RetrogeneDB ID: retro_dnov_712

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_100772:4145..4664(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000002575
• Aliases: None
• Description: None

Sequence

>retro_dnov_712
GTTCGACTGCATAAGACAGTATGGCTGAGGTCTGAGATTTTACAGCAGGTCATCCAAGAGCTGTTTGTGGACTACTATGT
GAAGACACAAGATACAAATTTAACTTCTGAGGTTAAAAAGTTTCTTGAGACCTCTTAACAGTGGCTACTTGTGATTAAAC
TGACATGGCTCTTAGGTTCCAGCCAGGAGAGAGACATACCTCCACTGTTCAGGCTCCAGAAAACAGATCTGCTGGAGCTC
ATGCCACCCTCAGAGGATTTTGTGTGGGTAAGAGCTCAGCTACAGCTGGAAGTGGAGGAACAGCTCAAGAAGAAGTGCTT
CAGTCTGCTCTGCTACCTTCATCCCAATTCATATTCAGCAAATGAAACCCTGAGGGCAGTAAAGGTATGGAAATTGACAG
ATATCCTGGTGGGTGAGAAGCAGCAGTGACAAGACTCCAAAGGCCAGAAGAAGGAGTAGATGGTATTGCTGGAGAAACAG
TGCCACCTATTCCCAGAGCCTTCTCCAGAAGCACTGGCT

Alignment

ORF - retro_dnov_712 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.99 %
• Parental protein coverage: 50.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VRLHKTVWLRSEILQRVIQELLVDYYVKTQDTDLTSEDKKFHETLEQRLLVTELTRLVGPSQEREMPPLL
          VRLHKTVWLRSEILQ.VIQEL.VDYYVKTQDT.LTSE.KKF.ET..Q.LLV..LT.L.G.SQER..PPL.
Retrocopy VRLHKTVWLRSEILQQVIQELFVDYYVKTQDTNLTSEVKKFLETS*QWLLVIKLTWLLGSSQERDIPPLF

Parental  RLQKADLLELMPPSEDFVWMRARLQLEVEEQLKKKCFTLLCYHDPNSDSDNEILKAAKVWKLAEILVGEK
          RLQK.DLLELMPPSEDFVW.RA.LQLEVEEQLKKKCF.LLCY..PNS.S.NE.L.A.KVWKL..ILVGEK
Retrocopy RLQKTDLLELMPPSEDFVWVRAQLQLEVEEQLKKKCFSLLCYLHPNSYSANETLRAVKVWKLTDILVGEK

Parental  QQCQDTKNQQKEQMVLLEKQSATYSQVLLRCLA
          QQ.QD.K.Q.KE.MVLLEKQ...........LA
Retrocopy QQ*QDSKGQKKE*MVLLEKQCHLFPEPSPEALA

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	12.45 RPM
SRP012922_cerebellum	0.00 RPM	7.15 RPM
SRP012922_heart	0.00 RPM	5.57 RPM
SRP012922_kidney	0.00 RPM	8.49 RPM
SRP012922_liver	0.00 RPM	5.57 RPM
SRP012922_lung	0.00 RPM	10.54 RPM
SRP012922_quadricep_muscle	0.17 RPM	5.71 RPM
SRP012922_spleen	0.00 RPM	24.61 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_712 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000008389	1 retrocopy	retro_cjac_757,
Dasypus novemcinctus	ENSDNOG00000002575	1 retrocopy	retro_dnov_712 ,
Homo sapiens	ENSG00000092036	1 retrocopy	retro_hsap_469,
Gorilla gorilla	ENSGGOG00000007504	1 retrocopy	retro_ggor_447,
Myotis lucifugus	ENSMLUG00000012934	1 retrocopy	retro_mluc_1946,
Otolemur garnettii	ENSOGAG00000000586	1 retrocopy	retro_ogar_382,
Pongo abelii	ENSPPYG00000005651	1 retrocopy	retro_pabe_265,
Pan troglodytes	ENSPTRG00000006153	1 retrocopy	retro_ptro_352,