RetrogeneDB ID: retro_dnov_1556

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_234241:408..1180(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMD4
• Ensembl ID: ENSDNOG00000007446
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, non-ATPase, 4 [Source:HGNC Symbol;Acc:9561]

Sequence

>retro_dnov_1556
CTGGTGAAACTGTCCATATGTCTCAAGAAGGAGAAAGTAAATGTTGACATTATCAATTTTGGGGAAGAGGAGGTGAACAA
AGAGAAGATGATGTTTCTTTGTATACATACTGAATGGCAAAGTTGGAACTGGGTCTCATCTGATGACAGTGCCTCCTGGG
CCTAGCTTGGCGGATGCCCTCATCAGTTCTCCAATTCTGGCTGGTGAAAGTGGTGTCTTGCTGGGGCTTGGTGCCACTGA
CTTTGAATTCGGAGTGGATCCCAGTGCTGATCCCAAGCTGGCTTTGGCCCTTTGTGTTTCCATGGAAGAGCAGCAGCAGC
GGCAGGAAGAGAGGCACGGAGTGCAGCTGTAGCCTCTGCTGCTGAGGGTGGGATTGCTACAACTGGGACTGAACGTGCAA
GAGATTCAGATGATGCTCTTGCTGAAGATGACCATCAGTCAGCAGGAGTTTGGTCGCACCAGGCTCCCTTACCTGAGCAG
TATGACTGAAGAAGAGCAGATTGCTTATGCCCACGCAGAAGTCCCTGCAGGGAGCAGAGTTTGGCCCAGGCAGAATCAGC
GGATATTGACGCCAACTCAGCCCATGGACACATCTGAGCCAGGCAAGGAGGAGGAGGATTTTGATGTGATGCAGGATCCT
GGGTTCCTTAAGAGTGTCTTAGAGAACCTTCCAGATGTGGATCGCAACCATGAGGCCATTCGAAATGCCATGGGCTCCCT
GGCCACCCAGGTCACAAAGGAGAGCAAAAAGGACAAGAAGGAGGAGGACAGG

Alignment

ORF - retro_dnov_1556 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.68 %
• Parental protein coverage: 67.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  LVKLAKRLKKEKVNVDIINFGEEEVNTEKLTA-FVNTLNGKDGTGSHLVTVPPGPSLADALISSPILAGE
          LVKL...LKKEKVNVDIINFGEEEVN.EK....FV..LNGK.GTGSHL.TVPPGPSLADALISSPILAGE
Retrocopy LVKLSICLKKEKVNVDIINFGEEEVNKEKMMF>FVYILNGKVGTGSHLMTVPPGPSLADALISSPILAGE

Parental  GGAMLGLGASDFEFGVDPSADPELALALRVSMEEQRQRQEE-EARRAAAASAAEAGIATAGTEGERDSDD
          .G..LGLGA.DFEFGVDPSADP.LALAL.VSMEEQ.QRQEE.EAR.AA.ASAAE.GIAT.GTE..RDSDD
Retrocopy SGVLLGLGATDFEFGVDPSADPKLALALCVSMEEQQQRQEE<EARSAAVASAAEGGIATTGTERARDSDD

Parental  A-LLKMTISQQEFGRTGLPDLSSMTEEEQIAYA-MQMSLQGAEIG-QAESADIDASSA-MDTSEPAKEED
          A.LLKMTISQQEFGRT.LP.LSSMTEEEQIAYA..Q.SLQGAE.G.QAESADIDA.SA.MDTSEP.KEE.
Retrocopy A>LLKMTISQQEFGRTRLPYLSSMTEEEQIAYA>TQKSLQGAEFG>QAESADIDANSA>MDTSEPGKEEE

Parental  DYDVMQDPEFLQSVLENLPGVDPNNEAIRNAMGSLASQATKDSKKDKKEEDK
          D.DVMQDP.FL.SVLENLP.VD.N.EAIRNAMGSLA.Q.TK.SKKDKKEED.
Retrocopy DFDVMQDPGFLKSVLENLPDVDRNHEAIRNAMGSLATQVTKESKKDKKEEDR

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
SRP012922_ascending_colon	0.19 RPM	45.12 RPM
SRP012922_cerebellum	0.14 RPM	51.55 RPM
SRP012922_heart	0.70 RPM	46.41 RPM
SRP012922_kidney	0.00 RPM	57.22 RPM
SRP012922_liver	0.00 RPM	22.60 RPM
SRP012922_lung	0.15 RPM	57.73 RPM
SRP012922_quadricep_muscle	0.17 RPM	55.73 RPM
SRP012922_spleen	0.23 RPM	51.05 RPM

ChIP-Seq

Dasypus novemcinctus was not studied using ChIP-Seq data.

EST

Dasypus novemcinctus was not studied using EST data.

TSS

Dasypus novemcinctus was not studied using FANTOM5 data.

Lab

retro_dnov_1556 was not experimentally validated.

Homology

Retrocopy orthology:

Dasypus novemcinctus does not belong to any of the species groups (eutheria, teleost or neognath), studied for retrocopy-based homology. For more information about studied groups, please go to help section.

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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,