RetrogeneDB ID: retro_dnov_1451

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_20667:40584..40910(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPD52
• Ensembl ID: ENSDNOG00000017379
• Aliases: None
• Description: tumor protein D52 [Source:HGNC Symbol;Acc:12005]

Sequence

>retro_dnov_1451
AAGGATTATAGTAAGATAGATTTATATGAGGACTACAAATCACCATTTGATTTTGACAAAAGCTATCTCTACTTGACTCC
TAGTGGAAATTTATCTCCACCTGGATCACCTTCCCTTCAGAAATATGGTCTGCTGTGAGCAGACCCAGTACTGGAGGAAG
GAGAAGATGTTGCTGCCACAATCAGTGCCACAGAGACCCTGTCAGAGGAAAAGCAAAAAGAGACCTTGCAAAGGTAGAAG
AAAAAAATCCAGACTCTGTCTCAGAGGTAGCAGCAAAAGAGAAGCTTCTAGCAGAAACCAAACAGAAATTTAGAATCAAC
AGAATC

Alignment

ORF - retro_dnov_1451 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.1 %
• Parental protein coverage: 51.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RDYREMDSYEDYKSPFDFDKGVNKNYLYLSPSGNSSPPGSPTLQKHGLLRTDSVPEEGEDVAAAISATEA
          .DY...D.YEDYKSPFDFD....K.YLYL.PSGN.SPPGSP.LQK.GLL..D.V.EEGEDVAA.ISATE.
Retrocopy KDYSKIDLYEDYKSPFDFD----KSYLYLTPSGNLSPPGSPSLQKYGLL*ADPVLEEGEDVAATISATET

Parental  LSEEEQEELRRELAKVEEEIQTLSQ-VLAAKEKHLAEIKRKLGINSL
          LSEE.Q.E....L......IQTLSQ...AAKEK.LAE.K.K..IN..
Retrocopy LSEEKQKE---TLQR*KKKIQTLSQ<EVAAKEKLLAETKQKFRINRI

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	171.52 RPM
SRP012922_cerebellum	0.00 RPM	55.40 RPM
SRP012922_heart	0.00 RPM	2.55 RPM
SRP012922_kidney	0.00 RPM	141.83 RPM
SRP012922_liver	0.00 RPM	14.09 RPM
SRP012922_lung	0.00 RPM	8.55 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.38 RPM
SRP012922_spleen	0.00 RPM	19.57 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_1451 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000014930	1 retrocopy	retro_dnov_1582,
Dasypus novemcinctus	ENSDNOG00000017379	2 retrocopies	retro_dnov_1294, retro_dnov_1451 ,
Mus musculus	ENSMUSG00000027506	1 retrocopy	retro_mmus_3221,
Oryctolagus cuniculus	ENSOCUG00000008247	1 retrocopy	retro_ocun_325,
Otolemur garnettii	ENSOGAG00000016601	2 retrocopies	retro_ogar_1677, retro_ogar_348,