RetrogeneDB ID: retro_dnov_2606

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_89713:4077..4424(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LEPROTL1
• Ensembl ID: ENSDNOG00000014538
• Aliases: None
• Description: leptin receptor overlapping transcript-like 1 [Source:HGNC Symbol;Acc:6555]

Sequence

>retro_dnov_2606
TCCTTTGAAGGAGCAATTGGACTGATGTTTTTGATATTTGGATATGCACTTCCAATATACAACCAATACTAGCTCCTCTT
TGTTTTATTATTTTTTTACATCCCTTCACCCCTTCCATACTGCATAGCAAGATTATTGGATGATACAAATGATATGAGTA
ATGCTTGTAAGGAAATTACCATATTTCTTACAAAAACGCCATTGTTGTCTCAGCTTTTGGACTCCCTATTATATTTGCCA
GAGCACATCTGATTGAGTGAGAAGCTTGTGCACTTGTCGTCACAGGAAACAGAGTCATCTTTGCAACTATAATAGGCTTT
TACTTGGTCTTTAGCAGCACTGGTGAA

Alignment

ORF - retro_dnov_2606 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.88 %
• Parental protein coverage: 92.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SFGGAIGLMFLMLGCALPIYNQYWPLFVL-FFYVLSPIPYCIARRLVDDTDAMSNACKE-LAIFLT-TGI
          SF.GAIGLMFL..G.ALPIYNQY..LFVL.FFY..SP.PYCIAR.L.DDT..MSNACKE.L..FL....I
Retrocopy SFEGAIGLMFLIFGYALPIYNQY*LLFVLLFFYIPSPLPYCIAR-LLDDTNDMSNACKE>LPYFLQ>NAI

Parental  VVSAFGLPIVFARAHLIEWGACALVLTGNTVIFATILGFFLVFGSNDD
          VVSAFGLPI.FARAHLIE..ACALV.TGN.VIFATI.GF.LVF.S...
Retrocopy VVSAFGLPIIFARAHLIE*EACALVVTGNRVIFATIIGFYLVFSSTGE

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	13.88 RPM
SRP012922_heart	0.00 RPM	9.51 RPM
SRP012922_kidney	0.00 RPM	26.56 RPM
SRP012922_liver	0.00 RPM	19.35 RPM
SRP012922_lung	0.00 RPM	33.14 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.40 RPM
SRP012922_spleen	0.00 RPM	57.80 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_2606 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
Canis familiaris	ENSCAFG00000006530	1 retrocopy	retro_cfam_2171,
Choloepus hoffmanni	ENSCHOG00000012299	1 retrocopy	retro_chof_1305,
Dasypus novemcinctus	ENSDNOG00000014538	3 retrocopies	retro_dnov_1528, retro_dnov_2606 , retro_dnov_876,
Erinaceus europaeus	ENSEEUG00000001360	1 retrocopy	retro_eeur_139,
Oryctolagus cuniculus	ENSOCUG00000013931	1 retrocopy	retro_ocun_832,