RetrogeneDB ID: retro_dnov_306

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3460:167331..167766(+)
• Located in intron of: ENSDNOG00000003488

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL26L1
• Ensembl ID: ENSDNOG00000002289
• Aliases: None
• Description: ribosomal protein L26-like 1 [Source:HGNC Symbol;Acc:17050]

Sequence

>retro_dnov_306
ATGTAGTTCAATCCCTTTCTGACTTGTGATCGGAGCAAGAACCGTAAGAGGCATTTCAATGCACCTTCCCACATTCAGAG
GAAGATTATGTCTTCCCCTCTTTCCAAGAAGCTGAGACAGAACTATAATGTTTGATTCATGCCTATCTGAAAAGATCATG
AAGTTCAGGATGTGCGAGGACACTACAAAGGTCAGCAAATTGGCAAAGTAGTCTAGGTTTACAGCAAGAAATATGTCATC
TACCTTGAATGGGTGCAGCGGTAGAAGGCTAATGGCACCACTGTCCATATGGGCATTCACCTCAGCAAGGTGGTTATCAC
TAGGCTAAAATTGGATAAAGACCGCAAAAAGATCCTTGAATGTAAAGCCAAATCTAGCCAAGTAGGAAAGGAAAAGGGCA
AATATAAGGAAGAAACAATTGAGAAGATGCAGAAA

Alignment

ORF - retro_dnov_306 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.14 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFNPFVTSDRSKNRKRHFNAPSHVRRKIMSSPLSKELRQKYNVRSMPIRKDDEVQVVRGHYKGQQIGKV
          M.FNPF.T.DRSKNRKRHFNAPSH..RKIMSSPLSK.LRQ.YNV..MPI.KD.EVQ.VRGHYKGQQIGKV
Retrocopy M*FNPFLTCDRSKNRKRHFNAPSHIQRKIMSSPLSKKLRQNYNV*FMPI*KDHEVQDVRGHYKGQQIGKV

Parental  VQVYRKKYVIYIERVQREKANGTTVHVGIHPSKVVITRLKLDKDRKKILERKAKSRQVGKEKGKYKEELI
          V.VY.KKYVIY.E.VQR.KANGTTVH.GIH.SKVVITRLKLDKDRKKILE.KAKS.QVGKEKGKYKEE.I
Retrocopy V*VYSKKYVIYLEWVQR*KANGTTVHMGIHLSKVVITRLKLDKDRKKILECKAKSSQVGKEKGKYKEETI

Parental  EKMQE
          EKMQ.
Retrocopy EKMQK

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	12.64 RPM
SRP012922_cerebellum	0.00 RPM	13.33 RPM
SRP012922_heart	0.00 RPM	5.34 RPM
SRP012922_kidney	0.00 RPM	10.68 RPM
SRP012922_liver	0.00 RPM	6.04 RPM
SRP012922_lung	0.00 RPM	16.04 RPM
SRP012922_quadricep_muscle	0.00 RPM	9.17 RPM
SRP012922_spleen	0.11 RPM	13.62 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_306 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 17 parental genes, and 100 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000011270	7 retrocopies	retro_amel_1106, retro_amel_1477, retro_amel_172, retro_amel_272, retro_amel_560, retro_amel_788, retro_amel_887,
Dasypus novemcinctus	ENSDNOG00000002289	35 retrocopies	retro_dnov_1106, retro_dnov_1147, retro_dnov_1171, retro_dnov_1258, retro_dnov_1304, retro_dnov_1319, retro_dnov_1344, retro_dnov_1381, retro_dnov_1501, retro_dnov_1676, retro_dnov_1819, retro_dnov_1959, retro_dnov_2039, retro_dnov_2041, retro_dnov_2061, retro_dnov_2078, retro_dnov_2103, retro_dnov_2116, retro_dnov_2121, retro_dnov_2287, retro_dnov_2297, retro_dnov_2438, retro_dnov_2545, retro_dnov_2580, retro_dnov_2632, retro_dnov_300, retro_dnov_306 , retro_dnov_467, retro_dnov_646, retro_dnov_666, retro_dnov_681, retro_dnov_760, retro_dnov_850, retro_dnov_970, retro_dnov_985,
Dasypus novemcinctus	ENSDNOG00000002470	3 retrocopies	retro_dnov_2054, retro_dnov_2174, retro_dnov_378,
Felis catus	ENSFCAG00000026949	1 retrocopy	retro_fcat_524,
Homo sapiens	ENSG00000037241	2 retrocopies	retro_hsap_586, retro_hsap_837,
Latimeria chalumnae	ENSLACG00000007599	2 retrocopies	retro_lcha_5, retro_lcha_8,
Microcebus murinus	ENSMICG00000011312	10 retrocopies	retro_mmur_1020, retro_mmur_1144, retro_mmur_313, retro_mmur_327, retro_mmur_346, retro_mmur_412, retro_mmur_471, retro_mmur_623, retro_mmur_72, retro_mmur_75,
Myotis lucifugus	ENSMLUG00000009799	1 retrocopy	retro_mluc_1556,
Macaca mulatta	ENSMMUG00000003070	1 retrocopy	retro_mmul_676,
Mustela putorius furo	ENSMPUG00000012729	2 retrocopies	retro_mputfur_1624, retro_mputfur_190,
Oryctolagus cuniculus	ENSOCUG00000006172	4 retrocopies	retro_ocun_1015, retro_ocun_1224, retro_ocun_354, retro_ocun_845,
Procavia capensis	ENSPCAG00000002246	10 retrocopies	retro_pcap_137, retro_pcap_157, retro_pcap_188, retro_pcap_204, retro_pcap_337, retro_pcap_404, retro_pcap_419, retro_pcap_42, retro_pcap_422, retro_pcap_448,
Pteropus vampyrus	ENSPVAG00000003253	8 retrocopies	retro_pvam_1062, retro_pvam_1208, retro_pvam_122, retro_pvam_353, retro_pvam_688, retro_pvam_71, retro_pvam_769, retro_pvam_877,
Sus scrofa	ENSSSCG00000016989	3 retrocopies	retro_sscr_1104, retro_sscr_462, retro_sscr_685,
Ictidomys tridecemlineatus	ENSSTOG00000026876	1 retrocopy	retro_itri_1141,
Tarsius syrichta	ENSTSYG00000001655	2 retrocopies	retro_tsyr_1805, retro_tsyr_759,
Tursiops truncatus	ENSTTRG00000010624	8 retrocopies	retro_ttru_1070, retro_ttru_1124, retro_ttru_1694, retro_ttru_1818, retro_ttru_364, retro_ttru_386, retro_ttru_474, retro_ttru_646,