RetrogeneDB ID: retro_dnov_1717

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_274328:251..597(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000025221
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS8
• Ensembl ID: ENSDNOG00000025236
• Aliases: None
• Description: ribosomal protein S8 [Source:HGNC Symbol;Acc:10441]

Sequence

>retro_dnov_1717
TTTCCTCTTTTCAGGCAGCGCCATGTGACTGGCATCTCCTGGGACAACTGGCACAAGTGCTGCAAGACTGGGGCAAGAGA
AAGCCCTACCACAAGAAGCGGAAGTATGGGCTAGGACGTCCAGCTGTCAACACCAAGATTGGTCCCCCTGCATACACACA
CAGTTTGTGTGCAAGGAGGCAACAAGTACTATGCCCTGAGGTTGATGTGAGGAACTTCTCCTGGGGTTCTGAGTGCTGTA
CTCACAAAAGAAGGATCATAATGTTGTTTACAATGCACCCAATAATGAGCTGGTCCACAACAAGACACTGGTGAAGAACT
GTATTGTGTTCATTGACAGCACACCA

Alignment

ORF - retro_dnov_1717 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.21 %
• Parental protein coverage: 53.7 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FPLSSQRLAMGISRDNWHKRRKTG-GKRKPYHKKRKYELGRPAANT-IG-PRRIHTVRVRGGNKKYRALR
          FPL..QR...GIS.DNWHK..KTG.GKRKPYHKKRKY.LGRPA.NT.IG.P...HTV.V.GGN.KY.ALR
Retrocopy FPLFRQRHVTGISWDNWHKCCKTG<GKRKPYHKKRKYGLGRPAVNTKIG>PLHTHTVCVQGGN-KYYALR

Parental  L-DVGNFSWGSECCTRKTRII-DVVYNASNNELVRTKTLVKNCIVLIDSTP
          L.DV.NFSWGSECCT.K.RII..VVYNA.NNELV..KTLVKNCIV.IDSTP
Retrocopy L<DVRNFSWGSECCTHKRRII<NVVYNAPNNELVHNKTLVKNCIVFIDSTP

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	0.58 RPM	666.05 RPM
SRP012922_cerebellum	0.14 RPM	396.60 RPM
SRP012922_heart	0.00 RPM	393.99 RPM
SRP012922_kidney	0.00 RPM	728.57 RPM
SRP012922_liver	0.00 RPM	389.96 RPM
SRP012922_lung	0.00 RPM	975.76 RPM
SRP012922_quadricep_muscle	0.00 RPM	562.18 RPM
SRP012922_spleen	0.11 RPM	1128.24 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_1717 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 85 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015697	1 retrocopy	retro_acar_124,
Canis familiaris	ENSCAFG00000004745	8 retrocopies	retro_cfam_1336, retro_cfam_1662, retro_cfam_1730, retro_cfam_2139, retro_cfam_2177, retro_cfam_261, retro_cfam_589, retro_cfam_791,
Callithrix jacchus	ENSCJAG00000004197	5 retrocopies	retro_cjac_1068, retro_cjac_181, retro_cjac_3138, retro_cjac_6, retro_cjac_951,
Dasypus novemcinctus	ENSDNOG00000025236	3 retrocopies	retro_dnov_1717 , retro_dnov_802, retro_dnov_908,
Dipodomys ordii	ENSDORG00000009287	1 retrocopy	retro_dord_429,
Felis catus	ENSFCAG00000022996	4 retrocopies	retro_fcat_1222, retro_fcat_200, retro_fcat_456, retro_fcat_962,
Gorilla gorilla	ENSGGOG00000005645	5 retrocopies	retro_ggor_1127, retro_ggor_1170, retro_ggor_1357, retro_ggor_1465, retro_ggor_556,
Microcebus murinus	ENSMICG00000008024	4 retrocopies	retro_mmur_1180, retro_mmur_1434, retro_mmur_1501, retro_mmur_380,
Myotis lucifugus	ENSMLUG00000001559	30 retrocopies	retro_mluc_1114, retro_mluc_1132, retro_mluc_1165, retro_mluc_1277, retro_mluc_1288, retro_mluc_1418, retro_mluc_1467, retro_mluc_1476, retro_mluc_1486, retro_mluc_1634, retro_mluc_1656, retro_mluc_1689, retro_mluc_1808, retro_mluc_1911, retro_mluc_1938, retro_mluc_2043, retro_mluc_2055, retro_mluc_2085, retro_mluc_2111, retro_mluc_2153, retro_mluc_2182, retro_mluc_2209, retro_mluc_2414, retro_mluc_460, retro_mluc_662, retro_mluc_730, retro_mluc_773, retro_mluc_820, retro_mluc_821, retro_mluc_906,
Macaca mulatta	ENSMMUG00000015270	2 retrocopies	retro_mmul_275, retro_mmul_70,
Monodelphis domestica	ENSMODG00000028389	1 retrocopy	retro_mdom_998,
Nomascus leucogenys	ENSNLEG00000014147	1 retrocopy	retro_nleu_34,
Oryctolagus cuniculus	ENSOCUG00000012476	1 retrocopy	retro_ocun_168,
Otolemur garnettii	ENSOGAG00000006922	16 retrocopies	retro_ogar_1156, retro_ogar_1746, retro_ogar_1895, retro_ogar_2501, retro_ogar_2529, retro_ogar_2556, retro_ogar_2699, retro_ogar_2723, retro_ogar_2947, retro_ogar_308, retro_ogar_3291, retro_ogar_3436, retro_ogar_394, retro_ogar_521, retro_ogar_730, retro_ogar_805,
Pan troglodytes	ENSPTRG00000000659	1 retrocopy	retro_ptro_30,
Rattus norvegicus	ENSRNOG00000018768	2 retrocopies	retro_rnor_222, retro_rnor_235,