RetrogeneDB ID: retro_sscr_518

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 16:7129804..7130635(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSSSCG00000016796
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RNF167
• Ensembl ID: ENSSSCG00000017906
• Aliases: None
• Description: ring finger protein 167 [Source:HGNC Symbol;Acc:24544]

Sequence

>retro_sscr_518
ATGCACCCTGCTGCTTCCCTCCTTTCTGTGTTTGTGGCCACTGTGCTGTGGGGAGTGGCCCCTATCAGGGGGCTTATTCG
AGCGACTTCATACCACAATGCAAGCATGAACTTTGCAGACCTCCCAGCTCTCTTTGGGACTGCCTTGAGCCCAGAGGGAC
TTAAGGGGTTCCTTGTGGAGGCTCACCCAGCCAATGCCTGCAGCCCTATTGCCCCACCGCCTCCAGCCTGGGTCAACGGG
TCAGTTTTCATTGCACTGCTTCGAAGATTTGACTGCAGTTTTGACCTCAAAGTCCTAAATGCTCAGAAGGCTGGGTATGA
TGCCGCTGTGGTCCACAATGTGGATTCTGATGAACTTGTGAACATGGTGTGGAACAATGAGGAAATCCAGCAGCAGATCT
GGATCCCGTCGGTGTTTATCGGCGAGAAGAGCTCTAAATACCTGCGTGCCCTCTTCGTCTACCAGAATAGGGCTCAGGTG
CTTCTGGTTCCCGAAAATACATTCCTTTTGGGCTATCGCCTCATCCTTTTCTCTGGGATTTTGGGCGTGCTAATTTTGGG
CATGGGAGCGATTGTGACAGTTTGTTGTATCCAATTCCAGAAACAGCACCGGGGGAACCGACTAACTGAAGAACAACTGA
AGCAGATTCCTACACGTGACTATCACAAGGGAGACCAGTATGATGTCTGTGCCATCTGCCTGGAGGAATATGAAGTTGGG
GACAAACTGAGGGTACTTCCTTGCACTCATGCCTATCATTGCTGCTGTGTGGACAGGTGGCTCACTCAGACCCGGGAGAC
TTGTCCTATCTGCAAACAGCCTGTTCAGCGG

Alignment

ORF - retro_sscr_518 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.06 %
• Parental protein coverage: 79.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MHPAAFPLPVVVATVLWGVAPSQGLIRAISDHNASMDFADLPALFGAALSQEGLQGFLVEAHPDNACSPI
          MHPAA..L.V.VATVLWGVAP..GLIRA.S.HNASM.FADLPALFG.ALS.EGL.GFLVEAHP.NACSPI
Retrocopy MHPAASLLSVFVATVLWGVAPIRGLIRATSYHNASMNFADLPALFGTALSPEGLKGFLVEAHPANACSPI

Parental  APPPPAPVNGSVFIALLRRFDCNFDLKVLNAQKAGYGAAVVHNVNSNELLNMVWNSEEIQQQIWIPSVFI
          APPPPA.VNGSVFIALLRRFDC.FDLKVLNAQKAGY.AAVVHNV.S.EL.NMVWN.EEIQQQIWIPSVFI
Retrocopy APPPPAWVNGSVFIALLRRFDCSFDLKVLNAQKAGYDAAVVHNVDSDELVNMVWNNEEIQQQIWIPSVFI

Parental  GERSSQYLRALFVYEKGARVLLVPDNSFPLGYYLIPFTGIVGLLVLAMGAVMIVRCIQHRKRLQRNRLTK
          GE.SS.YLRALFVY...A.VLLVP.N.F.LGY.LI.F.GI.G.L.L.MGA...V.CIQ..K....NRLT.
Retrocopy GEKSSKYLRALFVYQNRAQVLLVPENTFLLGYRLILFSGILGVLILGMGAIVTVCCIQFQKQHRGNRLTE

Parental  EQLKQIPTHDYQKGDQYDVCAICLDEYEDGDRLRVLPCAHAYHSRCVDPWLTQTRKTCPICKQPVHR
          EQLKQIPT.DY.KGDQYDVCAICL.EYE.GD.LRVLPC.HAYH..CVD.WLTQTR.TCPICKQPV.R
Retrocopy EQLKQIPTRDYHKGDQYDVCAICLEEYEVGDKLRVLPCTHAYHCCCVDRWLTQTRETCPICKQPVQR

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	126.76 RPM
SRP014902_testis	0.14 RPM	82.18 RPM
SRP018288_heart	0.00 RPM	28.34 RPM
SRP018288_kidney	0.00 RPM	76.74 RPM
SRP018288_liver	0.00 RPM	65.72 RPM
SRP018288_lung	0.00 RPM	85.43 RPM
SRP018856_adipose	0.18 RPM	96.87 RPM
SRP035408_brain	0.00 RPM	40.65 RPM
SRP035408_liver	0.00 RPM	59.71 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_518 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_518 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_518 has 2 orthologous retrocopies within eutheria group .

Species	RetrogeneDB ID
Canis familiaris	retro_cfam_84
Equus caballus	retro_ecab_583

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Parental genes homology:

Parental genes homology involve 13 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006392	1 retrocopy	retro_amel_43,
Bos taurus	ENSBTAG00000004913	1 retrocopy	retro_btau_217,
Canis familiaris	ENSCAFG00000015830	2 retrocopies	retro_cfam_1053, retro_cfam_84,
Dipodomys ordii	ENSDORG00000011757	2 retrocopies	retro_dord_277, retro_dord_432,
Equus caballus	ENSECAG00000021567	1 retrocopy	retro_ecab_583,
Felis catus	ENSFCAG00000011173	1 retrocopy	retro_fcat_99,
Mustela putorius furo	ENSMPUG00000010940	1 retrocopy	retro_mputfur_95,
Pteropus vampyrus	ENSPVAG00000003781	1 retrocopy	retro_pvam_1206,
Sorex araneus	ENSSARG00000011216	1 retrocopy	retro_sara_517,
Sus scrofa	ENSSSCG00000012551	1 retrocopy	retro_sscr_597,
Sus scrofa	ENSSSCG00000014013	3 retrocopies	retro_sscr_150, retro_sscr_253, retro_sscr_254,
Sus scrofa	ENSSSCG00000017906	1 retrocopy	retro_sscr_518 ,
Tursiops truncatus	ENSTTRG00000001298	1 retrocopy	retro_ttru_1062,