RetrogeneDB ID: retro_dnov_2453

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_76059:5166..5867(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DCAF7
• Ensembl ID: ENSDNOG00000001071
• Aliases: None
• Description: DDB1 and CUL4 associated factor 7 [Source:HGNC Symbol;Acc:30915]

Sequence

>retro_dnov_2453
CGCGTTCAGCTTGTTGGTTTAGATGAGGAGAGCTCAGAACTTATTTGCCAAAATACCTTTGACCATCTGTACCCCACCAT
GAAGCTCACGTGGACCCCCAACACAGAAGGCGCCTATCCAGACCTACAGCAACAGGTGGCAACCATCTCCGTGTGGCGGG
TTGGTGGAGCAGAGCCCAGGCTGCAATTTTTTGCTAAATAGTAACAGAACTCTGACTTCCGGGCTCCTCTGACCTCCTTG
TCTGGAATGAGGTGAAGCCTTATCTTTTAGGTACTTCCAGCACAGGTAGGACTTGTACCTCCTGGGCTCTGGTGACAGAG
CAGGTGTTAGGGTGAGGGAATCTCATGTCTGGTTATGTGAAGACCCAGCTGAGCGCCCACTACAAAGAAGTCTGTAATAC
TCCCCTTAGCCGGGCTGGGGGTGGCAGGGACAGGTTTGCCTCCGTGGGCGCCGACGTCTCGCTGTGGATGTTTGACCTCA
GCCATCTAGAACACAGCCCCATTATTTACGAGGCCCCACAGCACCACCTGCTGCTTCGTCTCTGCTGGAACACGCAGGAC
CCTAACTACCTGGCCACCATGGCCATAGCTGGAATGGAGCTGGTCGTTCTGGATGTGCGAGTTCCGTGCACATCTGTTGC
CAGGTTAAACAACCGCTGAGCGTGTGTCAATGGCACATTCATCCTGCCACATCTGTACTGC

Alignment

ORF - retro_dnov_2453 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.49 %
• Parental protein coverage: 71.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KVQLVGLDEESSEFICRNTFDHPYPTTKLMWIPDTKGVYPDLLATSGDYLRVWRVGETETRLEC-LLNNN
          .VQLVGLDEESSE.IC.NTFDH.YPT.KL.W.P.T.G.YPDL.........VWRVG..E.RL...LLN.N
Retrocopy RVQLVGLDEESSELICQNTFDHLYPTMKLTWTPNTEGAYPDLQQQVAT-ISVWRVGGAEPRLQF>LLNSN

Parental  K-NSDFCAPLTSFD-WNEVDPYLLGTSSIDTTCTIWGLETGQVLGRVNLVSGHVKTQLIAHDKEVYDIAF
          ..NSDF.APLTS...WNEV.PYLLGTSS...TCT.W.L.T.QVLG..NL.SG.VKTQL.AH.KEV.....
Retrocopy R<NSDFRAPLTSLS<WNEVKPYLLGTSSTGRTCTSWALVTEQVLG*GNLMSGYVKTQLSAHYKEVCNTPL

Parental  SR--GGRDMFASVGADGSVRMFDLRHLEHSTIIYEDPQHHPLLRLCWNKQDPNYLATMAMDGMEVVILDV
          SR..GGRD.FASVGAD.S..MFDL.HLEHS.IIYE.PQHH.LLRLCWN.QDPNYLATMA..GME.V.LDV
Retrocopy SRAGGGRDRFASVGADVSLWMFDLSHLEHSPIIYEAPQHHLLLRLCWNTQDPNYLATMAIAGMELVVLDV

Parental  RVPCTPVARLNNHRACVNGIAWAPHSSC
          RVPCT.VARLNN..ACVNG....PH..C
Retrocopy RVPCTSVARLNNR*ACVNGTFILPHLYC

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	0.19 RPM	34.23 RPM
SRP012922_cerebellum	0.14 RPM	22.27 RPM
SRP012922_heart	0.00 RPM	6.73 RPM
SRP012922_kidney	0.00 RPM	17.80 RPM
SRP012922_liver	0.00 RPM	7.43 RPM
SRP012922_lung	0.00 RPM	16.49 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.92 RPM
SRP012922_spleen	0.00 RPM	23.69 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_2453 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001071	1 retrocopy	retro_dnov_2453 ,
Monodelphis domestica	ENSMODG00000009994	1 retrocopy	retro_mdom_5,