0.28 RPM	0.85 RPM
SRP018288_heart	0.00 RPM	0.03 RPM
SRP018288_kidney	0.00 RPM	0.00 RPM
SRP018288_liver	0.00 RPM	0.00 RPM
SRP018288_lung	0.20 RPM	0.00 RPM
SRP018856_adipose	0.35 RPM	0.02 RPM
SRP035408_brain	0.00 RPM	0.00 RPM
SRP035408_liver	0.06 RPM	0.00 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_678 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_678 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_678 has 3 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Pan troglodytes	retro_ptro_2132
Gorilla gorilla	retro_ggor_2275
Equus caballus	retro_ecab_301

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Parental genes homology:

Parental genes homology involve 25 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010377	3 retrocopies	retro_amel_1057, retro_amel_1213, retro_amel_1616,
Bos taurus	ENSBTAG00000021111	2 retrocopies	retro_btau_1576, retro_btau_951,
Canis familiaris	ENSCAFG00000000485	1 retrocopy	retro_cfam_1538,
Callithrix jacchus	ENSCJAG00000019789	1 retrocopy	retro_cjac_123,
Dipodomys ordii	ENSDORG00000009549	1 retrocopy	retro_dord_65,
Equus caballus	ENSECAG00000008967	1 retrocopy	retro_ecab_301,
Erinaceus europaeus	ENSEEUG00000015357	2 retrocopies	retro_eeur_196, retro_eeur_558,
Felis catus	ENSFCAG00000001078	3 retrocopies	retro_fcat_1372, retro_fcat_1422, retro_fcat_275,
Gorilla gorilla	ENSGGOG00000027662	3 retrocopies	retro_ggor_2275, retro_ggor_295, retro_ggor_852,
Macropus eugenii	ENSMEUG00000013221	3 retrocopies	retro_meug_1146, retro_meug_1475, retro_meug_692,
Microcebus murinus	ENSMICG00000001511	1 retrocopy	retro_mmur_1423,
Myotis lucifugus	ENSMLUG00000011028	3 retrocopies	retro_mluc_1465, retro_mluc_2382, retro_mluc_515,
Mustela putorius furo	ENSMPUG00000001202	2 retrocopies	retro_mputfur_253, retro_mputfur_96,
Mus musculus	ENSMUSG00000024406	2 retrocopies	retro_mmus_2201, retro_mmus_250,
Oryctolagus cuniculus	ENSOCUG00000017160	3 retrocopies	retro_ocun_1175, retro_ocun_1696, retro_ocun_463,
Otolemur garnettii	ENSOGAG00000000621	3 retrocopies	retro_ogar_1406, retro_ogar_1436, retro_ogar_2229,
Ochotona princeps	ENSOPRG00000003926	2 retrocopies	retro_opri_1213, retro_opri_556,
Pongo abelii	ENSPPYG00000017210	3 retrocopies	retro_pabe_2761, retro_pabe_3294, retro_pabe_898,
Pan troglodytes	ENSPTRG00000017953	5 retrocopies	retro_ptro_1798, retro_ptro_204, retro_ptro_2132, retro_ptro_2721, retro_ptro_733,
Pteropus vampyrus	ENSPVAG00000007334	2 retrocopies	retro_pvam_724, retro_pvam_74,
Rattus norvegicus	ENSRNOG00000046487	4 retrocopies	retro_rnor_1474, retro_rnor_2186, retro_rnor_2968, retro_rnor_921,
Sus scrofa	ENSSSCG00000001393	2 retrocopies	retro_sscr_252, retro_sscr_678 ,
Ictidomys tridecemlineatus	ENSSTOG00000026103	3 retrocopies	retro_itri_1076, retro_itri_1705, retro_itri_951,
Tupaia belangeri	ENSTBEG00000013044	4 retrocopies	retro_tbel_3628, retro_tbel_3718, retro_tbel_3779, retro_tbel_4614,
Tarsius syrichta	ENSTSYG00000007340	4 retrocopies	retro_tsyr_1508, retro_tsyr_1630, retro_tsyr_814, retro_tsyr_817,