RetrogeneDB ID: retro_dnov_1925

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_37204:6146..6817(-)
• Located in intron of: None

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_1925
GCAGACAACTTCTGTGCTGCTGACAGGAATGTGGAGATCTGGAAGATCAAGAAGTTCATCAAGTGTTTGGAGGCAGCCCA
CGGCAGTGGTGTAAGCATGATTTCATTGATCTTTCCACCCAAAGACACAAGTGGCAAAAATGTTAGCAGATGAGTTTGGA
ACTACATCTAATACTAAGCCATGAGTAAACCTCCTTTCAGTCCTGGAGCCATTACATCTGTACAAAAAGACTCAAACTTT
ATAACAAAGTACCTCCAAATGATCTGGTTGTTTACTGTGGAACAAGTATAATGGAAGAAGGAAAGGAAAAGAAAGTCAAT
GTTGACTTTCAGCCTTTCAAACCAATTGATATGTCATTACATTTGTGTGACAACAAATTTCATATCGAGGTTCATACAGT
GCTACTTTTGGATGATAGAAAGTTGGTTTCATTGTGATAAATGGTAAGGGTGCATTTTTTGGCACACTGCAAGGAAACAC
AGGAGGAGTCCTACGCAATTCACTGTGGATATCCCAAAGAAACATAGTAGAGGAGGTCAGAATGCCATGTGTTTTGCCCA
TTTAAGAATGGAAAAATGAGATAACTATGTTCAGAAAGTAGCTGAGACTGTGTACAGCTGTTCATTTCTGGGGACAAAGT
GAATGTGGCTGGTCTCATTTTAGCTGGATCC

Alignment

ORF - retro_dnov_1925 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.09 %
• Parental protein coverage: 52.09 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  ADSPRVAHRSVE---LKRPSKSWEA-RGNGTSMISLIIP-PKDQISRVAKMLADEFGTASNIKSRVNRLS
          AD....A.R.VE....K...K..EA..G.G.SMISLI.P.PK.Q...VAKMLADEFGT.SN.K..VN.LS
Retrocopy ADNFCAADRNVEIWKIKKFIKCLEAAHGSGVSMISLIFP>PKTQ---VAKMLADEFGTTSNTKP*VNLLS

Parental  VL-GAITSVQQ-RLKLYNKVPPNGLVVYCGTIVTEEGKEKKVNIDFEPFKPINTSLYLCDNKFHTEALTA
          VL.GAITSVQ..RLKLYNKVPPN.LVVYCGT...EEGKEKKVN.DF.PFKPI..SL.LCDNKFH.E..T.
Retrocopy VL<GAITSVQK<RLKLYNKVPPNDLVVYCGTSIMEEGKEKKVNVDFQPFKPIDMSLHLCDNKFHIEVHTV

Parental  LLSDDSKF-GFIVIDGSGALFGTLQGNTREVLH-KFTVDLPKKHGRGGQSALRFARLRMEKRHNYVRKVA
          LL.DD.K..GFIVI.G.GA.FGTLQGNT..VL...FTVD.PKKH.RGGQ.A..FA.LRMEK..NYV.KVA
Retrocopy LLLDDRKL<GFIVINGKGAFFGTLQGNTGGVLR<QFTVDIPKKHSRGGQNAMCFAHLRMEK*DNYVQKVA

Parental  ET-AVQLFISGDKVNVAGLVLAGS
          ET..VQLFISGDKVNVAGL.LAGS
Retrocopy ET<CVQLFISGDKVNVAGLILAGS

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	0.00 RPM	18.17 RPM
SRP012922_quadricep_muscle	0.00 RPM	23.37 RPM
SRP012922_spleen	0.00 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_1925 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 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,