RetrogeneDB ID: retro_dnov_573

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_6342:648493..649111(-)
• Located in intron of: ENSDNOG00000006713

Retrocopy information

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

Parental gene information

• Parental gene symbol: RALA
• Ensembl ID: ENSDNOG00000017413
• Aliases: None
• Description: v-ral simian leukemia viral oncogene homolog A (ras related) [Source:HGNC Symbol;Acc:9839]

Sequence

>retro_dnov_573
ATGGCTGCAAATAAACCCAAGGGTCAGAATTCTTTGGCCTTACACAAAGTCATCATGGTGGGCAGTGGTGGTGTGGGGAA
GTCTGCCCTGACTCTCCAGTTCATGTATGATGAGTTTGTGGAGGACTATGAGCCTACCAAAGCAGACAGCTATCGGAAGA
AGGTAGTGCTGGATGGAAAGGAAGTCCAGATTGATATCTTAGATACCGCTGGGCAGGAGGACTATGCTGCAATTAGAGAC
AACTACTTTCGAAGTGGGGAGGGTTTCCTCTGTGTGTTCTCTATTACAGAAATGGAATCCTTTGCAGCCACAGCTGACTT
CAGGGAACAGATTTTAAGAGTAAAAGAAGATGAAAATGTTCCATTTCTGCTGGTTGGTAACAAATCAGATTTAGAAGACA
AAAGGCAGGTTTCTGTAGAAGAGGCAAAAAACAGAGCCGATCAGTGGAATGTTAACTATGTGGAAACATCTGCTAAAACA
CGAGCTAATGTTGACAAGGTCTTTTTTGATTTAATGAGGGAAATTCGAGCCAGAAAGATGGAAGACAGCAAGGAAAAGAA
TGGAGAAAAGAAGAGGAAATGTTTAGCCAAGAGAATCAGAGAAAGATGCTGCATTTTA

Alignment

ORF - retro_dnov_573 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.54 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAANKPKGQNSLALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGEEVQIDILDTA
          MAANKPKGQNSLALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDG.EVQIDILDTA
Retrocopy MAANKPKGQNSLALHKVIMVGSGGVGKSALTLQFMYDEFVEDYEPTKADSYRKKVVLDGKEVQIDILDTA

Parental  GQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVE
          GQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVE
Retrocopy GQEDYAAIRDNYFRSGEGFLCVFSITEMESFAATADFREQILRVKEDENVPFLLVGNKSDLEDKRQVSVE

Parental  EAKNRADQWNVNYVETSAKTRANVDKVFFDLMREIRARKMEDSKEKNGKKKRKSLAKRIRERCCIL
          EAKNRADQWNVNYVETSAKTRANVDKVFFDLMREIRARKMEDSKEKNG.KKRK.LAKRIRERCCIL
Retrocopy EAKNRADQWNVNYVETSAKTRANVDKVFFDLMREIRARKMEDSKEKNGEKKRKCLAKRIRERCCIL

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	2.53 RPM	8.17 RPM
SRP012922_cerebellum	1.79 RPM	6.05 RPM
SRP012922_heart	2.32 RPM	2.78 RPM
SRP012922_kidney	1.92 RPM	7.39 RPM
SRP012922_liver	0.77 RPM	3.41 RPM
SRP012922_lung	2.90 RPM	7.64 RPM
SRP012922_quadricep_muscle	1.38 RPM	3.29 RPM
SRP012922_spleen	2.52 RPM	8.01 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_573 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 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007630	1 retrocopy	retro_cjac_3313,
Dasypus novemcinctus	ENSDNOG00000007809	5 retrocopies	retro_dnov_101, retro_dnov_1617, retro_dnov_1764, retro_dnov_628, retro_dnov_94,
Dasypus novemcinctus	ENSDNOG00000015293	3 retrocopies	retro_dnov_1358, retro_dnov_154, retro_dnov_2354,
Dasypus novemcinctus	ENSDNOG00000017413	1 retrocopy	retro_dnov_573 ,
Dasypus novemcinctus	ENSDNOG00000019724	18 retrocopies	retro_dnov_1243, retro_dnov_1249, retro_dnov_1323, retro_dnov_1395, retro_dnov_1574, retro_dnov_1710, retro_dnov_1763, retro_dnov_1841, retro_dnov_186, retro_dnov_1976, retro_dnov_2033, retro_dnov_217, retro_dnov_2679, retro_dnov_298, retro_dnov_318, retro_dnov_719, retro_dnov_761, retro_dnov_84,
Homo sapiens	ENSG00000006451	2 retrocopies	retro_hsap_1136, retro_hsap_3707,
Macropus eugenii	ENSMEUG00000000259	1 retrocopy	retro_meug_1638,
Macaca mulatta	ENSMMUG00000016059	2 retrocopies	retro_mmul_1706, retro_mmul_882,
Nomascus leucogenys	ENSNLEG00000003055	1 retrocopy	retro_nleu_935,
Pongo abelii	ENSPPYG00000017619	3 retrocopies	retro_pabe_3148, retro_pabe_3208, retro_pabe_945,
Pan troglodytes	ENSPTRG00000019108	1 retrocopy	retro_ptro_2511,
Sus scrofa	ENSSSCG00000029741	1 retrocopy	retro_sscr_634,
Ictidomys tridecemlineatus	ENSSTOG00000020292	2 retrocopies	retro_itri_1314, retro_itri_1315,
Vicugna pacos	ENSVPAG00000002810	1 retrocopy	retro_vpac_211,