RetrogeneDB ID: retro_dnov_1989

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_40671:3172..3721(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000011403
• Aliases: None
• Description: None

Sequence

>retro_dnov_1989
AAACACCAGCCCAAAAAGAACCTGGAGCTCATTTTCATTCAATCTTTAAAGGAGCTTGGGGTCTGGGGCGACTCGGTCTC
GGTGAAGATATCTGCGGGCAGGAATCAACTCCTTCCTCAAAGACTGACTGTATGTGCATCCCCTGAAAACAAGAAGCTGT
TTGAAGAGGATCAATTGCTGAGACAAGATGGAAAATTAGAGAAGATCCATTCCAAGGCAGGTGAGGTGACAGTGAAATTT
TTGAGGAGCTGTCTGTCACCTGAAGGTGGGGCTGAAGGACAAAGTCAAGTGGAGCCAACTCCTGAAACAGCTGTCAGCCA
CTTCCTTAACAATCATGGTGTTGTGGTAACCCCACAGGCATTAAAGTTACCAGAAGAGCCCATCCCATGGTGGTGTGGGG
GGAACAGCTGGTGTGAGGGGACAGTAAATGGGCTTGGCACTGGGAGGGTGCCTATGTCCATGATGAACTTTTGAACCAAG
GCCAAAAGTTAGAAGTACTGGTTGGCTCAGCAAGCTGCCCAGGGAATGACCCCCACCGGAGCTCTCATA

Alignment

ORF - retro_dnov_1989 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.5 %
• Parental protein coverage: 68.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KHRPKENLELILTQSVEEIGVRGDLVSVKKSLARNRLLPQGLAVYASPENKKLFEEEKSLRQEGKLEKIQ
          KH.PK.NLELI..QS..E.GV.GD.VSVK.S..RN.LLPQ.L.V.ASPENKKLFEE...LRQ.GKLEKI.
Retrocopy KHQPKKNLELIFIQSLKELGVWGDSVSVKISAGRNQLLPQRLTVCASPENKKLFEEDQLLRQDGKLEKIH

Parental  TMAGEATVKFLRSC-HLEVGMKNNVKWELNPEIVARHFLKNLGVVVAPHALKLPEEPITRW--GEYWCEV
          ..AGE.TVKFLRSC...E.G.......E..PE....HFL.N.GVVV.P.ALKLPEEPI..W..G..WCE.
Retrocopy SKAGEVTVKFLRSCLSPEGGAEGQSQVEPTPETAVSHFLNNHGVVVTPQALKLPEEPIPWWCGGNSWCEG

Parental  TVNGLDTVRVPMSVVNFERPKTKRYKYWLAQQAAKGTAPTNSQV
          TVNGL.T.RVPMS..NF...K.K..KYWLAQQAA.G..PT....
Retrocopy TVNGLGTGRVPMSMMNF-*TKAKS*KYWLAQQAAQGMTPTGALI

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	32.48 RPM
SRP012922_cerebellum	0.00 RPM	19.93 RPM
SRP012922_heart	0.00 RPM	18.33 RPM
SRP012922_kidney	0.00 RPM	27.93 RPM
SRP012922_liver	0.00 RPM	13.78 RPM
SRP012922_lung	0.00 RPM	17.72 RPM
SRP012922_quadricep_muscle	0.00 RPM	18.69 RPM
SRP012922_spleen	0.00 RPM	20.60 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_1989 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000258	1 retrocopy	retro_chof_10,
Dasypus novemcinctus	ENSDNOG00000011403	1 retrocopy	retro_dnov_1989 ,
Homo sapiens	ENSG00000143436	1 retrocopy	retro_hsap_4078,
Gorilla gorilla	ENSGGOG00000001902	1 retrocopy	retro_ggor_2735,
Loxodonta africana	ENSLAFG00000006271	2 retrocopies	retro_lafr_498, retro_lafr_563,
Nomascus leucogenys	ENSNLEG00000010275	1 retrocopy	retro_nleu_2045,
Oryctolagus cuniculus	ENSOCUG00000001383	1 retrocopy	retro_ocun_725,
Otolemur garnettii	ENSOGAG00000030456	1 retrocopy	retro_ogar_159,
Pongo abelii	ENSPPYG00000000857	1 retrocopy	retro_pabe_3347,
Pan troglodytes	ENSPTRG00000001295	2 retrocopies	retro_ptro_2765, retro_ptro_2996,
Vicugna pacos	ENSVPAG00000000664	1 retrocopy	retro_vpac_123,