RetrogeneDB ID: retro_dnov_94

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1498:68096..68457(+)
• Located in intron of: ENSDNOG00000019370

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAP1A
• Ensembl ID: ENSDNOG00000007809
• Aliases: None
• Description: RAP1A, member of RAS oncogene family [Source:HGNC Symbol;Acc:9855]

Sequence

>retro_dnov_94
GAGCAATTTACAGTGATGAGGGATTTGTATATGAAGAATGGCCAAGGATTTATGCTGGAATACTCTATTACAATTCAGAC
CACATTTACAGGACCTGAGGGAACAGATTTTATGGGTTAAGGACACAGAAGATGTTCCAAAGATTTTGGTTGGCAATAAA
TGCAACCTGAAAGATGAATGAGTGGTTGGCAAAGAACAGGGTCAGAATTTAGCAAGACAGTGGCTTGACCATGCCTTTTT
AGAATCTTCTGCAAAGTCAAAGATCAATATTAATGAGATAGTTTGTGAAATGGTCAGACAGATAAACAGAAAAACAGCAA
AGGAAAAGAAGAAACCTAAAAAGAAATCATGTCTGCTGCTC

Alignment

ORF - retro_dnov_94 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.74 %
• Parental protein coverage: 66.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EQFTAMRDLYMKNGQGFALVYSITAQSTF-NDLQDLREQILRVKDTEDVPMILVGNKCDLEDERVVGKEQ
          EQFT.MRDLYMKNGQGF.L.YSIT.Q.TF..DL.....QIL.VKDTEDVP.ILVGNKC.L.DE.VVGKEQ
Retrocopy EQFTVMRDLYMKNGQGFMLEYSITIQTTF>QDLRE---QILWVKDTEDVPKILVGNKCNLKDE*VVGKEQ

Parental  GQNLARQWCNCAFLESSAKSKINVNEIFYDLVRQINRKTPVEKKKPKKKSCLLL
          GQNLARQW...AFLESSAKSKIN.NEI....VRQ...............SCLLL
Retrocopy GQNLARQWLDHAFLESSAKSKININEIVCEMVRQXXXXXXXXXXXXXXXSCLLL

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	17.50 RPM
SRP012922_cerebellum	0.00 RPM	11.41 RPM
SRP012922_heart	0.00 RPM	9.05 RPM
SRP012922_kidney	0.27 RPM	11.50 RPM
SRP012922_liver	0.00 RPM	5.11 RPM
SRP012922_lung	0.15 RPM	20.47 RPM
SRP012922_quadricep_muscle	0.00 RPM	11.77 RPM
SRP012922_spleen	0.00 RPM	22.55 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_94 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 22 parental genes, and 64 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005384	1 retrocopy	retro_amel_1764,
Canis familiaris	ENSCAFG00000013686	1 retrocopy	retro_cfam_696,
Callithrix jacchus	ENSCJAG00000013392	7 retrocopies	retro_cjac_1671, retro_cjac_2218, retro_cjac_3376, retro_cjac_3707, retro_cjac_3843, retro_cjac_3844, retro_cjac_728,
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,
Equus caballus	ENSECAG00000016434	1 retrocopy	retro_ecab_99,
Erinaceus europaeus	ENSEEUG00000010446	2 retrocopies	retro_eeur_306, retro_eeur_361,
Echinops telfairi	ENSETEG00000016893	2 retrocopies	retro_etel_1196, retro_etel_176,
Homo sapiens	ENSG00000116473	1 retrocopy	retro_hsap_1364,
Myotis lucifugus	ENSMLUG00000010571	3 retrocopies	retro_mluc_2311, retro_mluc_2312, retro_mluc_2313,
Monodelphis domestica	ENSMODG00000001323	3 retrocopies	retro_mdom_1327, retro_mdom_139, retro_mdom_1777,
Mus musculus	ENSMUSG00000068798	2 retrocopies	retro_mmus_1963, retro_mmus_3027,
Nomascus leucogenys	ENSNLEG00000004018	1 retrocopy	retro_nleu_1069,
Ochotona princeps	ENSOPRG00000003999	3 retrocopies	retro_opri_321, retro_opri_460, retro_opri_875,
Pongo abelii	ENSPPYG00000001028	1 retrocopy	retro_pabe_1132,
Pan troglodytes	ENSPTRG00000001102	1 retrocopy	retro_ptro_937,
Rattus norvegicus	ENSRNOG00000032463	3 retrocopies	retro_rnor_1147, retro_rnor_1494, retro_rnor_1639,
Ictidomys tridecemlineatus	ENSSTOG00000027847	1 retrocopy	retro_itri_81,
Tarsius syrichta	ENSTSYG00000004521	3 retrocopies	retro_tsyr_1546, retro_tsyr_1829, retro_tsyr_2140,
Vicugna pacos	ENSVPAG00000010033	1 retrocopy	retro_vpac_491,