RetrogeneDB ID: retro_dnov_610

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_68:52301..53013(-)
• Located in intron of: ENSDNOG00000013570

Retrocopy information

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

Parental gene information

• Parental gene symbol: ETF1
• Ensembl ID: ENSDNOG00000010830
• Aliases: None
• Description: eukaryotic translation termination factor 1 [Source:HGNC Symbol;Acc:3477]

Sequence

>retro_dnov_610
TCACCCACTCATGGTAGGCTACTTTTGTACCTGGCCCTCCAATCCAGCTCCTCACTGGGCTCCAGCAATGGCACAAGCGT
AATTTTGTTGATCATTCCTCCCAAAGACCAGATTTTACGAGTGGCAAAAATGTTAACAGATGAGTCTGGACCTGCATCTA
ACATTAAGTCATAAGTAAAACAACTTTCAGTCCTGGAAGTCATTACATCTGTACAACAAAGACTCTAACTTCATAACAAA
GTACCTGCAAATGGTCTGGTTGTTTATTGTGGAACATTAGTAAGGGAAGAAGGAAAGGAAATGAAAGTCAACATTGACTT
AGAGCCTTTCAAACCAATTAATATGCCACTGTATTTGTGTGACAACAAATTCCAAACAGAGGCTCTTACAGTGTTACTTT
TGGATGATAGTAAGTTTGGCTTCAGTGTAATAGATAGTTGTAGTGCATTTCTTGGCACACTCCAAGGAAACACAAGAGAA
GTCTTGCACAAATTCACTGTGAATCTCCCAAAGAAACATGGTAGAGATGGTCAGTCTGCTTTGTGTTTTGCCCTTTTAAG
AATGGAAAAAGGACTTAACTATGTTTACAAAGTAGCTGATACTGCTGTGCAGTTGATTACTCCTGGGGAAAAAGCGAATG
TGGCTGGTCTCATTTTAGCTGAATCACCTGACTTTAAAACTGAACTAAGTCAATCTGATAATGTTTGATCAG

Alignment

ORF - retro_dnov_610 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.53 %
• Parental protein coverage: 55.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SPRVAHRSVELKRPSKSWEARGNGTSMISLIIPPKDQISRVAKMLADEFGTASNIKSRVNRLSVLGAITS
          SP........L...S.S.....NGTS.I.LIIPPKDQI.RVAKML.DE.G.ASNIKS.V..LSVL..ITS
Retrocopy SPTHGRLLLYLALQSSSSLGSSNGTSVILLIIPPKDQILRVAKMLTDESGPASNIKS*VKQLSVLEVITS

Parental  VQQRLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTALLSDDSKFG
          VQQRL.L.NKVP.NGLVVYCGT.V.EEGKE.KVNID.EPFKPIN..LYLCDNKF.TEALT.LL.DDSKFG
Retrocopy VQQRL*LHNKVPANGLVVYCGTLVREEGKEMKVNIDLEPFKPINMPLYLCDNKFQTEALTVLLLDDSKFG

Parental  FIVIDGSGALFGTLQGNTREVLHKFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVAETAVQLFISGD
          F.VID...A..GTLQGNTREVLHKFTV.LPKKHGR.GQSAL.FA.LRMEK..NYV.KVA.TAVQL...G.
Retrocopy FSVIDSCSAFLGTLQGNTREVLHKFTVNLPKKHGRDGQSALCFALLRMEKGLNYVYKVADTAVQLITPGE

Parental  KVNVAGLVLAGSADFKTELSQSD-MFDQ
          K.NVAGL.LA.S.DFKTELSQSD.MFDQ
Retrocopy KANVAGLILAESPDFKTELSQSD>MFDQ

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	22.75 RPM
SRP012922_cerebellum	0.00 RPM	12.23 RPM
SRP012922_heart	0.00 RPM	9.28 RPM
SRP012922_kidney	0.00 RPM	9.31 RPM
SRP012922_liver	0.00 RPM	15.95 RPM
SRP012922_lung	0.15 RPM	18.17 RPM
SRP012922_quadricep_muscle	0.00 RPM	23.37 RPM
SRP012922_spleen	0.11 RPM	19.92 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_610 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 10 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001282	1 retrocopy	retro_cfam_99,
Callithrix jacchus	ENSCJAG00000006776	2 retrocopies	retro_cjac_2316, retro_cjac_4133,
Dasypus novemcinctus	ENSDNOG00000010830	3 retrocopies	retro_dnov_1925, retro_dnov_2504, retro_dnov_610 ,
Equus caballus	ENSECAG00000013041	1 retrocopy	retro_ecab_740,
Echinops telfairi	ENSETEG00000007362	2 retrocopies	retro_etel_1237, retro_etel_1400,
Gorilla gorilla	ENSGGOG00000000657	4 retrocopies	retro_ggor_2326, retro_ggor_2561, retro_ggor_2562, retro_ggor_2919,
Macaca mulatta	ENSMMUG00000005871	2 retrocopies	retro_mmul_1658, retro_mmul_718,
Mustela putorius furo	ENSMPUG00000009338	1 retrocopy	retro_mputfur_1448,
Oryctolagus cuniculus	ENSOCUG00000006650	3 retrocopies	retro_ocun_1188, retro_ocun_1614, retro_ocun_462,
Rattus norvegicus	ENSRNOG00000019450	1 retrocopy	retro_rnor_2935,