RetrogeneDB ID: retro_dnov_482

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5177:352..812(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000006864
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000000943
• Aliases: None
• Description: None

Sequence

>retro_dnov_482
AATTTTGCTCCTCGAACTGAGATTTGGAAAGTTGTGGCTGAAAATAAGGAATGGCAAGAAAAATTCCTCACTCCAAATTT
GCCATTTATTGGTAAACAAGAGAATGTGATTACTTATCTGGTACTGTGGTACAAAACAGAAAAGCCTCCAAAGGAAAGAG
TCAGTGAACTGGTTACTCTTCGAATGAAACCTGGTGGACCAGCTCTGTGGAGTAATGCTTTTTCTAAGGGAAGTTAATGC
CCATGTCAACGTAGGCTACTCAAAACTAATTGGAGATTTCCACTCAGAACATGGCACACTCAACAGAGTTCACATTCTTT
GGTAGAATGAGAGTCTGGACAGTCATGCACCTGGGTGACATGAGTCTCATGAGGATCCCAGAGTTGTGGCAGCTGTTCTG
GAAAGTGCCAACTACCTAGTATCCCAGCAGAATATGCTTCTGACTCCTGTGTCTTTTTCA

Alignment

ORF - retro_dnov_482 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.68 %
• Parental protein coverage: 66.23 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NFAHRTEVRKAVAKDKEWQEKFIIPNLPFIDKQENEITYLVPWSKIEKPPKEGVYELVIFQMKPGGPAVW
          NFA.RTE..K.VA..KEWQEKF..PNLPFI.KQEN.ITYLV.W.K.EKPPKE.V.ELV...MKPGGPA.W
Retrocopy NFAPRTEIWKVVAENKEWQEKFLTPNLPFIGKQENVITYLVLWYKTEKPPKERVSELVTLRMKPGGPALW

Parental  GNAFQ-RAVNAHVSLGYSKLIGVFHSEYGTLNRVHVLWWNESLDSRAAGRHQSHEDPRVVGAVRDSANHL
          .NAF..R.VNAHV..GYSKLIG.FHSE.GTLNRVH.LW.NESLDS.A.G.H.SHEDPRVV.AV..SAN.L
Retrocopy SNAFS>REVNAHVNVGYSKLIGDFHSEHGTLNRVHILW*NESLDSHAPG*HESHEDPRVVAAVLESANYL

Parental  VSQQNMLLIPSSFS
          VSQQNMLL.P.SFS
Retrocopy VSQQNMLLTPVSFS

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	21.59 RPM
SRP012922_cerebellum	0.00 RPM	10.72 RPM
SRP012922_heart	0.00 RPM	35.27 RPM
SRP012922_kidney	0.00 RPM	50.93 RPM
SRP012922_liver	0.31 RPM	76.78 RPM
SRP012922_lung	0.00 RPM	9.62 RPM
SRP012922_quadricep_muscle	0.00 RPM	24.40 RPM
SRP012922_spleen	0.00 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_482 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000014253	1 retrocopy	retro_acar_133,
Ailuropoda melanoleuca	ENSAMEG00000005118	1 retrocopy	retro_amel_552,
Canis familiaris	ENSCAFG00000023949	1 retrocopy	retro_cfam_295,
Cavia porcellus	ENSCPOG00000009373	1 retrocopy	retro_cpor_690,
Dasypus novemcinctus	ENSDNOG00000000943	1 retrocopy	retro_dnov_482 ,
Equus caballus	ENSECAG00000008088	1 retrocopy	retro_ecab_978,
Echinops telfairi	ENSETEG00000016120	1 retrocopy	retro_etel_1335,
Myotis lucifugus	ENSMLUG00000010147	1 retrocopy	retro_mluc_924,
Mustela putorius furo	ENSMPUG00000007103	1 retrocopy	retro_mputfur_1471,
Oryctolagus cuniculus	ENSOCUG00000007880	1 retrocopy	retro_ocun_1385,
Tursiops truncatus	ENSTTRG00000012307	1 retrocopy	retro_ttru_1702,