RetrogeneDB ID: retro_dnov_1054

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_14149:33706..34142(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000012613
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: CHTOP
• Ensembl ID: ENSDNOG00000004834
• Aliases: None
• Description: chromatin target of PRMT1 [Source:HGNC Symbol;Acc:24511]

Sequence

>retro_dnov_1054
GGCATCTGCACCCTAGAGAGAAGCTTGCCCAGAGGAGGACTTCATGGGGGACGGGCCAAGAGAACCCTACTTAGGGGCAG
GATGCTGCTCCAAGGTCAAAACCTGTTCCAAGATGGACTAGCCATAGCTCTCCAAATGGGCATAAGAAGAGGTGGCGTTC
AAGGTCGTGGAGGTCCTAGGAGAGGGACCCCAAGGTGTGGAGCTATAGGTCATGGTGGAATCAGTGGTAGAGGTCAGGGT
GTGATAGATATGGGAAGAGAGGCCTTTGGAGGAAGAGGCAGAAGCCTGTGGCCAAGGGAGAGGTGCCCTTGCTTGCTCTG
TACTGACCAAGAAGCAGCTGGACAACCATTTGGATGCCTACATGTCAAAAACGAAGGGACACCTGGATGCACAGTTGGTC
GCCTACATGGCACAGACAGATCCTGAAACCAGTGAT

Alignment

ORF - retro_dnov_1054 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.49 %
• Parental protein coverage: 58.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLPIIQRGLPRGGLRGGRATRTLLRGGMSLRGQNLLRGGRAVAPRMGLRRGGVRGRGGPGRGGLGRGAMG
          G.....R.LPRGGL.GGRA.RTLLRG.M.L.GQNL...G.A.A..MG.RRGGV.GRGGP.RG....GA.G
Retrocopy GICTLERSLPRGGLHGGRAKRTLLRGRMLLQGQNLFQDGLAIALQMGIRRGGVQGRGGPRRGTPRCGAIG

Parental  RGGIGGRGRGMIGRGRGGFGGRGRGR-GRGRGALTRPVLTKEQLDNQLDAYMSKTKGHLDAELDAYMAQT
          .GGI.GRG.G.I..GR..FGGRGR...G.GRGAL...VLTK.QLDN.LDAYMSKTKGHLDA.L.AYMAQT
Retrocopy HGGISGRGQGVIDMGREAFGGRGRSL>GQGRGALACSVLTKKQLDNHLDAYMSKTKGHLDAQLVAYMAQT

Parental  DPETND
          DPET.D
Retrocopy DPETSD

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	52.90 RPM
SRP012922_cerebellum	0.00 RPM	82.21 RPM
SRP012922_heart	0.00 RPM	19.72 RPM
SRP012922_kidney	0.00 RPM	27.38 RPM
SRP012922_liver	0.00 RPM	24.61 RPM
SRP012922_lung	0.00 RPM	60.33 RPM
SRP012922_quadricep_muscle	0.00 RPM	48.81 RPM
SRP012922_spleen	0.00 RPM	75.66 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_1054 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 7 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013518	1 retrocopy	retro_chof_6,
Dasypus novemcinctus	ENSDNOG00000004834	1 retrocopy	retro_dnov_1054 ,
Equus caballus	ENSECAG00000020889	1 retrocopy	retro_ecab_729,
Loxodonta africana	ENSLAFG00000002658	3 retrocopies	retro_lafr_131, retro_lafr_282, retro_lafr_656,
Myotis lucifugus	ENSMLUG00000016098	2 retrocopies	retro_mluc_201, retro_mluc_247,
Rattus norvegicus	ENSRNOG00000012760	1 retrocopy	retro_rnor_1095,
Vicugna pacos	ENSVPAG00000010259	1 retrocopy	retro_vpac_353,