RetrogeneDB ID: retro_dnov_710

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_100470:388..804(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: THEM4
• Ensembl ID: ENSDNOG00000005970
• Aliases: None
• Description: thioesterase superfamily member 4 [Source:HGNC Symbol;Acc:17947]

Sequence

>retro_dnov_710
GAAGGAAAACAATGTTCACAGGCCTACCTCTTCACCAGAAGCTTTGAGGGTGGCCTAAGCTTTGAATATGTGATATTCTA
TAATGAGGATGAGAAAAAAATTGTTTGCTTGTTTCATGGAGGCACTTACCTGTGTGGAGTGCCTGGATTCTTCCATGAAG
GCACCACTGCAACCTTGATTGATATTACTTTCGGCATGTGTGCTTACAGCTGGGAGAATTGCCATGACCACCAATCTCAT
CATCAATTTTAGAAGACATATCTCCTTTTGTTCTGTTGTTGTGAGAAATAGCCAGCTTGATAAAGTTGAAGGAAGGAAAC
GTTTTGTTTCCTGTAATATTTGAAGCGTTCATAAGAAGATCCTATACTCAAGAGGCAACAAGCTTTTTTGTTAAGTTGGA
TCCTGATAAAAGTTTG

Alignment

ORF - retro_dnov_710 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.08 %
• Parental protein coverage: 97.89 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EGKQRSQAPFFTRSFEDGLGFENAIFYNEDEKRAVCSFQGGPYLQGARGFLHGGTTSTMIDNTLSVYA-L
          EGKQ.SQA..FTRSFE.GL.FE..IFYNEDEK..VC.F.GG.YL.G..GF.H.GTT.T.ID.T....A.L
Retrocopy EGKQCSQAYLFTRSFEGGLSFEYVIFYNEDEKKIVCLFHGGTYLCGVPGFFHEGTTATLIDITFGMCA<L

Parental  LSGE-FAMTANLNINFKRPIPLNSVVVINGQLDKIEGREVFLSYSVQSVDEKILYS-EATSIFVQLDPDK
          ..GE..AMT.NL.INF.R.I...SVVV.N.QLDK.EGR..F.S....SV..KILYS.EATS.FV.LDPDK
Retrocopy QLGE<IAMTTNLIINFRRHISFCSVVVRNSQLDKVEGRKRFVSCNI*SVHKKILYS>EATSFFVKLDPDK

Parental  SL
          SL
Retrocopy SL

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	25.86 RPM
SRP012922_cerebellum	0.00 RPM	15.26 RPM
SRP012922_heart	0.00 RPM	15.78 RPM
SRP012922_kidney	0.00 RPM	20.81 RPM
SRP012922_liver	0.00 RPM	10.53 RPM
SRP012922_lung	0.00 RPM	6.41 RPM
SRP012922_quadricep_muscle	0.00 RPM	17.65 RPM
SRP012922_spleen	0.00 RPM	7.33 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_710 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 13 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000355	1 retrocopy	retro_amel_1301,
Choloepus hoffmanni	ENSCHOG00000000818	1 retrocopy	retro_chof_841,
Dasypus novemcinctus	ENSDNOG00000005970	1 retrocopy	retro_dnov_710 ,
Felis catus	ENSFCAG00000003443	1 retrocopy	retro_fcat_387,
Homo sapiens	ENSG00000159445	2 retrocopies	retro_hsap_1569, retro_hsap_978,
Gorilla gorilla	ENSGGOG00000008114	2 retrocopies	retro_ggor_1195, retro_ggor_782,
Microcebus murinus	ENSMICG00000010696	4 retrocopies	retro_mmur_1241, retro_mmur_1436, retro_mmur_1505, retro_mmur_1574,
Nomascus leucogenys	ENSNLEG00000010322	1 retrocopy	retro_nleu_1737,
Oryctolagus cuniculus	ENSOCUG00000005194	1 retrocopy	retro_ocun_1341,
Pongo abelii	ENSPPYG00000000851	1 retrocopy	retro_pabe_1295,
Pan troglodytes	ENSPTRG00000001301	2 retrocopies	retro_ptro_1056, retro_ptro_768,
Tupaia belangeri	ENSTBEG00000003352	2 retrocopies	retro_tbel_2412, retro_tbel_3266,
Tarsius syrichta	ENSTSYG00000005739	1 retrocopy	retro_tsyr_579,