RetrogeneDB ID: retro_dnov_1204

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_162389:69..586(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000025786
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SSR4
• Ensembl ID: ENSDNOG00000025714
• Aliases: None
• Description: signal sequence receptor, delta [Source:HGNC Symbol;Acc:11326]

Sequence

>retro_dnov_1204
ATGGCAGCAGTGGCATCGGTAGGGCCCTGGCACTGCTTCTGCTGCCCAGCCTCTCCTGCTGCCCAGCCAAGGCCTGCATG
GAGCCCCAGATCACCCCTTCCTATTACACCACCTCAGATGCTATCATCTCCACTGAGACCATCTTTATTGTGGATATCTC
CCTGATGTGCAAGAACAGGGTCCAGAACATGACTCTTTATGCTGACGTCAGTGGGAAACAGTTTCCTGCCACTTGGGGCC
AGGATATTGGGCACTATCAGGTGTCTGGAGCCTGGACCACAAGAGCGCCCATGCAGGCACCTACGAGATCCATTTCTTCC
ACAAGGAATCCTACAGCCTCCTGCAGAAGGCTCAGAGAAATAATGAGGACGTCTCTGTCATCCCACCCCTGTTCACAGTC
AGCATGGGCCATCAGAGCACATGGAACAGACCCTGGGTCTCCACCAAGGTGCTGGCCACGGTCATCAACCTGGTCATCTA
CTACCTGGCCTTCAGCACCAAGAGTCACATTCAGGCC

Alignment

ORF - retro_dnov_1204 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAVASLG-ALALLLLSSLSCCSAEACMEPQITPSYYTTSDAVISTETVFIVEISLTCKNRVQNMVLYAD
          MAAVAS.G.ALALLLL.SLSCC.A.ACMEPQITPSYYTTSDA.ISTET.FIV.ISL.CKNRVQNM.LYAD
Retrocopy MAAVASVG<ALALLLLPSLSCCPAKACMEPQITPSYYTTSDAIISTETIFIVDISLMCKNRVQNMTLYAD

Parental  VGGKQFPVTRGQDVGRYQVS-WSLDHKSAHAGTYEVRFFDEESYSLLRKAQRNNEDVSVIPPLFTVSVDH
          V.GKQFP.T.GQD.G.YQVS.WSLDHKSAHAGTYE..FF..ESYSLL.KAQRNNEDVSVIPPLFTVS..H
Retrocopy VSGKQFPATWGQDIGHYQVS<WSLDHKSAHAGTYEIHFFHKESYSLLQKAQRNNEDVSVIPPLFTVSMGH

Parental  RGTWNGPWVSTEVLAAVIGLVIYYLAFSAKSHIQA
          ..TWN.PWVST.VLA.VI.LVIYYLAFS.KSHIQA
Retrocopy QSTWNRPWVSTKVLATVINLVIYYLAFSTKSHIQA

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	0.19 RPM	318.73 RPM
SRP012922_cerebellum	0.27 RPM	87.43 RPM
SRP012922_heart	0.00 RPM	89.10 RPM
SRP012922_kidney	0.00 RPM	223.96 RPM
SRP012922_liver	0.15 RPM	208.52 RPM
SRP012922_lung	0.15 RPM	213.81 RPM
SRP012922_quadricep_muscle	0.35 RPM	84.64 RPM
SRP012922_spleen	0.23 RPM	293.25 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_1204 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000011328	1 retrocopy	retro_acar_97,
Callithrix jacchus	ENSCJAG00000011167	1 retrocopy	retro_cjac_2056,
Dasypus novemcinctus	ENSDNOG00000025714	2 retrocopies	retro_dnov_1204 , retro_dnov_922,
Homo sapiens	ENSG00000180879	1 retrocopy	retro_hsap_2536,
Gorilla gorilla	ENSGGOG00000024329	1 retrocopy	retro_ggor_1585,
Loxodonta africana	ENSLAFG00000006908	1 retrocopy	retro_lafr_337,
Mustela putorius furo	ENSMPUG00000008803	1 retrocopy	retro_mputfur_148,
Nomascus leucogenys	ENSNLEG00000013602	1 retrocopy	retro_nleu_2738,
Otolemur garnettii	ENSOGAG00000006738	1 retrocopy	retro_ogar_691,
Procavia capensis	ENSPCAG00000009037	1 retrocopy	retro_pcap_139,
Sus scrofa	ENSSSCG00000012784	1 retrocopy	retro_sscr_866,