RetrogeneDB ID: retro_dnov_1508

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_220464:9..635(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMC5
• Ensembl ID: ENSDNOG00000002393
• Aliases: None
• Description: proteasome (prosome, macropain) 26S subunit, ATPase, 5 [Source:HGNC Symbol;Acc:9552]

Sequence

>retro_dnov_1508
ATGGCGCTTGACGGACCAGAGCACATGGAGCTGGAAGAGGGGAAGGCAGGCAGTGGTCTCCACCAATATTACCTATCCAA
GATTGAAGAACTTCAGCTGATTGTGAATGACAAGAGTCAGAACCTTCAGTGGCTGCAAGCACAGAGAAATGAGCTAAATG
CAAAAGTTCGTCTGTTGCAGGAGGAGCTCCACCTGCTGCAGGAACAGGGCTCCTATGTGGGGGAAGTTGTCCGGGCTATG
GATAAGAAGAAAGTGTTGGTTAAGTACATCCCGAGGGCAAGTTTGTTGTAGATGTGGATAAGAACATAGATAACAGTGAT
ATGACTCCCAATTGCCGGGTGGCTCTAAGAAATGACAGTTGTACTTTACACAAGATCCTGCCCAACAAGATGGACCCTCT
GGTGTCATTGATGATGGTGGAGAAGTGCCAGACTCAACTTATGAGATGAATGGTGGACTGGACAAGCAGATCAAGAGATC
AAGGAAATGATCGAGCTGCCTGTTAAACATTCCTGAGCTCTTTGAGCACTGGGCATTGCATAACCCAAGGGAATGCTGCT
GTATGGACCTAGTCCTGGGAAGACACTATTGGGCTTGGGCTGTAGCTCATTCCTATGGATTGCACC

Alignment

ORF - retro_dnov_1508 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.1 %
• Parental protein coverage: 51.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 7

Retrocopy - Parental Gene Alignment:

Parental  MALDGPEQMELEEGKAGSGLRQYYLSKIEELQLIVNDKSQNLRRLQAQRNELNAKVRLLREELQLLQEQG
          MALDGPE.MELEEGKAGSGL.QYYLSKIEELQLIVNDKSQNL..LQAQRNELNAKVRLL.EEL.LLQEQG
Retrocopy MALDGPEHMELEEGKAGSGLHQYYLSKIEELQLIVNDKSQNLQWLQAQRNELNAKVRLLQEELHLLQEQG

Parental  SYVGEVVRAMDKKKVLVK-VHPEGKFVVDVDKNIDINDVTPNCRVALRNDSYTLHKILPNKVDPLVSLMM
          SYVGEVVRAMDKKKVLVK.VHPEGKFVVDVDKNID..D.TPNCRVALRNDS.TLHKILPNK.DPLVSLMM
Retrocopy SYVGEVVRAMDKKKVLVK<VHPEGKFVVDVDKNIDNSDMTPNCRVALRNDSCTLHKILPNKMDPLVSLMM

Parental  VEK-VPDSTYEMIGGLDKQIK-EIKEVIELPVKH-PELFE-ALGIAQPKGVLLYGPPGTGKTLL-ARAVA
          VEK.VPDSTYEM.GGLDKQIK.EIKE.IELPVKH.PELFE.ALGIA.PKG.LLYG.P..GKTLL.A.AVA
Retrocopy VEK<VPDSTYEMNGGLDKQIK<EIKEMIELPVKH>PELFE<ALGIA*PKGMLLYG-PSPGKTLL>AWAVA

Parental  HH-TDCT
          H...DCT
Retrocopy HS>MDCT

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	0.00 RPM	84.98 RPM
SRP012922_cerebellum	0.00 RPM	182.97 RPM
SRP012922_heart	0.00 RPM	89.10 RPM
SRP012922_kidney	0.00 RPM	115.82 RPM
SRP012922_liver	0.00 RPM	63.01 RPM
SRP012922_lung	0.00 RPM	114.85 RPM
SRP012922_quadricep_muscle	0.00 RPM	86.37 RPM
SRP012922_spleen	0.00 RPM	100.38 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_1508 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 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002393	1 retrocopy	retro_dnov_1508 ,
Homo sapiens	ENSG00000087191	1 retrocopy	retro_hsap_1949,
Gorilla gorilla	ENSGGOG00000006803	1 retrocopy	retro_ggor_1418,
Macaca mulatta	ENSMMUG00000016769	1 retrocopy	retro_mmul_1354,
Monodelphis domestica	ENSMODG00000009873	2 retrocopies	retro_mdom_1411, retro_mdom_1583,
Nomascus leucogenys	ENSNLEG00000004150	1 retrocopy	retro_nleu_1480,
Oryctolagus cuniculus	ENSOCUG00000004329	1 retrocopy	retro_ocun_78,
Otolemur garnettii	ENSOGAG00000008296	1 retrocopy	retro_ogar_911,
Procavia capensis	ENSPCAG00000002653	1 retrocopy	retro_pcap_352,
Pongo abelii	ENSPPYG00000008533	1 retrocopy	retro_pabe_1606,
Pan troglodytes	ENSPTRG00000009525	1 retrocopy	retro_ptro_1303,
Ictidomys tridecemlineatus	ENSSTOG00000008945	1 retrocopy	retro_itri_1046,
Tupaia belangeri	ENSTBEG00000010546	3 retrocopies	retro_tbel_1411, retro_tbel_2422, retro_tbel_3450,
Tursiops truncatus	ENSTTRG00000006984	1 retrocopy	retro_ttru_1532,