RetrogeneDB ID: retro_dnov_1233

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_16727:350..666(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL27
• Ensembl ID: ENSDNOG00000023845
• Aliases: None
• Description: mitochondrial ribosomal protein L27 [Source:HGNC Symbol;Acc:14483]

Sequence

>retro_dnov_1233
ACAACCCTGCTGAACATCCCTCAGGCTGCAGGTCTTGCTGTCAGATACACATCCAAGAAGGCGGGTTGCAGCTCCAGAAA
CCTCACTGGGAAGTCACCAGCAAACATTGTGGCATCAACAAAGGGGAGGGTCACTGCGTTCATGCTGGCAACGTCCTCGG
GACTCAGCGCCAGGCTGGCTGGCCCCCAGGAGCCCACGTTGGACTGGGGGAGAGGAGATGCCCTTGTGCCCTGGAGGGGG
GGGTGGTCCGCTACGCAAAGAAAGTCTGCCCGCCAATACCACCAGCTGCCAGGCTGTGGATCTGGTCGCCAAGCTG

Alignment

ORF - retro_dnov_1233 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.04 %
• Parental protein coverage: 79.1 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TTLLNPPQATALTVRYASKKTGGSSKNLGGKSPG-KRFGIKKMEGHYVHAGNILGTQRQFRWHPGAHVGL
          TTLLN.PQA..L.VRY.SKK.G.SS.NL.GKSP..K..GI.K.EGH.VHAGN.LGTQRQ..W.PGAHVGL
Retrocopy TTLLNIPQAAGLAVRYTSKKAGCSSRNLTGKSPA<KHCGINKGEGHCVHAGNVLGTQRQAGWPPGAHVGL

Parental  GRRKCLYALEEGVVHYTKEVYVPSP-SNSEAMDLVTKL
          G.R.C..AL....V.Y.K.V..P.P.....A.DLV.KL
Retrocopy GERRCPCALXXXXVRYAKKVCPPIP<TSCQAVDLVAKL

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	54.84 RPM
SRP012922_cerebellum	0.00 RPM	47.56 RPM
SRP012922_heart	0.00 RPM	45.94 RPM
SRP012922_kidney	0.00 RPM	82.69 RPM
SRP012922_liver	0.31 RPM	44.74 RPM
SRP012922_lung	0.15 RPM	46.89 RPM
SRP012922_quadricep_muscle	0.00 RPM	45.52 RPM
SRP012922_spleen	0.00 RPM	47.73 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_1233 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 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017031	1 retrocopy	retro_cfam_1454,
Choloepus hoffmanni	ENSCHOG00000005103	1 retrocopy	retro_chof_943,
Callithrix jacchus	ENSCJAG00000018851	2 retrocopies	retro_cjac_28, retro_cjac_378,
Dasypus novemcinctus	ENSDNOG00000023845	2 retrocopies	retro_dnov_1233 , retro_dnov_1731,
Erinaceus europaeus	ENSEEUG00000010549	3 retrocopies	retro_eeur_126, retro_eeur_22, retro_eeur_9,
Echinops telfairi	ENSETEG00000014252	2 retrocopies	retro_etel_13, retro_etel_893,
Microcebus murinus	ENSMICG00000009698	1 retrocopy	retro_mmur_624,
Macaca mulatta	ENSMMUG00000017231	1 retrocopy	retro_mmul_64,
Mus musculus	ENSMUSG00000024414	2 retrocopies	retro_mmus_1696, retro_mmus_2918,
Oryctolagus cuniculus	ENSOCUG00000004601	2 retrocopies	retro_ocun_1026, retro_ocun_1936,
Otolemur garnettii	ENSOGAG00000005385	1 retrocopy	retro_ogar_53,