RetrogeneDB ID: retro_dnov_2583

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_87471:3208..3704(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DPPA2
• Ensembl ID: ENSDNOG00000010745
• Aliases: None
• Description: developmental pluripotency associated 2 [Source:HGNC Symbol;Acc:19197]

Sequence

>retro_dnov_2583
AAACACGGTATTTCTGACATACCACAGGAGGCCAATGTGCCATCATGTTCAAAGAAATGCAAGACAGTAACCAAGACAGC
AAGGAATCAGAAAAGTTGTAAGAGAAGGGAGAAAGAGGAAGAGATAACTGAAGTGGTAACTTCAGCTCAGTAGGCAAAAT
TGTCATCATGGACAAGAATTGCTGCATGAACTGCTCAGGCTAAGACCTTGAATTCATGTCCCATTCCTTCTTCTGTTAGA
CCATTTTGCTGCAAGCCTCTGGTGTCAGATGGTGTGTGGTTCATGGCAGTTCTCCCTGCAGATACAAAGGGCTGGGTTCA
CTTGCAGTTCTATGCAGAGCAGGCCTGGGTACTGACACTCCCAAGAGGATGATCTCTCTCTTCTTGTAACCAGCCTACAA
TTTCCCATCCCCAGATGAAGAAGATAATATATTGTGTCCTGAATGTGTGAAAAAGAATAAGAAGTTAATGAAAGATTAAT
TATAATGGGTAAGGAG

Alignment

ORF - retro_dnov_2583 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.47 %
• Parental protein coverage: 58.3 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  KQDIPDTPQEAKLQSCTKRC----KAAKDQKSCKKREKEEVTNTVEVISSAQEAILASWTRIAARAAQPK
          K..I.D.PQEA...SC.K.C....K.A..QKSCK.REKEE.....EV..SAQ.A.L.SWTRIAA..AQ.K
Retrocopy KHGISDIPQEANVPSCSKKCKTVTKTARNQKSCKRREKEE--EITEVVTSAQ*AKLSSWTRIAA*TAQAK

Parental  TVNSCPIPTSVE-TFLLQASGVRWCVVHGRVLPADTKG-WVRLQFHAGQVWV-PDTPKRMISLFLLPACT
          T.NSCPIP.SV..T.LLQASGVRWCVVHG...P...KG.WV.LQF.A.Q.WV..DTPKRMISLFL.PA..
Retrocopy TLNSCPIPSSVR<TILLQASGVRWCVVHGS-SPCRYKG>WVHLQFYAEQAWV<TDTPKRMISLFL*PAYN

Parental  FPSADVEDNMLCPDCVKRNKKLMK-RLIIIGKE
          FPS.D.EDN.LCP.CVK.NKKLMK.RLII.GKE
Retrocopy FPSPDEEDNILCPECVKKNKKLMK<RLIIMGKE

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	0.00 RPM
SRP012922_cerebellum	0.00 RPM	0.00 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	0.00 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.00 RPM	0.00 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	0.00 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_2583 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 20 parental genes, and 63 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020460	2 retrocopies	retro_btau_435, retro_btau_529,
Callithrix jacchus	ENSCJAG00000020168	4 retrocopies	retro_cjac_1378, retro_cjac_1991, retro_cjac_3832, retro_cjac_944,
Dasypus novemcinctus	ENSDNOG00000010745	6 retrocopies	retro_dnov_1248, retro_dnov_1626, retro_dnov_1714, retro_dnov_2462, retro_dnov_2583 , retro_dnov_2656,
Erinaceus europaeus	ENSEEUG00000008944	4 retrocopies	retro_eeur_205, retro_eeur_415, retro_eeur_426, retro_eeur_616,
Echinops telfairi	ENSETEG00000007985	4 retrocopies	retro_etel_2051, retro_etel_2058, retro_etel_506, retro_etel_918,
Homo sapiens	ENSG00000163530	3 retrocopies	retro_hsap_1642, retro_hsap_2903, retro_hsap_357,
Microcebus murinus	ENSMICG00000013744	6 retrocopies	retro_mmur_1171, retro_mmur_156, retro_mmur_1634, retro_mmur_213, retro_mmur_598, retro_mmur_955,
Myotis lucifugus	ENSMLUG00000007444	1 retrocopy	retro_mluc_1706,
Macaca mulatta	ENSMMUG00000022112	3 retrocopies	retro_mmul_1550, retro_mmul_342, retro_mmul_475,
Monodelphis domestica	ENSMODG00000018083	3 retrocopies	retro_mdom_1057, retro_mdom_1478, retro_mdom_999,
Mus musculus	ENSMUSG00000072419	7 retrocopies	retro_mmus_1303, retro_mmus_1832, retro_mmus_1847, retro_mmus_2391, retro_mmus_2935, retro_mmus_3699, retro_mmus_394,
Nomascus leucogenys	ENSNLEG00000004020	2 retrocopies	retro_nleu_1329, retro_nleu_633,
Oryctolagus cuniculus	ENSOCUG00000003175	1 retrocopy	retro_ocun_61,
Otolemur garnettii	ENSOGAG00000031228	7 retrocopies	retro_ogar_1678, retro_ogar_1722, retro_ogar_1953, retro_ogar_2404, retro_ogar_2567, retro_ogar_2900, retro_ogar_586,
Ochotona princeps	ENSOPRG00000005059	1 retrocopy	retro_opri_433,
Pongo abelii	ENSPPYG00000013566	3 retrocopies	retro_pabe_1360, retro_pabe_2401, retro_pabe_346,
Pan troglodytes	ENSPTRG00000015199	3 retrocopies	retro_ptro_1113, retro_ptro_1962, retro_ptro_281,
Sarcophilus harrisii	ENSSHAG00000017398	1 retrocopy	retro_shar_542,
Tupaia belangeri	ENSTBEG00000006212	1 retrocopy	retro_tbel_3864,
Tursiops truncatus	ENSTTRG00000009500	1 retrocopy	retro_ttru_1524,