RetrogeneDB ID: retro_dnov_216

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2704:163143..163697(+)
• Located in intron of: ENSDNOG00000019725

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000011999
• Aliases: None
• Description: None

Sequence

>retro_dnov_216
GCTACTCCTCCGACTGGTATTTTGTTTTATCAGGGCGAACTGTGTTCCATGGCCGGAAACTTTTGGCGGAGCTCCCACTA
TTTGCAATGGATTTTGGATAAACAATATCTGTTGAAGGAGCGTCAAAAGGACTTAGAGTTTCTTTCAGAAGAAGAATATT
GGAAAATACAACTGTTTTTTACAAACGTTATTCAAGCACTAGGTGAACATCTTAAATTCAGACAACAAGTTATTGCCACA
GCTACAGTCTATTTCAAGAGATTTTATGTCAGGTATTCTCTGGAAAGTGTAGATCCTGTACTAATGGCTCCTATATGTGT
GTTTTTGGCATCCAAAGTAGAGGAATTGGGAGTAGTCTCAAATACAAGATTGATTTCTGCTGCTACTTCTCTATTAAAAA
CTAGATTTTCACATGCCTTTCCAAAAGAATTTCTTTATAGGATGAACCATATCTTCGAATGTGAATTCTGTCTTTTAGAA
TTAACGGATATTGCTTGATATTGAATTATCCTTACAGATCTTTGCTCCAGTATGGGCAGGACATGGGCCAAGAA

Alignment

ORF - retro_dnov_216 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.11 %
• Parental protein coverage: 75.42 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  APPLRRLVFYQG-LCM---NFWQSSHYLQWILDKQDLLKERQKDLKFLSEEEYWKLQIFFTNVIQALGEH
          A.P.....FYQG.LC....NFW.SSHYLQWILDKQ.LLKERQKDL.FLSEEEYWK.Q.FFTNVIQALGEH
Retrocopy ATPPTGILFYQGELCSMAGNFWRSSHYLQWILDKQYLLKERQKDLEFLSEEEYWKIQLFFTNVIQALGEH

Parental  LKLRQQVIATATVYFKRFYARYSLKSIDPVLMAPTCVFLASKVEEFGVVSNTRLTAAATSVLKTRFSYAF
          LK.RQQVIATATVYFKRFY.RYSL.S.DPVLMAP.CVFLASKVEE.GVVSNTRL..AATS.LKTRFS.AF
Retrocopy LKFRQQVIATATVYFKRFYVRYSLESVDPVLMAPICVFLASKVEELGVVSNTRLISAATSLLKTRFSHAF

Parental  PKEFPYRMNHILECEFYLLELMDC-CLIVYHPYRPLLQYVQDMGQE
          PKEF.YRMNHI.ECEF.LLEL.D..CLI...PYR.LLQY.QDMGQE
Retrocopy PKEFLYRMNHIFECEFCLLELTDI<CLILNYPYRSLLQYGQDMGQE

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	11.67 RPM
SRP012922_cerebellum	0.00 RPM	9.21 RPM
SRP012922_heart	0.00 RPM	4.18 RPM
SRP012922_kidney	0.00 RPM	5.75 RPM
SRP012922_liver	0.00 RPM	3.41 RPM
SRP012922_lung	0.00 RPM	7.64 RPM
SRP012922_quadricep_muscle	0.00 RPM	5.19 RPM
SRP012922_spleen	0.00 RPM	12.25 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_216 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008954	1 retrocopy	retro_amel_1828,
Bos taurus	ENSBTAG00000015744	3 retrocopies	retro_btau_1206, retro_btau_1536, retro_btau_1836,
Canis familiaris	ENSCAFG00000003525	1 retrocopy	retro_cfam_1774,
Callithrix jacchus	ENSCJAG00000001388	1 retrocopy	retro_cjac_780,
Dasypus novemcinctus	ENSDNOG00000011999	3 retrocopies	retro_dnov_1153, retro_dnov_216 , retro_dnov_2243,
Dipodomys ordii	ENSDORG00000008393	2 retrocopies	retro_dord_230, retro_dord_75,
Echinops telfairi	ENSETEG00000002643	1 retrocopy	retro_etel_1441,
Myotis lucifugus	ENSMLUG00000012815	1 retrocopy	retro_mluc_1582,
Oryctolagus cuniculus	ENSOCUG00000003309	2 retrocopies	retro_ocun_1753, retro_ocun_888,
Otolemur garnettii	ENSOGAG00000001116	1 retrocopy	retro_ogar_2123,
Ochotona princeps	ENSOPRG00000012972	2 retrocopies	retro_opri_1026, retro_opri_151,
Sorex araneus	ENSSARG00000004726	2 retrocopies	retro_sara_141, retro_sara_583,
Sus scrofa	ENSSSCG00000004353	1 retrocopy	retro_sscr_760,
Tupaia belangeri	ENSTBEG00000017525	1 retrocopy	retro_tbel_677,