RetrogeneDB ID: retro_dnov_2562

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_85721:1..580(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MDH1
• Ensembl ID: ENSDNOG00000013329
• Aliases: None
• Description: malate dehydrogenase 1, NAD (soluble) [Source:HGNC Symbol;Acc:6970]

Sequence

>retro_dnov_2562
GCACTTCCTCTCCTGAAAGATGACATCATAACAGATAAAGAAGAGGTTGCTTTCAAAGACTTGGATGTGGCCCTTCTCAT
GGGTCCTATGCCAAGAAGGACAGCATGGAGAGAAAAGATTTACTGAAAACAAACATGAAAATCTTTGAAGTCCAAAGTAC
TGCCTTGCAAACATATGCCAAGAAGTCAGTTAAGGTTATTGTCTGGGGAAACACAGTCAAAACTAACTGCCTTACTGCCT
CAAAGTTGGCTCCATCCACCACCAAAGAAAACTTCAGTTGCTTGACACGTTTGGATGAAAACCAAACTAAACCTCAAATT
GCTCTTAAACTTGGTGTGACTGCTGATAACATGAAGAAGGCCATCATCTGGGGAAACCATTCTTCAGCTCAGTATCCAGA
TGTCAGCCATGCCAAGCTGAAATGGCAGGGAAAGGAAGCTGGTGTTTATGAAGCTCTGAAAGGTGACAGCGGCTTAAAGG
GAGGCGTCATCATGACTGTGCAGCAGCACGGGGCTGCCGTCATCGAGACTCGAAACTGTCCGTGCAATGTCTGCTGCAAA
AGCCATCTGTGACCACGTC

Alignment

ORF - retro_dnov_2562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.16 %
• Parental protein coverage: 65.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ALPLLKDIIITDKEEVAFKDLDVAILVGSMPRR-DGMERKDLLKANVKIFKTQGAALEKYAKKSVKVIVV
          ALPLLKD.IITDKEEVAFKDLDVA.L.G.MPRR.D.MERKDLLK.N.KIF..Q..AL..YAKKSVKVIV.
Retrocopy ALPLLKDDIITDKEEVAFKDLDVALLMGPMPRR<DSMERKDLLKTNMKIFEVQSTALQTYAKKSVKVIVW

Parental  GNPANTNCLTASKSAPSIPKENFSCLTRLDQNRAKSQIALKLGVPADNVKNVIIWGNHSSTQYPDVNHAK
          GN...TNCLTASK.APS..KENFSCLTRLD.N..K.QIALKLGV.ADN.K..IIWGNHSS.QYPDV.HAK
Retrocopy GNTVKTNCLTASKLAPSTTKENFSCLTRLDENQTKPQIALKLGVTADNMKKAIIWGNHSSAQYPDVSHAK

Parental  VKMQGKEVGVYEALKDDSWLKGDFITTVQQRGAAVIKAR-KLS-SAMSAAKAICDHV
          .K.QGKE.GVYEALK.DS.LKG..I.TVQQ.GAAVI..R.KLS..AMSAAKAICDHV
Retrocopy LKWQGKEAGVYEALKGDSGLKGGVIMTVQQHGAAVIETR<KLS<RAMSAAKAICDHV

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	354.32 RPM
SRP012922_cerebellum	0.00 RPM	301.88 RPM
SRP012922_heart	0.00 RPM	929.05 RPM
SRP012922_kidney	0.00 RPM	277.63 RPM
SRP012922_liver	0.00 RPM	175.71 RPM
SRP012922_lung	0.00 RPM	49.64 RPM
SRP012922_quadricep_muscle	0.00 RPM	670.53 RPM
SRP012922_spleen	0.00 RPM	50.59 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_2562 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 15 parental genes, and 26 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000019295	1 retrocopy	retro_btau_466,
Choloepus hoffmanni	ENSCHOG00000007281	5 retrocopies	retro_chof_1260, retro_chof_1513, retro_chof_1892, retro_chof_2001, retro_chof_90,
Callithrix jacchus	ENSCJAG00000007018	4 retrocopies	retro_cjac_1848, retro_cjac_2407, retro_cjac_2418, retro_cjac_282,
Dasypus novemcinctus	ENSDNOG00000013329	2 retrocopies	retro_dnov_109, retro_dnov_2562 ,
Homo sapiens	ENSG00000014641	1 retrocopy	retro_hsap_3426,
Gorilla gorilla	ENSGGOG00000007085	1 retrocopy	retro_ggor_2316,
Loxodonta africana	ENSLAFG00000016504	2 retrocopies	retro_lafr_1134, retro_lafr_972,
Macaca mulatta	ENSMMUG00000006163	2 retrocopies	retro_mmul_1750, retro_mmul_2496,
Nomascus leucogenys	ENSNLEG00000009823	1 retrocopy	retro_nleu_1363,
Otolemur garnettii	ENSOGAG00000014487	1 retrocopy	retro_ogar_741,
Pongo abelii	ENSPPYG00000012373	1 retrocopy	retro_pabe_2839,
Pan troglodytes	ENSPTRG00000011974	1 retrocopy	retro_ptro_2326,
Sorex araneus	ENSSARG00000007690	1 retrocopy	retro_sara_361,
Sus scrofa	ENSSSCG00000025751	1 retrocopy	retro_sscr_779,
Tarsius syrichta	ENSTSYG00000001215	2 retrocopies	retro_tsyr_1790, retro_tsyr_190,