RetrogeneDB ID: retro_dnov_152

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2135:159412..159768(+)
• Located in intron of: ENSDNOG00000025601

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS18C
• Ensembl ID: ENSDNOG00000018326
• Aliases: None
• Description: mitochondrial ribosomal protein S18C [Source:HGNC Symbol;Acc:16633]

Sequence

>retro_dnov_152
ATGGCGACTTCCTGGACTCACACGGTGCTGTGGAGATCGGTTGTTCACAGCATCAACAGGTGACCAGCCATGAGGATCTG
CCCATTCCAATGGAAAATCCTTTTAAGGAACTTCTTAAAAAATGTATCTTATGTGGAAAATGTGTAGCTTATAAGAATGT
ACAGCTTTTGTCCCAGTTTATTTCTCCATTTACTGGATGCATTTATGGAAGGCACATAACAGGTCTTTGTGGGAAGAAAT
AGAAAGAAATCACAAAAGCAATTAAGAGGGCTCAAATAATGGGTTTTATGCCAGTTACATATAAGGATCCTGCATATCGC
AAAGACCCCAAAATTTGTAATATCAGATACCAAGAA

Alignment

ORF - retro_dnov_152 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90. %
• Parental protein coverage: 95.97 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTASWTHTVLWRR-GCSQHKQVTSHEDLPVPMENPFKEPLKKCILCGKCVDYKNVQLLSQFISPFTGCIY
          ...SWTHTVLWR..GCSQH.QVTSHEDLP.PMENPFKE.LKKCILCGKCV.YKNVQLLSQFISPFTGCIY
Retrocopy MATSWTHTVLWRS<GCSQHQQVTSHEDLPIPMENPFKELLKKCILCGKCVAYKNVQLLSQFISPFTGCIY

Parental  GRHITGLCGKKQKEISKAIKRAQIMGFMPVTYKDPAYRKDPKICNIRYRE
          GRHITGLCGKK.KEI.KAIKRAQIMGFMPVTYKDPAYRKDPKICNIRY.E
Retrocopy GRHITGLCGKK*KEITKAIKRAQIMGFMPVTYKDPAYRKDPKICNIRYQE

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	24.70 RPM
SRP012922_cerebellum	0.00 RPM	17.05 RPM
SRP012922_heart	0.23 RPM	16.01 RPM
SRP012922_kidney	0.27 RPM	31.49 RPM
SRP012922_liver	0.00 RPM	17.49 RPM
SRP012922_lung	0.15 RPM	34.21 RPM
SRP012922_quadricep_muscle	0.00 RPM	11.08 RPM
SRP012922_spleen	0.00 RPM	32.85 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_152 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 21 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018155	3 retrocopies	retro_btau_1386, retro_btau_309, retro_btau_502,
Callithrix jacchus	ENSCJAG00000005286	3 retrocopies	retro_cjac_1419, retro_cjac_234, retro_cjac_3970,
Cavia porcellus	ENSCPOG00000009198	1 retrocopy	retro_cpor_178,
Dasypus novemcinctus	ENSDNOG00000018326	2 retrocopies	retro_dnov_1030, retro_dnov_152 ,
Homo sapiens	ENSG00000163319	5 retrocopies	retro_hsap_1540, retro_hsap_2597, retro_hsap_4019, retro_hsap_4684, retro_hsap_969,
Gorilla gorilla	ENSGGOG00000008603	2 retrocopies	retro_ggor_1173, retro_ggor_2908,
Macropus eugenii	ENSMEUG00000010972	2 retrocopies	retro_meug_104, retro_meug_1113,
Myotis lucifugus	ENSMLUG00000017057	1 retrocopy	retro_mluc_2360,
Macaca mulatta	ENSMMUG00000015353	4 retrocopies	retro_mmul_2203, retro_mmul_2494, retro_mmul_655, retro_mmul_793,
Mus musculus	ENSMUSG00000016833	2 retrocopies	retro_mmus_1546, retro_mmus_2127,
Nomascus leucogenys	ENSNLEG00000009119	4 retrocopies	retro_nleu_111, retro_nleu_1614, retro_nleu_2722, retro_nleu_3010,
Ochotona princeps	ENSOPRG00000004113	2 retrocopies	retro_opri_1041, retro_opri_966,
Pongo abelii	ENSPPYG00000025867	2 retrocopies	retro_pabe_1276, retro_pabe_70,
Pan troglodytes	ENSPTRG00000016233	3 retrocopies	retro_ptro_1039, retro_ptro_1521, retro_ptro_3113,
Pteropus vampyrus	ENSPVAG00000006439	2 retrocopies	retro_pvam_1326, retro_pvam_1412,
Rattus norvegicus	ENSRNOG00000002178	3 retrocopies	retro_rnor_2264, retro_rnor_2265, retro_rnor_477,
Sarcophilus harrisii	ENSSHAG00000007084	1 retrocopy	retro_shar_718,
Ictidomys tridecemlineatus	ENSSTOG00000007989	1 retrocopy	retro_itri_1231,
Tupaia belangeri	ENSTBEG00000012505	3 retrocopies	retro_tbel_1755, retro_tbel_4724, retro_tbel_508,
Tarsius syrichta	ENSTSYG00000012924	1 retrocopy	retro_tsyr_649,
Tursiops truncatus	ENSTTRG00000004897	2 retrocopies	retro_ttru_144, retro_ttru_1721,