RetrogeneDB ID: retro_dnov_536

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5887:44845..45186(-)
• Located in intron of: ENSDNOG00000025823

Retrocopy information

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

Parental gene information

• Parental gene symbol: TFAM
• Ensembl ID: ENSDNOG00000000535
• Aliases: None
• Description: transcription factor A, mitochondrial [Source:HGNC Symbol;Acc:11741]

Sequence

>retro_dnov_536
TTGGGTAGTTTTCCAAGAAGCCTTCGAATTCATATGTTCGCTTTGCTAAAGAACAGCTACCCATAATTAAAGCTCAGAAC
CCAGATGCAAAAAATACAGAACTAATTTTAAAAACTACCCAACTCTGGAGGGAACTTGCTGATTCACAGACAAAAATATA
TGAAGATGCTTACAGGGCAGACTGGCAGGCATACAAAGAAGCGATAAACAGAATTCAAGAGACTCTAACTCCAAGTCACA
TTATATCTTTAGAAAAAGAAATGCAAAAACGTTTACCAAAGGAAGTATTAATTAAAAAGCTTTTAACATTTTTGTGTCTG
AATGCTTCCAAGAAGCCAAGG

Alignment

ORF - retro_dnov_536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.41 %
• Parental protein coverage: 63.69 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LGSYP-KKPLSSYLRFTKEQLPIIKAQNPDAKIPEIIQKIAQQWRELPDSQKKIYEDAYRADWQAYKEEI
          LGS.P.KKP..SY.RF.KEQLPIIKAQNPDAK..E.I.K..Q.WREL.DSQ.KIYEDAYRADWQAYKE.I
Retrocopy LGSFP<KKPSNSYVRFAKEQLPIIKAQNPDAKNTELILKTTQLWRELADSQTKIYEDAYRADWQAYKEAI

Parental  NRIQEQLTPSQILSLEKEIMQKRLKKKALIKKRVLTM-LGKPKKPR
          NRIQE.LTPS.I.SLEKE.MQKRL.K..LIKK......L...KKPR
Retrocopy NRIQETLTPSHIISLEKE-MQKRLPKEVLIKKLLTFLCLNASKKPR

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	5.06 RPM	0.58 RPM
SRP012922_cerebellum	2.06 RPM	1.65 RPM
SRP012922_heart	1.62 RPM	0.23 RPM
SRP012922_kidney	3.56 RPM	0.27 RPM
SRP012922_liver	1.55 RPM	0.15 RPM
SRP012922_lung	2.14 RPM	0.46 RPM
SRP012922_quadricep_muscle	1.73 RPM	0.52 RPM
SRP012922_spleen	4.69 RPM	0.92 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_536 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.

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000535	1 retrocopy	retro_dnov_536 ,
Dipodomys ordii	ENSDORG00000014013	2 retrocopies	retro_dord_415, retro_dord_691,
Erinaceus europaeus	ENSEEUG00000006119	3 retrocopies	retro_eeur_103, retro_eeur_182, retro_eeur_652,
Homo sapiens	ENSG00000108064	2 retrocopies	retro_hsap_3692, retro_hsap_923,
Gorilla gorilla	ENSGGOG00000004948	2 retrocopies	retro_ggor_2496, retro_ggor_745,
Loxodonta africana	ENSLAFG00000012891	1 retrocopy	retro_lafr_1164,
Macropus eugenii	ENSMEUG00000008802	1 retrocopy	retro_meug_190,
Macaca mulatta	ENSMMUG00000019829	1 retrocopy	retro_mmul_1121,
Nomascus leucogenys	ENSNLEG00000012295	2 retrocopies	retro_nleu_2827, retro_nleu_288,
Oryctolagus cuniculus	ENSOCUG00000014405	1 retrocopy	retro_ocun_1278,
Pongo abelii	ENSPPYG00000002430	2 retrocopies	retro_pabe_3042, retro_pabe_796,
Pan troglodytes	ENSPTRG00000002519	1 retrocopy	retro_ptro_641,
Rattus norvegicus	ENSRNOG00000000613	1 retrocopy	retro_rnor_1936,
Tursiops truncatus	ENSTTRG00000009246	1 retrocopy	retro_ttru_1763,