RetrogeneDB ID: retro_dnov_1957

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_38881:10880..11758(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCE1
• Ensembl ID: ENSDNOG00000004274
• Aliases: None
• Description: RCE1 homolog, prenyl protein protease (S. cerevisiae) [Source:HGNC Symbol;Acc:13721]

Sequence

>retro_dnov_1957
GTCCCAGTGTTCTCCTGCCTCAGCCTCGCCTGCTCCTACGTGGGCAAACTCTACATCTGGAAGAGCAAGCTGCCCAGGGA
TGACCCCGCCGTTATCAAGCGGCACTTCACCAGTGTCCTGGTGGTGTCCAGTCTCTTGCCCCTCTGCGTACTTCTCTGGA
GGGAACTCACTGGCATCCAGCCAGGTGCATCCCTTCTCACCCTGATGGACTTCAGGTTGGAGGTCATTTTCCCAGCAGCA
CTGCTGACCCTGCTGCTGACCATGATCCTTTTCCTGGGCCCACTGATGCAGCTCTCTGTGGATTGCCCCTGTGATCTGGC
ATATGGGCTGAAGGTTGTTCTGACCCCCCACTCGTAGGCCTGCTGCCTCACAGGTATGTGCTGGCTGCGGAACCAAGTGA
CTGTGCCCCTAACAGAGGAGCTGCTGTTCTGGCCCTACGTGCTGCCCATGTTAGTGCCATGTGTGGGTATGGGCCCTGCT
GTATTCACCTGCCCACTCTTCTTTGGAGTTGCCCATTTTCACCACATTATTGAGCAGCTGTGGTTCTGCCAGAATAGTGT
GCGCAGTATCTTCTTGTCTGCAGTGTTCCAATTCTCCTACACAGCTGTCTTCGATGCTTACACTGCTTTCCTCTTCATCT
GCACAGGACACCTGATTGGGCCCATTCACTGCCACTCTTTCTGCAATTACATGGGCTTCTTTGCTGTATGTGTGGCCCTG
GAGTATCCACAGAGGCGGCCCTTGCTGGCTGGCTATGCCTGGGTATGGGACTCTTCCTGCTTCTATTCCAGCCCCTCACA
GACCCCAAGCTCTAGAGCAGCCTTCCCCTTCATGTGCTTTTGGAGCGGGCAGGAGACTCAGAGGCTCCCCTGTGCTCC

Alignment

ORF - retro_dnov_1957 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.99 %
• Parental protein coverage: 89.3 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VSVFSCLSLACSYVGSLYVWKSELPRDHPAVIKRRFTSVLVVSSLSPLCVLLWRELTGIQPGTSLLTLMG
          V.VFSCLSLACSYVG.LY.WKS.LPRD.PAVIKR.FTSVLVVSSL.PLCVLLWRELTGIQPG.SLLTLM.
Retrocopy VPVFSCLSLACSYVGKLYIWKSKLPRDDPAVIKRHFTSVLVVSSLLPLCVLLWRELTGIQPGASLLTLMD

Parental  FR-EGIFPAALLPLLLTMILFLGPLMQLSMDCPCDLADRLKVVLAPRSWAHCLTDMRWLRNQVIAPLTEE
          FR.E.IFPAALL.LLLTMILFLGPLMQLS.DCPCDLA..LKVVL.P.S.A.CLT.M.WLRNQV..PLTEE
Retrocopy FRLEVIFPAALLTLLLTMILFLGPLMQLSVDCPCDLAYGLKVVLTPHS*ACCLTGMCWLRNQVTVPLTEE

Parental  LVFRGCMLPMLAPCMGLGPAVFTCPLFFGVAHFHHIIEQLRFRQSSVGSIFLSAAFQFSYTAVFGAYTAF
          L.F....LPML.PC.G.GPAVFTCPLFFGVAHFHHIIEQL.F.Q.SV.SIFLSA.FQFSYTAVF.AYTAF
Retrocopy LLFWPYVLPMLVPCVGMGPAVFTCPLFFGVAHFHHIIEQLWFCQNSVRSIFLSAVFQFSYTAVFDAYTAF

Parental  LFIRTGHLIGPVLCHSFCNYMGFPAVCAALEHPQRWPLLAGYA-LGVGLFLLLLQPLTDPKLYGSLPLCV
          LFI.TGHLIGP..CHSFCNYMGF.AVC.ALE.PQR.PLLAGYA.LG.GLFLLL.QPLTDPKL..SLPL.V
Retrocopy LFICTGHLIGPIHCHSFCNYMGFFAVCVALEYPQRRPLLAGYA<LGMGLFLLLFQPLTDPKL*SSLPLHV

Parental  LLERAGDSEAPLCS
          LLERAGDSEAPLCS
Retrocopy LLERAGDSEAPLCS

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	13.03 RPM
SRP012922_cerebellum	0.00 RPM	18.42 RPM
SRP012922_heart	0.23 RPM	5.10 RPM
SRP012922_kidney	0.00 RPM	11.50 RPM
SRP012922_liver	0.00 RPM	5.73 RPM
SRP012922_lung	0.00 RPM	18.79 RPM
SRP012922_quadricep_muscle	0.00 RPM	5.19 RPM
SRP012922_spleen	0.00 RPM	19.80 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_1957 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 2 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004274	2 retrocopies	retro_dnov_106, retro_dnov_1957 ,
Oryctolagus cuniculus	ENSOCUG00000009821	1 retrocopy	retro_ocun_1897,