RetrogeneDB ID: retro_dnov_694

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_928:109255..109624(-)
• Located in intron of: ENSDNOG00000003821

Retrocopy information

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

Parental gene information

• Parental gene symbol: VBP1
• Ensembl ID: ENSDNOG00000019432
• Aliases: None
• Description: von Hippel-Lindau binding protein 1 [Source:HGNC Symbol;Acc:12662]

Sequence

>retro_dnov_694
ATGGCGGCCGGTAAGGACGCTGGTGTCTTTGGAGAAGTGGCGGCAGGGAACGGGCGGCAGCTCCACCCGAGGATTCCCCG
AGCTGTGTTTGTGGAGGATGTAGATTCCTTCATGAAACACCCTGGAAGTGAGACCGCAGATACGGTATTAAAGAAGCCGG
ATGAACAGTGTCAGAAGTGTAAGTTTAGGGAACTCAGTCTTAGAGGAAAAGGAGGCTAAAAGGTCAGATTCCTGAAATTA
AGCAGACTCTTGAAATTCTGAAATACATGCAGAAATAAAAAGAATCCACCGGTTCGTTGAAACCAGGTTCTAACTGGCAG
GTAACTTCTACTGCAAAGCTTCAGTCCTCCTACTGATCAAGTGTGTCTG

Alignment

ORF - retro_dnov_694 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.91 %
• Parental protein coverage: 63.27 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAAGKDACVFGDVAAGNGRRLHLGI-EAVFVEDVDSFMKQPGNETADIVLKKLDEQYQKYKFMELNLA-Q
          MAAGKDA.VFG.VAAGNGR.LH..I..AVFVEDVDSFMK.PG.ETAD.VLKK.DEQ.QK.KF.EL.L...
Retrocopy MAAGKDAGVFGEVAAGNGRQLHPRIPRAVFVEDVDSFMKHPGSETADTVLKKPDEQCQKCKFRELSLR<R

Parental  KKRRLKGQIPEIKQTLEILKYMQKKKESTGSL-ETRFLLADNLYCKASV-PPTDKVCL
          K.R.LKGQIPEIKQTLEILKYMQK.KESTGSL.ETRF.LA.N.YCKASV.PPTD.VCL
Retrocopy KRR-LKGQIPEIKQTLEILKYMQK*KESTGSL<ETRF*LAGNFYCKASV<PPTDQVCL

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	0.39 RPM	17.11 RPM
SRP012922_cerebellum	0.41 RPM	13.47 RPM
SRP012922_heart	0.00 RPM	14.85 RPM
SRP012922_kidney	0.27 RPM	10.13 RPM
SRP012922_liver	0.15 RPM	5.88 RPM
SRP012922_lung	0.31 RPM	11.30 RPM
SRP012922_quadricep_muscle	1.04 RPM	19.04 RPM
SRP012922_spleen	0.34 RPM	16.83 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_694 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 17 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009058	2 retrocopies	retro_amel_1232, retro_amel_1346,
Canis familiaris	ENSCAFG00000019639	2 retrocopies	retro_cfam_1030, retro_cfam_573,
Cavia porcellus	ENSCPOG00000013652	1 retrocopy	retro_cpor_466,
Dasypus novemcinctus	ENSDNOG00000019432	1 retrocopy	retro_dnov_694 ,
Dipodomys ordii	ENSDORG00000004628	2 retrocopies	retro_dord_213, retro_dord_587,
Latimeria chalumnae	ENSLACG00000016144	1 retrocopy	retro_lcha_18,
Macaca mulatta	ENSMMUG00000015095	1 retrocopy	retro_mmul_124,
Mus musculus	ENSMUSG00000031197	1 retrocopy	retro_mmus_2220,
Nomascus leucogenys	ENSNLEG00000014475	1 retrocopy	retro_nleu_537,
Oryctolagus cuniculus	ENSOCUG00000017448	2 retrocopies	retro_ocun_233, retro_ocun_747,
Otolemur garnettii	ENSOGAG00000016566	1 retrocopy	retro_ogar_3121,
Sarcophilus harrisii	ENSSHAG00000002823	1 retrocopy	retro_shar_7,
Sus scrofa	ENSSSCG00000012811	1 retrocopy	retro_sscr_131,
Ictidomys tridecemlineatus	ENSSTOG00000006684	1 retrocopy	retro_itri_1492,
Tupaia belangeri	ENSTBEG00000007833	5 retrocopies	retro_tbel_3084, retro_tbel_3369, retro_tbel_3652, retro_tbel_553, retro_tbel_632,
Tarsius syrichta	ENSTSYG00000002205	1 retrocopy	retro_tsyr_2032,
Tursiops truncatus	ENSTTRG00000016258	1 retrocopy	retro_ttru_988,