RetrogeneDB ID: retro_dnov_2467

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_77733:6052..6367(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RWDD1
• Ensembl ID: ENSDNOG00000007516
• Aliases: None
• Description: RWD domain containing 1 [Source:HGNC Symbol;Acc:20993]

Sequence

>retro_dnov_2467
CAATTATTTCATGGTACTCCTTTTACAATTGAAAATTTCTTAAGTTGGAAAGCTAAGTTTGATGCAGAGCTCTTAAAGAT
TAAAAAGAAACAAATAAAAGAAGAATAACAAGCAGGAAAAAATTAATTAAGTGGAAAGCAGCCTTTTGATACAGATCATA
ATCTTGACACATCCAATATCCAGTTCTTGGAGGATGCTGGAAACAATGTGGAGGTAGATAAGTCTTTGTTCTAGGAAGTG
GATGATTTGGAGCTGGAGGGTGATGAGGATAACCCAGACTGCAATCCTGATGACCCAGAGAGTGACTCAACTGAC

Alignment

ORF - retro_dnov_2467 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.81 %
• Parental protein coverage: 53.57 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QLFHGTPVTIENFLSWKAKFDAELLEIKKKRMKEEEQAGKNKLSGKQLFETDHNLDTSDIQFLEDAGNNV
          QLFHGTP.TIENFLSWKAKFDAELL.IKKK..KEE.QAGKN.LSGKQ.F.TDHNLDTS.IQFLEDAGNNV
Retrocopy QLFHGTPFTIENFLSWKAKFDAELLKIKKKQIKEE*QAGKN*LSGKQPFDTDHNLDTSNIQFLEDAGNNV

Parental  EVDESLFQEMDDLELEDDEDDPDYNPANPESDSTD
          EVD.SLF.E.DDLELE.DED.PD.NP..PESDSTD
Retrocopy EVDKSLF*EVDDLELEGDEDNPDCNPDDPESDSTD

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	23.14 RPM
SRP012922_cerebellum	0.14 RPM	20.07 RPM
SRP012922_heart	0.00 RPM	15.31 RPM
SRP012922_kidney	0.27 RPM	34.50 RPM
SRP012922_liver	0.15 RPM	14.55 RPM
SRP012922_lung	0.00 RPM	28.71 RPM
SRP012922_quadricep_muscle	0.17 RPM	29.25 RPM
SRP012922_spleen	0.00 RPM	29.99 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_2467 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004474	1 retrocopy	retro_cjac_1622,
Dasypus novemcinctus	ENSDNOG00000007516	1 retrocopy	retro_dnov_2467 ,
Loxodonta africana	ENSLAFG00000008170	1 retrocopy	retro_lafr_813,
Monodelphis domestica	ENSMODG00000017837	1 retrocopy	retro_mdom_1686,
Oryctolagus cuniculus	ENSOCUG00000013592	1 retrocopy	retro_ocun_691,
Ictidomys tridecemlineatus	ENSSTOG00000020231	2 retrocopies	retro_itri_121, retro_itri_365,
Ictidomys tridecemlineatus	ENSSTOG00000022124	1 retrocopy	retro_itri_596,
Tupaia belangeri	ENSTBEG00000002543	2 retrocopies	retro_tbel_2986, retro_tbel_4366,