RetrogeneDB ID: retro_dnov_2245

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_58114:10647..10916(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000010776
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SPCS1
• Ensembl ID: ENSDNOG00000012421
• Aliases: None
• Description: signal peptidase complex subunit 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:23401]

Sequence

>retro_dnov_2245
GATTACAAGGGCCAGAAGCTAGCTGAACAGATGTTTCAGGGAATTATTCTTTTTTCCGCAATAGTTGGATTTATCTATGG
GTACGTGGCCAAACAGTTCGGATGGACTGTCTATACAGTTATGGCTGGATTTGCTTTTTCATGTTTGCTGACACTTCCTC
CATGGCCCATCTATTGCCGACATCCCCTCAAGTGGTTACCTGTTCAAGACTCAGGAACAGAAGACAAGAAACCAGAAGAT
AGAAAAATAAGAGGCATGCTAAAAATAAT

Alignment

ORF - retro_dnov_2245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.31 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DYKGQKLAEQMFQGIILFSAIVGFIYGYVAEQFGWTVYIVMAGFAFSCLLTLPPWPIYRRHPLK-LPVQD
          DYKGQKLAEQMFQGIILFSAIVGFIYGYVA.QFGWTVY.VMAGFAFSCLLTLPPWPIY.RHPLK.LPVQD
Retrocopy DYKGQKLAEQMFQGIILFSAIVGFIYGYVAKQFGWTVYTVMAGFAFSCLLTLPPWPIYCRHPLKWLPVQD

Parental  SGTEDKKPGDRKL-KRHAKNN
          SGTEDKKP.DRK..KRHAKNN
Retrocopy SGTEDKKPEDRKI<KRHAKNN

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	0.97 RPM	39.28 RPM
SRP012922_cerebellum	0.27 RPM	17.46 RPM
SRP012922_heart	0.93 RPM	25.99 RPM
SRP012922_kidney	0.55 RPM	23.27 RPM
SRP012922_liver	0.77 RPM	26.94 RPM
SRP012922_lung	0.76 RPM	29.48 RPM
SRP012922_quadricep_muscle	0.52 RPM	34.79 RPM
SRP012922_spleen	1.37 RPM	38.46 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_2245 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012421	3 retrocopies	retro_dnov_2086, retro_dnov_2245 , retro_dnov_698,
Dipodomys ordii	ENSDORG00000000678	4 retrocopies	retro_dord_273, retro_dord_274, retro_dord_686, retro_dord_734,
Equus caballus	ENSECAG00000023559	1 retrocopy	retro_ecab_86,
Erinaceus europaeus	ENSEEUG00000007914	1 retrocopy	retro_eeur_25,
Echinops telfairi	ENSETEG00000004020	1 retrocopy	retro_etel_1056,
Loxodonta africana	ENSLAFG00000016073	2 retrocopies	retro_lafr_575, retro_lafr_625,
Mus musculus	ENSMUSG00000021917	2 retrocopies	retro_mmus_2758, retro_mmus_2928,
Vicugna pacos	ENSVPAG00000007380	1 retrocopy	retro_vpac_269,