RetrogeneDB ID: retro_dnov_2007

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_4183:6184..6598(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS10
• Ensembl ID: ENSDNOG00000006067
• Aliases: None
• Description: mitochondrial ribosomal protein S10 [Source:HGNC Symbol;Acc:14502]

Sequence

>retro_dnov_2007
ATAACCATTTCTGTTAAACCAGACACACTATATAAGCTCTTGTAGGTTTTAGTAAAAGATCATAATAAAACTGAATTGGA
CAGCTATGAATATTTTGCCATGCTTGCTGCTAAGGAATTTGGTATCTCTATTAAAGTTGATGAACCTCCAAGGAAAACAC
AGCAATTTACTTTTCTCAAATTAGTGCATATTTTCAGGAAGCACAGAGCCCGTTATGATATGAGAACACTGTACAGATGT
TTAGAGTTAGGACATCTAACTGGAAGTACAGCAGAAGTCTGTTTGGAATATATTCAGAGAAACTCACCTGAAGGAGTTGC
CCTGGAAGTTACAAAGACAAAGTTAGAAAGGTTACCAGAACACATCAAAGAGCCAATCTGGGAAAGGGTACCAGAAGAAA
AAGAAGAAAGTAAG

Alignment

ORF - retro_dnov_2007 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.54 %
• Parental protein coverage: 68.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ITISDEPDTLYKRLSVLVKGHDKAVLDSYEYFATLAAKELGISVKVHEPPRKIERFTLLKSVHIYKKHRV
          ITIS..PDTLYK.L.VLVK.H.K..LDSYEYFA.LAAKE.GIS.KV.EPPRK...FT.LK.VHI..KHR.
Retrocopy ITISVKPDTLYKLL*VLVKDHNKTELDSYEYFAMLAAKEFGISIKVDEPPRKTQQFTFLKLVHIFRKHRA

Parental  QYEMRTLYRCLELEHVTGSTADVYLEYIQRNLPEGVAMEVTKTKLEQLPEHIKEPIWEAVPEEKEASK
          .Y.MRTLYRCLEL.H.TGSTA.V.LEYIQRN.PEGVA.EVTKTKLE.LPEHIKEPIWE.VPEEKE.SK
Retrocopy RYDMRTLYRCLELGHLTGSTAEVCLEYIQRNSPEGVALEVTKTKLERLPEHIKEPIWERVPEEKEESK

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	28.20 RPM
SRP012922_cerebellum	0.00 RPM	29.69 RPM
SRP012922_heart	0.00 RPM	19.49 RPM
SRP012922_kidney	0.00 RPM	15.06 RPM
SRP012922_liver	0.00 RPM	10.99 RPM
SRP012922_lung	0.00 RPM	22.60 RPM
SRP012922_quadricep_muscle	0.00 RPM	13.33 RPM
SRP012922_spleen	0.00 RPM	25.30 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_2007 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001638	1 retrocopy	retro_cfam_598,
Choloepus hoffmanni	ENSCHOG00000006109	1 retrocopy	retro_chof_1964,
Dasypus novemcinctus	ENSDNOG00000006067	1 retrocopy	retro_dnov_2007 ,
Macaca mulatta	ENSMMUG00000014661	1 retrocopy	retro_mmul_48,
Mus musculus	ENSMUSG00000034729	1 retrocopy	retro_mmus_1654,
Nomascus leucogenys	ENSNLEG00000004800	1 retrocopy	retro_nleu_1385,
Rattus norvegicus	ENSRNOG00000022609	1 retrocopy	retro_rnor_2284,
Tursiops truncatus	ENSTTRG00000014063	1 retrocopy	retro_ttru_1203,