RetrogeneDB ID: retro_dnov_2086

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_4655:62649..62919(-)
• Located in intron of: None

Retrocopy information

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

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_2086
GATTACAAGGGCCAGAAGCTAGCTGAACAGATGTTTCAGGGAATTATTCTGTTTTCCGCAATAGTTGGATTTATCTACGG
GTACGCGGCCGAACAGTTCGAATGGGCTGTCTATATAGTTATGGCCAGATTTGCTTTTTCATGTTTGCTGACACTTCCTC
CATGGCCCATCTATCGCCGACATCCCCTCAAGTGGTTACCTGTTCAAGACTCAGGAACAGAAGACAGGAAACCAGGAGAT
AGAAAACTTAAGAGGCATGCTAAAAATAAT

Alignment

ORF - retro_dnov_2086 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.33 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DYKGQKLAEQMFQGIILFSAIVGFIYGYVAEQFGWTVYIVMAGFAFSCLLTLPPWPIYRRHPLK-LPVQD
          DYKGQKLAEQMFQGIILFSAIVGFIYGY.AEQF.W.VYIVMA.FAFSCLLTLPPWPIYRRHPLK.LPVQD
Retrocopy DYKGQKLAEQMFQGIILFSAIVGFIYGYAAEQFEWAVYIVMARFAFSCLLTLPPWPIYRRHPLKWLPVQD

Parental  SGTEDKKPGDRKLKRHAKNN
          SGTED.KPGDRKLKRHAKNN
Retrocopy SGTEDRKPGDRKLKRHAKNN

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	24.31 RPM	39.28 RPM
SRP012922_cerebellum	9.90 RPM	17.46 RPM
SRP012922_heart	10.44 RPM	25.99 RPM
SRP012922_kidney	14.24 RPM	23.27 RPM
SRP012922_liver	15.64 RPM	26.94 RPM
SRP012922_lung	14.66 RPM	29.48 RPM
SRP012922_quadricep_muscle	18.35 RPM	34.79 RPM
SRP012922_spleen	27.70 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_2086 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,