RetrogeneDB ID: retro_dnov_555

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_6083:294174..294430(-)
• Located in intron of: ENSDNOG00000004435

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM254
• Ensembl ID: ENSDNOG00000024625
• Aliases: None
• Description: transmembrane protein 254 [Source:HGNC Symbol;Acc:25804]

Sequence

>retro_dnov_555
GCCACAATGGGGAGCACAGCAAGTGAAGCAGCTTATTTCCGGAAGGTCAGTTTGTTCTGGCTCACAATCATCACCCTCTC
TATGGGCTGCTACATGTGGGTTGTCTTCCAGCCTCAGAGTATCCCCTATCAGAGCCTTGGGCTTCTGGGCCCCTTCAATC
AATACTTGGGACCACCATCACACCCTCCTGAGCAATGGGTTTTGGCTTGCCTGGCTGATTCACATGGTAGAGTCCTTGCA
TGCCATGGTATTGTGC

Alignment

ORF - retro_dnov_555 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.09 %
• Parental protein coverage: 84.31 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AKSGAGRATAAYFRIARPLPLLVTVLGLGCYTWVVFWPQSIPYQRLGPL-GPFTQYLV-DNHPTLLRNGF
          A..G.....AAYFR......L....L..GCY.WVVF.PQSIPYQ.LG.L.GP....L..D.H.TLL.NGF
Retrocopy ATMGSTASEAAYFRKVSLFWLTIITLSMGCYMWVVFQPQSIPYQSLGLL<GPLQSILG<DHHHTLLSNGF

Parental  WLAWLIHVGESLYAMVLC
          WLAWLIH..ESL.AMVLC
Retrocopy WLAWLIHMVESLHAMVLC

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	1.17 RPM
SRP012922_cerebellum	0.00 RPM	0.96 RPM
SRP012922_heart	0.00 RPM	0.46 RPM
SRP012922_kidney	0.00 RPM	1.64 RPM
SRP012922_liver	0.00 RPM	2.94 RPM
SRP012922_lung	0.00 RPM	1.68 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.17 RPM
SRP012922_spleen	0.00 RPM	0.23 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_555 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 28 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015748	3 retrocopies	retro_cfam_602, retro_cfam_635, retro_cfam_637,
Callithrix jacchus	ENSCJAG00000007670	1 retrocopy	retro_cjac_3839,
Dasypus novemcinctus	ENSDNOG00000024625	1 retrocopy	retro_dnov_555 ,
Felis catus	ENSFCAG00000026147	1 retrocopy	retro_fcat_401,
Myotis lucifugus	ENSMLUG00000007585	16 retrocopies	retro_mluc_1178, retro_mluc_2482, retro_mluc_2491, retro_mluc_2492, retro_mluc_2528, retro_mluc_2532, retro_mluc_2550, retro_mluc_2551, retro_mluc_2552, retro_mluc_2572, retro_mluc_2573, retro_mluc_2583, retro_mluc_2586, retro_mluc_2603, retro_mluc_2623, retro_mluc_766,
Macaca mulatta	ENSMMUG00000003015	1 retrocopy	retro_mmul_1583,
Mus musculus	ENSMUSG00000072676	1 retrocopy	retro_mmus_2102,
Oryctolagus cuniculus	ENSOCUG00000013679	1 retrocopy	retro_ocun_453,
Otolemur garnettii	ENSOGAG00000028898	1 retrocopy	retro_ogar_59,
Tarsius syrichta	ENSTSYG00000006920	1 retrocopy	retro_tsyr_103,
Tursiops truncatus	ENSTTRG00000006122	1 retrocopy	retro_ttru_454,