RetrogeneDB ID: retro_dnov_2087

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_46582:3406..4056(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB1
• Ensembl ID: ENSDNOG00000019502
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 1 [Source:HGNC Symbol;Acc:9537]

Sequence

>retro_dnov_2087
GGGCCGGGTAGAGAACTGGGGATAGAACCTTACAGAGCCGTGGGTCCCTCGCAGCTTCACTTTTTGCCCTTCGCTTTCAA
CGGAGGTACTGTATTGGCGTTTGCTGGAGAAGGTTTTTCAGTTGTTGCTTTTGACACTTGACTGAGTGAAGGGTTTTCAA
TTCATACCCGGGACAGCCCCCAAGTGTTACAAATTAACAGACAAAACAGTCATCGGATGTAGCGGTTTTCATGGGGACTG
CCTTACACTTACAAAAATTATTGAAGCACATCTAAAGAAGTATAAGCATTCCAATAATAAGGCCATGACTACTGGGGCAA
TTGCTGCAATGTTATCTACAATCCTCTATTCAAGACTCTTCTTTCCATATTAGGTTTACCACATCATCAGAGGACTTGAC
AAAGAAGGGAAGGGGGCCCTGTACAGCTTTGATCCAGTAGGATCCTACCAGAGAGACTCCTTCAAAGCCTGGAGGCTCAG
CAAGTACCATGATGCAACCCCTACTTGACAACCAGCTTGGTTTTAAGAATATGAAAGATGTAGAACATGTTTTGCTGTCC
CTGGACAGAGACAAGCAGCTGGTGAAAGATGTCTTTATCTCTGCAGTGAAGAGAGATGGATATACTGGAGACATACTTCA
GAACTGCATC

Alignment

ORF - retro_dnov_2087 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.94 %
• Parental protein coverage: 89.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GPGRELGMEPYRAAGPSQLRFSPYAFNGGTVLAIAGEDFSIVASDTRLSEGFSIHTRDS-PKCYKLTDKT
          GPGRELG.EPYRA.GPSQL.F.P.AFNGGTVLA.AGE.FS.VA.DT.LSEGFSIHTRDS.PKCYKLTDKT
Retrocopy GPGRELGIEPYRAVGPSQLHFLPFAFNGGTVLAFAGEGFSVVAFDT*LSEGFSIHTRDS>PKCYKLTDKT

Parental  VIGCSGFHGDCLTLTKIIEARLKMYKHSNNKAMTTGAIAAMLSTILYSRRFFPYYVYNIIGGLDEEGKGA
          VIGCSGFHGDCLTLTKIIEA.LK.YKHSNNKAMTTGAIAAMLSTILYSR.FFPY.VY.II.GLD.EGKGA
Retrocopy VIGCSGFHGDCLTLTKIIEAHLKKYKHSNNKAMTTGAIAAMLSTILYSRLFFPY*VYHIIRGLDKEGKGA

Parental  VYSFDPVGSYQRDSFKA-GGSASAMLQPLLDNQVGFKNMQNVEHVPLSLDRAMRLVKDVFISAAERDVYT
          .YSFDPVGSYQRDSFKA.GGSAS.M.QPLLDNQ.GFKNM..VEHV.LSLDR...LVKDVFISA..RD.YT
Retrocopy LYSFDPVGSYQRDSFKA>GGSASTMMQPLLDNQLGFKNMKDVEHVLLSLDRDKQLVKDVFISAVKRDGYT

Parental  GDALKICI
          GD.L..CI
Retrocopy GDILQNCI

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	127.57 RPM
SRP012922_cerebellum	0.14 RPM	67.36 RPM
SRP012922_heart	0.00 RPM	58.47 RPM
SRP012922_kidney	0.00 RPM	75.57 RPM
SRP012922_liver	0.00 RPM	60.84 RPM
SRP012922_lung	0.00 RPM	110.88 RPM
SRP012922_quadricep_muscle	0.00 RPM	63.70 RPM
SRP012922_spleen	0.00 RPM	95.35 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_2087 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 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017047	1 retrocopy	retro_amel_1066,
Canis familiaris	ENSCAFG00000004116	1 retrocopy	retro_cfam_2108,
Callithrix jacchus	ENSCJAG00000020644	1 retrocopy	retro_cjac_632,
Dasypus novemcinctus	ENSDNOG00000019502	1 retrocopy	retro_dnov_2087 ,
Felis catus	ENSFCAG00000031269	1 retrocopy	retro_fcat_911,
Gorilla gorilla	ENSGGOG00000022128	1 retrocopy	retro_ggor_1661,
Microcebus murinus	ENSMICG00000007469	1 retrocopy	retro_mmur_173,
Macaca mulatta	ENSMMUG00000019919	1 retrocopy	retro_mmul_1135,
Mustela putorius furo	ENSMPUG00000007150	1 retrocopy	retro_mputfur_1196,
Mus musculus	ENSMUSG00000014769	2 retrocopies	retro_mmus_1784, retro_mmus_3664,
Oryctolagus cuniculus	ENSOCUG00000007973	2 retrocopies	retro_ocun_1029, retro_ocun_620,
Procavia capensis	ENSPCAG00000000344	1 retrocopy	retro_pcap_329,
Pongo abelii	ENSPPYG00000017191	1 retrocopy	retro_pabe_130,
Vicugna pacos	ENSVPAG00000006517	1 retrocopy	retro_vpac_521,