RetrogeneDB ID: retro_dnov_85

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1394:122764..123180(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS15
• Ensembl ID: ENSDNOG00000000706
• Aliases: None
• Description: ribosomal protein S15 [Source:HGNC Symbol;Acc:10388]

Sequence

>retro_dnov_85
ATGGCGGAAGTGGAGCAAAAGAAGAAGTGCACCTTCCGCAAGTTCACCTACCGCGGTGTGGACTTCGACCAGCTGCTGGA
CATGTCCTACGAGCAGCTGATGCAGCTGTACAGCGCAGGGCAGCGGAGACTGCTGAACCATGGCCTACGGCGGAAGCAGC
ACTCCCTGCTGAAGCAGCTGCACAAGGCCAAGAAGGCGGCGCCGCCCATGGAGAAGCTGGAGGTGGTGAAGACGCATCTG
CATGACATCATCATCCTGCCCAGATGGTGGGCAGCATGGTGGGCATCTACAACGGCAAGACGTTCAACCAGGTGGAAATC
AAGCCTGAGATGATCGGCCACTACCTGGGCGAGTTCTCCATCACCTACAAGCCCGTGAAGCATGGCCGGCCCGGCATTGG
GGCCACCCACTCCTCC

Alignment

ORF - retro_dnov_85 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.0 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAEVEQKKKRTFRKFTYRGVDLDQLLDMSYEQLMQLYSARQRRRLNRGLRRKQHSLLKRLRKAKKEAPPM
          MAEVEQKKK.TFRKFTYRGVD.DQLLDMSYEQLMQLYSA.QRR.LN.GLRRKQHSLLK.L.KAKK.APPM
Retrocopy MAEVEQKKKCTFRKFTYRGVDFDQLLDMSYEQLMQLYSAGQRRLLNHGLRRKQHSLLKQLHKAKKAAPPM

Parental  EKPEVVKTHLRDMIILP-EMVGSMVGVYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHGRPGIGATHSS
          EK.EVVKTHL.D.IILP..MVGSMVG.YNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHGRPGIGATHSS
Retrocopy EKLEVVKTHLHDIIILP<QMVGSMVGIYNGKTFNQVEIKPEMIGHYLGEFSITYKPVKHGRPGIGATHSS

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	19.25 RPM	619.77 RPM
SRP012922_cerebellum	9.76 RPM	286.90 RPM
SRP012922_heart	10.21 RPM	297.23 RPM
SRP012922_kidney	28.47 RPM	738.15 RPM
SRP012922_liver	11.92 RPM	357.76 RPM
SRP012922_lung	28.41 RPM	639.76 RPM
SRP012922_quadricep_muscle	12.12 RPM	560.62 RPM
SRP012922_spleen	23.46 RPM	870.02 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_85 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 14 parental genes, and 58 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000005632	13 retrocopies	retro_cjac_143, retro_cjac_151, retro_cjac_1517, retro_cjac_1607, retro_cjac_1672, retro_cjac_1714, retro_cjac_2069, retro_cjac_2236, retro_cjac_2596, retro_cjac_2656, retro_cjac_48, retro_cjac_756, retro_cjac_86,
Cavia porcellus	ENSCPOG00000003968	1 retrocopy	retro_cpor_495,
Dasypus novemcinctus	ENSDNOG00000000706	2 retrocopies	retro_dnov_173, retro_dnov_85 ,
Echinops telfairi	ENSETEG00000008645	1 retrocopy	retro_etel_2,
Gorilla gorilla	ENSGGOG00000002818	4 retrocopies	retro_ggor_1136, retro_ggor_116, retro_ggor_141, retro_ggor_1851,
Monodelphis domestica	ENSMODG00000005119	1 retrocopy	retro_mdom_1335,
Mus musculus	ENSMUSG00000063457	8 retrocopies	retro_mmus_1270, retro_mmus_208, retro_mmus_2734, retro_mmus_2786, retro_mmus_3166, retro_mmus_3642, retro_mmus_520, retro_mmus_917,
Nomascus leucogenys	ENSNLEG00000001651	8 retrocopies	retro_nleu_105, retro_nleu_1858, retro_nleu_1922, retro_nleu_2390, retro_nleu_2465, retro_nleu_2559, retro_nleu_461, retro_nleu_544,
Otolemur garnettii	ENSOGAG00000015776	4 retrocopies	retro_ogar_194, retro_ogar_210, retro_ogar_2237, retro_ogar_96,
Pongo abelii	ENSPPYG00000009317	4 retrocopies	retro_pabe_1233, retro_pabe_2321, retro_pabe_67, retro_pabe_893,
Pan troglodytes	ENSPTRG00000010200	1 retrocopy	retro_ptro_122,
Rattus norvegicus	ENSRNOG00000024603	8 retrocopies	retro_rnor_1384, retro_rnor_1711, retro_rnor_1712, retro_rnor_178, retro_rnor_2086, retro_rnor_2114, retro_rnor_2642, retro_rnor_700,
Sus scrofa	ENSSSCG00000023248	1 retrocopy	retro_sscr_271,
Ictidomys tridecemlineatus	ENSSTOG00000006423	2 retrocopies	retro_itri_722, retro_itri_939,