RetrogeneDB ID: retro_sscr_981

Retrocopy location

• Organism: Pig (Sus scrofa)
• Coordinates: 8:116364646..116365244(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD4
• Ensembl ID: ENSSSCG00000006628
• Aliases: None
• Description: Sus scrofa proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 (PSMD4), mRNA. [Source:RefSeq mRNA;Acc:NM_001044535]

Sequence

>retro_sscr_981
CCAACTCAAAGGCAAGATTACTGCACTGGCATCTATGTGGCCCATCTGGCCCTGAAGCATCAGTGGGGCAAGAATCAGAA
GACTCGAATCACTGCCTTTGTGAGAAGCCCTATAGAGGACAATGAGAAGGATCTGGTGAAAGTGGCTAAATGCCTCAAGA
AGGAGAAAGTAAATGTTGACATTATTAATTTTGGGGAAGAGGAGGTGAACACAGAAGAGGTGCCTGTCTTCATAAACACA
ATGAATGGTAAAGATGGAACAGGCTCTCATCTGGTGACAGTGCCCTCTGGGCCCAGCTTGGCTGATGCCCTCATTGGTTC
TCTGATTCTGGCTGGGGGAAGGTGGTGCCATACTGCATCTTGGTGCCAGTGACTTTGAATTTGGAGTGGATCCCAGTGCT
TATCCTGACCTGGGCCTGGCCCTGTGTGTTTCTTTGGAAGAGCAGTGGTGGTGGCAGCAGGAAGTGGTGTGGTGGGCAGC
TGCCACCTCTGCTGCTGAGACCAGGATTGCTACAACTGGGACTGAAGGTGAAAGAGACTAGGACCATGCCCTGCTAAAGA
TGACCATCAGCCAGCAGGAGTCTGGTCACACTGGGGTC

Alignment

ORF - retro_sscr_981 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74. %
• Parental protein coverage: 51.99 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PKGKITFCTGIRVAHLALKHRQGKNHKMRIIAFVGSPVEDNEKDLVKLAKRLKKEKVNVDIINFGEEEVN
          P......CTGI.VAHLALKH..GKN.K.RI.AFV.SP.EDNEKDLVK.AK.LKKEKVNVDIINFGEEEVN
Retrocopy PTQRQDYCTGIYVAHLALKHQWGKNQKTRITAFVRSPIEDNEKDLVKVAKCLKKEKVNVDIINFGEEEVN

Parental  TEKLTAFVNTLNGKDGTGSHLVTVPPGPSLADALISSPILA-GEGGAMLGLGASDFEFGVDPSADPELAL
          TE....F.NT.NGKDGTGSHLVTVP.GPSLADALI.S.ILA.GEGGA.L.LGASDFEFGVDPSA.P.L.L
Retrocopy TEEVPVFINTMNGKDGTGSHLVTVPSGPSLADALIGSLILA>GEGGAILHLGASDFEFGVDPSAYPDLGL

Parental  ALRVSMEEQRQRQEEEARRAAAASAAEAGIATTGTE---DSDDALLKMTISQQEFGRTGL
          AL.VS.EEQ...Q.E....AAA.SAAE..IATTGTE...D.D.ALLKMTISQQE.G.TG.
Retrocopy ALCVSLEEQWWWQQEVVWWAAATSAAETRIATTGTEGERD*DHALLKMTISQQESGHTGV

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	104.33 RPM
SRP014902_testis	0.00 RPM	123.20 RPM
SRP018288_heart	0.00 RPM	55.29 RPM
SRP018288_kidney	0.00 RPM	88.06 RPM
SRP018288_liver	0.00 RPM	55.33 RPM
SRP018288_lung	0.00 RPM	71.79 RPM
SRP018856_adipose	0.00 RPM	202.39 RPM
SRP035408_brain	0.00 RPM	136.32 RPM
SRP035408_liver	0.00 RPM	59.18 RPM

ChIP-Seq

Sus scrofa was not studied using ChIP-Seq data.

EST

No EST(s) were mapped for retro_sscr_981 retrocopy.

TSS

Sus scrofa was not studied using FANTOM5 data.

Lab

retro_sscr_981 was not experimentally validated.

Homology

Retrocopy orthology:

Retrocopy retro_sscr_981 has 0 orthologous retrocopies within eutheria group .

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Parental genes homology:

Parental genes homology involve 10 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012565	1 retrocopy	retro_cfam_591,
Callithrix jacchus	ENSCJAG00000007357	1 retrocopy	retro_cjac_2808,
Dasypus novemcinctus	ENSDNOG00000007446	1 retrocopy	retro_dnov_1556,
Homo sapiens	ENSG00000159352	1 retrocopy	retro_hsap_2531,
Nomascus leucogenys	ENSNLEG00000010139	1 retrocopy	retro_nleu_1450,
Pongo abelii	ENSPPYG00000000871	1 retrocopy	retro_pabe_1862,
Pan troglodytes	ENSPTRG00000013893	1 retrocopy	retro_ptro_1474,
Sus scrofa	ENSSSCG00000006628	1 retrocopy	retro_sscr_981 ,
Tupaia belangeri	ENSTBEG00000016911	1 retrocopy	retro_tbel_238,
Tursiops truncatus	ENSTTRG00000007019	1 retrocopy	retro_ttru_903,