RetrogeneDB ID: retro_dnov_2643

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_93820:8025..8359(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000023580
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: POP5
• Ensembl ID: ENSDNOG00000012668
• Aliases: None
• Description: processing of precursor 5, ribonuclease P/MRP subunit (S. cerevisiae) [Source:HGNC Symbol;Acc:17689]

Sequence

>retro_dnov_2643
CGTCCCCATGCGGGACTTTCATGAAGCCAAAGCTTCGTGGGCTTTGCAGTGAGCTCCCTCAGCGCCTACACTGGAATAGT
GCTAACACCATGCCCGACGGAAGTCTGCAGCTTGTGTGGCCAGCGCTTCCCTTCATCACATTCTTGGAAAACAAAGGACG
CCGCTTGCCTTGTTTTTCAACACCTTGCACGGGGGAGGTACAATTAGAACACGTCAGAGGTGCCTGGTTCAGTATCACAG
GAGGCAACTGTTGGTCTTGTTGCAGAACTGCACTGATGCAGGAGAGCAGGAGGCGATCCAGAGAGCTGTCACAAGAAGCT
CTTTGCTAGAGGAG

Alignment

ORF - retro_dnov_2643 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.91 %
• Parental protein coverage: 65.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RVHGTFGAAACSIGFAVRYLNAYTGIVLLRCRKEF-YQLVWSALPFITYLENKGHRYPC-FFNTLHVGGT
          R.H..........GFAV..L.AYTGIVL..C..E...QLVW.ALPFIT.LENKG.R.PC.FFNTLH.GGT
Retrocopy RPHAGLS*SQSFVGFAVSSLSAYTGIVLTPCPTEV<LQLVWPALPFITFLENKGRRLPC<FFNTLHGGGT

Parental  IRTCQKFLIQYNRRQLLILLQNCNDEGQREAIQKSVTKSSLLEE
          IRT.Q..L.QY.RRQLL.LLQNC.D.G..EAIQ..VT.SSLLEE
Retrocopy IRTRQRCLVQYHRRQLLVLLQNCTDAGEQEAIQRAVTRSSLLEE

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	16.34 RPM
SRP012922_cerebellum	0.55 RPM	11.82 RPM
SRP012922_heart	0.00 RPM	2.09 RPM
SRP012922_kidney	0.00 RPM	7.12 RPM
SRP012922_liver	0.00 RPM	5.42 RPM
SRP012922_lung	0.00 RPM	12.68 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.87 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_2643 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012668	1 retrocopy	retro_dnov_2643 ,
Echinops telfairi	ENSETEG00000009283	1 retrocopy	retro_etel_569,
Tarsius syrichta	ENSTSYG00000006138	1 retrocopy	retro_tsyr_1763,