RetrogeneDB ID: retro_dnov_1681

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_2653:122630..123362(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3D
• Ensembl ID: ENSDNOG00000013488
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide D, 44kDa [Source:HGNC Symbol;Acc:1080]

Sequence

>retro_dnov_1681
AGGAGACACCATGGGGAAGCTCAGCCCCCAGGAGGGCCCCAACCCCTTCTCTCTGGGGCCTGGGGCTTGGAGGCAGCCAG
CAACCCCCTCACTCAGTGCTGCCTTCCTTCCATCTGTTCAAGGGACCTCATCTTTGGGGGAATCAAGAAGAAAATCTTCA
TCTTGAACATTAGCAGATGGAAGATTAAAGAAGAGCCCAAGGAATACGTGACGGTCAAAAAGGAGAAGTGCGAAAGGGAC
AGAGACTTGCAGCAAGAAGGGCATGGATGGGGTCAGGGTCATTCAGAAGGGATCCAGTCCCACTCCATCTTCGAGCAAGG
CCAAGCCGAGTTGATGAAGGAAAAAGGAGCTGGATAAGACAGTGGATGTGTGAGACATGGGGCCTGCTCTTACCATCAAT
ATCACATAAGAGCAGAGGGAGATGGATGAGGAAACCAACAAATCCTGTGCATCCTGGAGAAGGGTGAGTTCGTCCATGAC
CACGGGCTGAGGAATGACCCTCGAAATCTGCCTGTGCAGCTGCCTCTGGCTCACTCAGGGCGACTTTCTAAGAAGAGAAT
GAAGAACCCGATGGTATGCCTTGGTGGGCTGGCCCCAAGGACTTGGAAGTAGATGTCCCTGTTTGTGAAGTGAAGGTGGA
GCCATGAGATGAGGAGGAAGAAGCCAAGGAGAAGGCCCCTCCAGAGCAGCCAGAAAGACCTTGACCTCCCAACGGCCATA
TCTGTGGCTCAG

Alignment

ORF - retro_dnov_1681 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.45 %
• Parental protein coverage: 62.81 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  RNAAGEPSAPRGPRPLLPGARGLIERRPAPPLTPGRLPSIRSRDLTLGGVKKKTFTPNIISRKIKEEPKE
          R...GE...P.GP.PLL.GA.GL.......PLT...LPSI.SRDL..GG.KKK.F..NI...KIKEEPKE
Retrocopy RRHHGEAQPPGGPQPLLSGAWGL--EAASNPLTQCCLPSICSRDLIFGGIKKKIFILNISRWKIKEEPKE

Parental  DMTVKKEKRERDRDRQREGHGRGRGRPEVIQSHSIFEQGPAEMMKKKG-NW-DKTVDMSDMGPSHIINIK
          ..TVKKEK.ERDRD.Q.EGHG.G.G..E.IQSHSIFEQG.AE.MK.KG..W.DKTVD..DMGP...INI.
Retrocopy YVTVKKEKCERDRDLQQEGHGWGQGHSEGIQSHSIFEQGQAELMKEKG<SW<DKTVDV*DMGPALTINIT

Parental  KEKRETDEET-KQILRMLEKDDFIDDPGLRNDMRNMPVQLPLAYSGWLFK-EESEEPDVKPWPAGPKEED
          .E.RE.DEET..QIL..LEK..F..D.GLRND.RN.PVQLPLA.SG.L.K.EE.EEPD..PW.AGPK..D
Retrocopy *EQREMDEET<QQILCILEKGEFVHDHGLRNDPRNLPVQLPLAHSGRLSK<EENEEPDGMPWWAGPK--D

Parental  MEVDTPVTKVKEEPRDEEEEAKAKAPP-RAARKT-PGLPKEVSVAE
          .EVD.PV..VK.EP.DEEEEAK.KAPP.RAARKT...LP...SVA.
Retrocopy LEVDVPVCEVKVEP*DEEEEAKEKAPP<RAARKT<LDLPTAISVAQ

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	0.00 RPM	17.50 RPM
SRP012922_cerebellum	0.00 RPM	29.83 RPM
SRP012922_heart	0.00 RPM	9.51 RPM
SRP012922_kidney	0.00 RPM	12.32 RPM
SRP012922_liver	0.00 RPM	13.00 RPM
SRP012922_lung	0.00 RPM	28.41 RPM
SRP012922_quadricep_muscle	0.00 RPM	17.48 RPM
SRP012922_spleen	0.00 RPM	23.12 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_1681 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013488	1 retrocopy	retro_dnov_1681 ,
Equus caballus	ENSECAG00000025090	1 retrocopy	retro_ecab_43,
Erinaceus europaeus	ENSEEUG00000007632	2 retrocopies	retro_eeur_277, retro_eeur_705,
Homo sapiens	ENSG00000168495	1 retrocopy	retro_hsap_596,
Macropus eugenii	ENSMEUG00000000465	1 retrocopy	retro_meug_1550,
Myotis lucifugus	ENSMLUG00000002109	1 retrocopy	retro_mluc_2339,
Macaca mulatta	ENSMMUG00000023226	1 retrocopy	retro_mmul_2449,
Monodelphis domestica	ENSMODG00000009491	1 retrocopy	retro_mdom_988,
Nomascus leucogenys	ENSNLEG00000015502	1 retrocopy	retro_nleu_2218,
Pongo abelii	ENSPPYG00000018419	1 retrocopy	retro_pabe_594,
Pan troglodytes	ENSPTRG00000020056	1 retrocopy	retro_ptro_439,
Tursiops truncatus	ENSTTRG00000012745	1 retrocopy	retro_ttru_1189,