RetrogeneDB ID: retro_dnov_159

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2222:66416..66814(+)
• Located in intron of: ENSDNOG00000013415

Retrocopy information

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

Parental gene information

• Parental gene symbol: PSMB2
• Ensembl ID: ENSDNOG00000017663
• Aliases: None
• Description: proteasome (prosome, macropain) subunit, beta type, 2 [Source:HGNC Symbol;Acc:9539]

Sequence

>retro_dnov_159
CATAACAAGATGTTTAAGATGAGTGAAAAAATCTTACTCCTACGTGTCGGAGAGGCTGGAGACCCTGTGCAATTTACAGG
ATATATTCAGAAAAATGTACAACTTTATAAGATGATAAATGGATATGAATTGTCTCCCACAGTAGCAGCTAATTTCACTC
ACCGAAACTTGGCTGACTGCCTTCAGAGTCGGACCCCGTATCATGTCAGCCTCCTGGCTGGCAATGATGAGCATGAAGGT
CCAGCACTCTACTACATGGACTACCTGGCAGCCTTGGCCAAGGGCCCTTTTGCAGCCCAAGGCTATGGTGCCTTCTTTAC
TCTCAGTATCCTGGACCAATGCTATATACCACTCTCTCACATGAGAGGGCAGTGGAGCTTCTTGGGAATTGTCTTGAG

Alignment

ORF - retro_dnov_159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 99.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HDKMFKMSEKILLLCVGEAGDTVQFAEYIQKNVQLYKMRNXXXXXXTAAANFTRRNL-DCLRSRTPYHVN
          H.KMFKMSEKILLL.VGEAGD.VQF..YIQKNVQLYKM.N......T.AANFT.RNL.DCL.SRTPYHV.
Retrocopy HNKMFKMSEKILLLRVGEAGDPVQFTGYIQKNVQLYKMINGYELSPTVAANFTHRNLADCLQSRTPYHVS

Parental  LLLAGYDEHEGPALYYMDYLAALAKAPFAAHGYGAFLTLSILDRYYTP-TISRERAVELLRKCLE
          LL.AG.DEHEGPALYYMDYLAALAK.PFAA.GYGAF.TLSILD..Y.P.T.S.ERAVELL..CLE
Retrocopy LL-AGNDEHEGPALYYMDYLAALAKGPFAAQGYGAFFTLSILDQCYIP<TLSHERAVELLGNCLE

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	2.72 RPM	71.18 RPM
SRP012922_cerebellum	2.06 RPM	41.10 RPM
SRP012922_heart	2.09 RPM	48.26 RPM
SRP012922_kidney	2.19 RPM	58.32 RPM
SRP012922_liver	1.39 RPM	41.95 RPM
SRP012922_lung	2.14 RPM	45.05 RPM
SRP012922_quadricep_muscle	1.04 RPM	43.96 RPM
SRP012922_spleen	3.89 RPM	78.75 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_159 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 16 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000715	1 retrocopy	retro_amel_743,
Canis familiaris	ENSCAFG00000003543	1 retrocopy	retro_cfam_1291,
Callithrix jacchus	ENSCJAG00000001547	1 retrocopy	retro_cjac_2110,
Dasypus novemcinctus	ENSDNOG00000017663	1 retrocopy	retro_dnov_159 ,
Equus caballus	ENSECAG00000021615	1 retrocopy	retro_ecab_769,
Echinops telfairi	ENSETEG00000019511	1 retrocopy	retro_etel_1529,
Felis catus	ENSFCAG00000030845	1 retrocopy	retro_fcat_1803,
Macropus eugenii	ENSMEUG00000000421	1 retrocopy	retro_meug_1235,
Monodelphis domestica	ENSMODG00000017902	1 retrocopy	retro_mdom_79,
Mustela putorius furo	ENSMPUG00000014891	1 retrocopy	retro_mputfur_1550,
Ochotona princeps	ENSOPRG00000012259	2 retrocopies	retro_opri_76, retro_opri_762,
Pteropus vampyrus	ENSPVAG00000001871	1 retrocopy	retro_pvam_909,
Sorex araneus	ENSSARG00000000409	2 retrocopies	retro_sara_557, retro_sara_660,
Sarcophilus harrisii	ENSSHAG00000016996	1 retrocopy	retro_shar_794,
Tupaia belangeri	ENSTBEG00000005230	1 retrocopy	retro_tbel_4039,
Tarsius syrichta	ENSTSYG00000005648	2 retrocopies	retro_tsyr_403, retro_tsyr_912,