RetrogeneDB ID: retro_dnov_1052

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_14136:86151..86733(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRDX3
• Ensembl ID: ENSDNOG00000001359
• Aliases: None
• Description: peroxiredoxin 3 [Source:HGNC Symbol;Acc:9354]

Sequence

>retro_dnov_1052
TCATACTATGCTCCTGCTGTCACCCAGCATGTGTCTTATTTTAAGGATACAGTGTTGTCAACGGAGAGTTCAAAGAACTG
AGCTTTGATGACTTTAAGGGGAAATATTTGGTACTTTTCTTCCATCCTTTGGATTTTACCTTTGGGTGTCCTACAGAAAG
TGTTGCTTTTAGTGACAAAACCAATGAATTTCATGTGAACTGTGAAGTTGTTGCTGTTTCAATGGTTTCCTACTTTATCC
ACTTTGCCTGGATAAATACATCAAGGAAGAACAGTGATTTGGGCCACATGAACATCACATCCTTGTAAGATTTAACAAAA
CAAATCTCTAATACTGTGGTGTGCTATTAGACCTTGTTGGTCTTGTACTACATGGTCTCTCATTATTGACCCCAATGGAA
TCATCCAGCATTTGAGTGTCAGTGATCCCCCAATGGAAAGTGTGGAAGGGATCCTCTGCTTTGTGAAGTCATTCCAGTTG
TGGAGGCCATGGAGGAGTCTGTCCCACAAACTGACACCAAATTCTCCTAAGATCAAGCCAAACTTAACTGCTTCCAAAGA
AAACTTTGAAATGATGAATCAG

Alignment

ORF - retro_dnov_1052 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.61 %
• Parental protein coverage: 99.48 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  SYCAPAVTQHAPYFKGT-AVVNGEFKELSLDDFKGKYLVLFFYPLDF-FVC-TEIVAFSDKHD---VNCE
          SY.APAVTQH..YFK.T..VVNGEFKELS.DDFKGKYLVLFF.PLDF.F.C.TE.VAFSDK.....VNCE
Retrocopy SYYAPAVTQHVSYFKDT<SVVNGEFKELSFDDFKGKYLVLFFHPLDFTFGCPTESVAFSDKTNEFHVNCE

Parental  VXXXXXXXXXXXXXXXXXXXXNGGLGHMNIALLSDLTKQISRDY-GVLLEGAGLALRGL-FIIDPNGVIK
          V....................N..LGHMNI..L.DLTKQIS....GVLL...GL.L.GL..IIDPNG.I.
Retrocopy VVAVSMVSYFIHFAWINTSRKNSDLGHMNITSL*DLTKQISNTV<GVLLDLVGLVLHGL<LIIDPNGIIQ

Parental  HLSVNDLSVGRSVEETLRLVKAFQF-VETHGE-VCPANWTQIL-STIKPNPTASKEYFEKVNQ
          HLSV.D.....SVE..L..VK.FQ..VE...E.VCP.N..QIL...IKPN.TASKE.FE..NQ
Retrocopy HLSVSDPPM-ESVEGILCFVKSFQL<VEAMEE<VCPTN*HQIL<PKIKPNLTASKENFEMMNQ

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	56.01 RPM
SRP012922_cerebellum	0.00 RPM	33.68 RPM
SRP012922_heart	0.00 RPM	44.78 RPM
SRP012922_kidney	0.00 RPM	82.69 RPM
SRP012922_liver	0.00 RPM	53.41 RPM
SRP012922_lung	0.00 RPM	19.40 RPM
SRP012922_quadricep_muscle	0.00 RPM	88.10 RPM
SRP012922_spleen	0.00 RPM	38.57 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_1052 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 23 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008731	1 retrocopy	retro_btau_562,
Canis familiaris	ENSCAFG00000012109	3 retrocopies	retro_cfam_1322, retro_cfam_219, retro_cfam_9,
Callithrix jacchus	ENSCJAG00000019636	3 retrocopies	retro_cjac_1333, retro_cjac_3082, retro_cjac_653,
Ciona savignyi	ENSCSAVG00000001209	1 retrocopy	retro_csav_6,
Dasypus novemcinctus	ENSDNOG00000001359	3 retrocopies	retro_dnov_1052 , retro_dnov_2373, retro_dnov_745,
Dasypus novemcinctus	ENSDNOG00000018488	1 retrocopy	retro_dnov_2071,
Equus caballus	ENSECAG00000017026	1 retrocopy	retro_ecab_408,
Erinaceus europaeus	ENSEEUG00000009299	1 retrocopy	retro_eeur_238,
Homo sapiens	ENSG00000165672	3 retrocopies	retro_hsap_1253, retro_hsap_2587, retro_hsap_2653,
Gorilla gorilla	ENSGGOG00000026364	1 retrocopy	retro_ggor_986,
Macropus eugenii	ENSMEUG00000007732	3 retrocopies	retro_meug_1219, retro_meug_1735, retro_meug_62,
Microcebus murinus	ENSMICG00000007627	1 retrocopy	retro_mmur_475,
Myotis lucifugus	ENSMLUG00000012871	3 retrocopies	retro_mluc_1203, retro_mluc_1522, retro_mluc_2069,
Macaca mulatta	ENSMMUG00000008294	2 retrocopies	retro_mmul_1307, retro_mmul_1517,
Monodelphis domestica	ENSMODG00000009286	1 retrocopy	retro_mdom_1062,
Mustela putorius furo	ENSMPUG00000003074	1 retrocopy	retro_mputfur_1032,
Nomascus leucogenys	ENSNLEG00000016698	3 retrocopies	retro_nleu_1521, retro_nleu_2118, retro_nleu_2453,
Oryctolagus cuniculus	ENSOCUG00000017334	2 retrocopies	retro_ocun_135, retro_ocun_1434,
Pongo abelii	ENSPPYG00000002700	1 retrocopy	retro_pabe_1906,
Pan troglodytes	ENSPTRG00000002992	1 retrocopy	retro_ptro_29,
Ictidomys tridecemlineatus	ENSSTOG00000002537	2 retrocopies	retro_itri_1098, retro_itri_1753,
Tupaia belangeri	ENSTBEG00000011064	5 retrocopies	retro_tbel_3138, retro_tbel_3994, retro_tbel_710, retro_tbel_770, retro_tbel_811,
Tursiops truncatus	ENSTTRG00000010878	2 retrocopies	retro_ttru_1703, retro_ttru_881,