RetrogeneDB ID: retro_dnov_1454

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_207175:224..905(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000018584
• Aliases: None
• Description: None

Sequence

>retro_dnov_1454
TCTGGTCAGCTGAAATACAATATTGAAGTGTCTGTGAGTACATAGTAAAGAAAATTCCAATGCCCCAAAGAGACTTTACT
TCAGAACTCCGACTTATTGTTATTAGGTCCTTTGATGTCAACAAACCTGGCTGTGAAGTTGATGACCTTAAGGGTGGTGT
AGCTGGTGGCAGTATTCTAAAAGGAGTATTAAAGGTGGGCCAGGAGATAGAAGTCAGACCTGGTATTGTTTCCAGAGCTA
GTGAAGGAAAACTCATGTGTAAACCAATCTTTTCCAAAATTGTATCACTTTTTGCAGAACATAATGATCTTCAGTATGCT
GCTCCAGGGGGTCTTATTGGAGTTGGAACAAAAATTGACCCTACTTTGTGCCGGGCTGATAGAATGGTGGGACAGGTGGT
TGGTGCAGTTGGAGCGCTACCTGAGATCTTCACAGAATTGGAAATTTCCTATTTCCTACTTAGAGGGCTTCTAGGTGTCC
TCACTGAAGGAGATAAGAAAGCAGCAAAGGTGCAAAAACTGTCTAAGAATAAAGTGCTCATGGTGAACATAGAATCTCTG
TCAACTGGAGGAAGAGTTAGTGCAGTCAAGGCTGATGTGGGCAAAATTCTTTTGACTAATCCTGTGTGCACAGAAGTGGG
AGAAAAAAATAGCCCTTAGCCGAAGAGTTAAGAAACACTGG

Alignment

ORF - retro_dnov_1454 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.58 %
• Parental protein coverage: 53.04 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SAQLKYNIEV-VCEYIVKKIPVPPRDFTSEPRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQE
          S.QLKYNIEV.VCEYIVKKIP.P.RDFTSE.RLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQE
Retrocopy SGQLKYNIEV<VCEYIVKKIPMPQRDFTSELRLIVIRSFDVNKPGCEVDDLKGGVAGGSILKGVLKVGQE

Parental  IEVRPGIVSKDSEGKLMCKPIFSKIVSLFAEHNDLQYAAQGGLIGVGTKIDPTLCRADRMVGQVLGAVGA
          IEVRPGIVS..SEGKLMCKPIFSKIVSLFAEHNDLQYAA.GGLIGVGTKIDPTLCRADRMVGQV.GAVGA
Retrocopy IEVRPGIVSRASEGKLMCKPIFSKIVSLFAEHNDLQYAAPGGLIGVGTKIDPTLCRADRMVGQVVGAVGA

Parental  LPEIFTELEISYFLLRRLLGVRTEGDKKAAKVQKLSKNEVLMVNIGSLSTGGRVSAVKADLGKIVLTNPV
          LPEIFTELEISYFLLR.LLGV.TEGDKKAAKVQKLSKN.VLMVNI.SLSTGGRVSAVKAD.GKI.LTNPV
Retrocopy LPEIFTELEISYFLLRGLLGVLTEGDKKAAKVQKLSKNKVLMVNIESLSTGGRVSAVKADVGKILLTNPV

Parental  CTEVGE-KIALSRRVEKHW
          CTEVGE.KIALSRRV.KHW
Retrocopy CTEVGE>KIALSRRVKKHW

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	13.61 RPM	93.93 RPM
SRP012922_cerebellum	3.99 RPM	33.40 RPM
SRP012922_heart	4.87 RPM	29.93 RPM
SRP012922_kidney	7.94 RPM	66.81 RPM
SRP012922_liver	4.02 RPM	31.58 RPM
SRP012922_lung	10.54 RPM	71.78 RPM
SRP012922_quadricep_muscle	2.94 RPM	38.08 RPM
SRP012922_spleen	9.27 RPM	84.36 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_1454 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014337	1 retrocopy	retro_btau_1497,
Dasypus novemcinctus	ENSDNOG00000018584	1 retrocopy	retro_dnov_1454 ,
Equus caballus	ENSECAG00000017343	1 retrocopy	retro_ecab_810,
Echinops telfairi	ENSETEG00000000341	4 retrocopies	retro_etel_1061, retro_etel_126, retro_etel_1590, retro_etel_2017,
Loxodonta africana	ENSLAFG00000011052	1 retrocopy	retro_lafr_971,
Macaca mulatta	ENSMMUG00000006979	4 retrocopies	retro_mmul_1965, retro_mmul_2258, retro_mmul_473, retro_mmul_713,
Monodelphis domestica	ENSMODG00000007541	2 retrocopies	retro_mdom_1650, retro_mdom_732,
Pongo abelii	ENSPPYG00000020194	1 retrocopy	retro_pabe_10,
Pteropus vampyrus	ENSPVAG00000002533	1 retrocopy	retro_pvam_936,
Sus scrofa	ENSSSCG00000012178	1 retrocopy	retro_sscr_805,
Tursiops truncatus	ENSTTRG00000012474	4 retrocopies	retro_ttru_1080, retro_ttru_1638, retro_ttru_617, retro_ttru_686,