RetrogeneDB ID: retro_dnov_1935

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_3767:97970..98858(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IFI44
• Ensembl ID: ENSDNOG00000007317
• Aliases: None
• Description: interferon-induced protein 44 [Source:HGNC Symbol;Acc:16938]

Sequence

>retro_dnov_1935
GAGTGTGAAGTTTTTTGAACTGAAGGAATTAACAATAATCTAGGAAACATACAGAGGATAAAGGAAGTTACATAACACAG
AAAGAACCTCCTGACAGATCTCAGAACCTACAACCCCATTGCAGACTTGGTCCCAGAAATACATATTCTCTTGCTGGATC
CAATTGGGTCTGGAAATTCCAGTTTTTTCAATTCTGTGAAGTCAATTTTCTGAGGCCATGTGACTCACCAAGCTATAACA
GGATCCGATATCACCAGCATTACTGAACAGTTTAGAATATATTCCATTAAAGATAGAGAATAGGGTACATCTCTGCCTTT
TATATTTTGTGACTCAATGGGACTGGCTAAGAAAGGGGGAGTAGCATTGTGTGTGGATGACATACCTCACATCTTAAAAG
GTTGTGTGCCTGACAAATATCAGTTTAACCCCCATAAACCAATTATGTCCAATCATCCTGACTTCATCAGCTCTCCATCA
CTGAAGAAAAGGATTCACTGTGTGGTGTATGTCTTAGATATCAACTCTATCAATGAAATATCCTCTAAAATGGTGTCAAA
GTTCAAAAGAGTTCAAAAAGAAGTTTTAAACTATGGTATAGCACATGTGGCCTTGCTTACTAAAGTGAATAATTGCAATG
AAGTTCTTCAAGAGAACCTTCTAAACATGAATAGATCTATGACTTATCAAAGCTAGATATTGAATGTCAACAAAATGCTA
GGCGTTCCTCTTCTGAACATCTTGATGGTTGGAAATTATGCCTCAGAGTGGGAGCTGGACCCTTTAAAGGATGTTCGAAT
CCTCTCTACACTGAGGCAGATGTTGCAGGCTACAGATGACTCCTTAGAAGATTTGCCTCTTGAGAAAACAGATGAAATTA
CAAGAGCA

Alignment

ORF - retro_dnov_1935 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.04 %
• Parental protein coverage: 79.23 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ECEVFRCE----DLLNQRTIDGINVLRENLLSDLKTYKLYENLVHQARILLLGPFGAGKSSFFNSVKSVF
          ECEVF..E.....L.N...I......R.NLL.DL.TY.....LV....ILLL.P.G.G.SSFFNSVKS.F
Retrocopy ECEVF*TEGINNNLGNIQRIKEVT*HRKNLLTDLRTYNPIADLVPEIHILLLDPIGSGNSSFFNSVKSIF

Parental  RGHITNQAPVGFNTTGISEQYRIYSITDGKNGGSLPFILCDSMGLGVKEG--LCMDDIPYILQGHVPDRY
          .GH.T.QA..G...T.I.EQ.RIYSI.D...G.SLPFI.CDSMGL..K.G..LC.DDIP.IL.G.VPD.Y
Retrocopy *GHVTHQAITGSDITSITEQFRIYSIKDRE*GTSLPFIFCDSMGLAKKGGVALCVDDIPHILKGCVPDKY

Parental  KFNSIKPITPSHHDYIDSPLLKDRIHCVAFVFDANSVADFSSEMVANIKRIQKELIKYGMVHVALLTHVD
          .FN..KPI...H.D.I.SP.LK.RIHCV..V.D.NS....SS.MV...KR.QKE...YG..HVALLT.V.
Retrocopy QFNPHKPIMSNHPDFISSPSLKKRIHCVVYVLDINSINEISSKMVSKFKRVQKEVLNYGIAHVALLTKVN

Parental  DIDLITKGDLIDIYRCVPVKSKIEAVHTELGFSFLNILVVSKYTSEWELEPIKDVLILSALKQMLRIVDD
          .........L....R.....S.I..V...LG...LNIL.V..Y.SEWEL.P.KDV.ILS.L.QML...DD
Retrocopy NCNEVLQENLLNMNRSMTYQS*ILNVNKMLGVPLLNILMVGNYASEWELDPLKDVRILSTLRQMLQATDD

Parental  FLEDLPLATDQRKGRA
          .LEDLPL.......RA
Retrocopy SLEDLPLEKTDEITRA

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	0.58 RPM	5.83 RPM
SRP012922_cerebellum	0.00 RPM	0.55 RPM
SRP012922_heart	0.70 RPM	1.39 RPM
SRP012922_kidney	0.27 RPM	4.38 RPM
SRP012922_liver	0.62 RPM	5.57 RPM
SRP012922_lung	0.76 RPM	12.52 RPM
SRP012922_quadricep_muscle	0.17 RPM	0.17 RPM
SRP012922_spleen	1.03 RPM	9.84 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_1935 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007317	1 retrocopy	retro_dnov_1935 ,