RetrogeneDB ID: retro_sscr_102

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 1:32198217..32198610(+)
• Located in intron of: ENSSSCG00000004166

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOQ
• Ensembl ID: ENSSSCG00000008439
• Aliases: None
• Description: None

Sequence

>retro_sscr_102
CAAGAAGACTGTGATCATCTGAGGCTTTTATCTTGTCCAGTGATTGATGTCCTCTTACATGTTTCTCTGTGGAAAATCTA
GCCTCATTTCAAAATGTGAAAGAGGAGTAGGTACCAGAACTTAAGAAATACACATGAAATATACCCTTCATATTAATAGG
AACTCAGATTCATCTCTGAGGTGACCCCAAACCATAGCAAGACTGAAAGATACGAAAGGAGAAGCTATGTGTCTAGAACA
AGGATGGAAACTAGCAAACGAAATGGGAGCATGCTGCCAGGTGGTATGTTCAACTGTAACCCATCAGGGATTGAGGTGTT
TGGTGAGGTTATCATAGCCATTTTAACTCCAAAGAAACATACAGTTAAAAAAAAAAATGGATTGGGATGTGTA

Alignment

ORF - retro_sscr_102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 63.03 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QEDYDRLRPLSYPMTDVFL-ICFSVVNPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDDPK-TLAR
          QED.D.LR.LS.P..DV.L..CFSV.N.ASFQNVKEE.VPELK.Y..N.PF.LIGTQI.L..DPK.T.AR
Retrocopy QEDCDHLRLLSCPVIDVLL<TCFSVENLASFQNVKEE*VPELKKYT*NIPFILIGTQIHL*GDPK<TIAR

Parental  LNDMKEKPICVEQGQKLAKEIGACCYVECSALTQK-GLKTVFDEAIIAILTPKKHTVKKRIGSRCI
          L.D.K....C.EQG.KLA.E.GACC.V.CS..T...G...VF.E.IIAILTPKKHTV....G..C.
Retrocopy LKDTKGEAMCLEQGWKLANEMGACCQVVCSTVTHQ<GIE-VFGEVIIAILTPKKHTVXXXXGLGCV

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	10.35 RPM
SRP014902_testis	0.00 RPM	9.05 RPM
SRP018288_heart	0.00 RPM	104.01 RPM
SRP018288_kidney	0.00 RPM	6.60 RPM
SRP018288_liver	0.00 RPM	1.44 RPM
SRP018288_lung	0.00 RPM	32.28 RPM
SRP018856_adipose	0.11 RPM	19.91 RPM
SRP035408_brain	0.06 RPM	24.20 RPM
SRP035408_liver	0.00 RPM	4.76 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_102 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_102 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_102 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 19 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006082	1 retrocopy	retro_amel_383,
Choloepus hoffmanni	ENSCHOG00000000549	3 retrocopies	retro_chof_2030, retro_chof_457, retro_chof_914,
Callithrix jacchus	ENSCJAG00000000685	1 retrocopy	retro_cjac_2403,
Erinaceus europaeus	ENSEEUG00000015226	1 retrocopy	retro_eeur_129,
Echinops telfairi	ENSETEG00000019234	3 retrocopies	retro_etel_1468, retro_etel_596, retro_etel_672,
Felis catus	ENSFCAG00000015608	1 retrocopy	retro_fcat_795,
Homo sapiens	ENSG00000119729	3 retrocopies	retro_hsap_1333, retro_hsap_2158, retro_hsap_2316,
Loxodonta africana	ENSLAFG00000004327	1 retrocopy	retro_lafr_316,
Microcebus murinus	ENSMICG00000009124	1 retrocopy	retro_mmur_29,
Myotis lucifugus	ENSMLUG00000001567	1 retrocopy	retro_mluc_595,
Otolemur garnettii	ENSOGAG00000033272	1 retrocopy	retro_ogar_742,
Pongo abelii	ENSPPYG00000012439	2 retrocopies	retro_pabe_1107, retro_pabe_2195,
Pteropus vampyrus	ENSPVAG00000013691	1 retrocopy	retro_pvam_611,
Rattus norvegicus	ENSRNOG00000015415	1 retrocopy	retro_rnor_473,
Sus scrofa	ENSSSCG00000003520	1 retrocopy	retro_sscr_899,
Sus scrofa	ENSSSCG00000008439	1 retrocopy	retro_sscr_102 ,
Sus scrofa	ENSSSCG00000021944	4 retrocopies	retro_sscr_40, retro_sscr_565, retro_sscr_582, retro_sscr_882,
Tarsius syrichta	ENSTSYG00000002837	1 retrocopy	retro_tsyr_1609,
Tursiops truncatus	ENSTTRG00000011892	1 retrocopy	retro_ttru_805,