RetrogeneDB ID: retro_dnov_956

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_126544:3830..4287(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000015360
• Aliases: None
• Description: None

Sequence

>retro_dnov_956
CTCCACCTGGAGCTGAGGCACCGGACCCTGGCAGCTGTTCCAGAACTTGTCCTGCACAATTGCAAATCAAATGATGGGAA
AATTGAGGGCTTAACAGCTGAATTTGTGAACTTAGAGTTCCTCAGCTTAATAAATGTAGGCTTGATTTCAGTTTCAAAGC
TCCCCAAACTACCTAAATTGAAAGAGCTTGATCTCAGTGACAACACAATCTTTGGAAGTCTGGACATGTTTGCAGAAAAA
ACTTCTGAATCTAACACATCTAAACTTAAATGGAAATAAATTGAAAGATATCAGCACCTTGGAACCTTTGAAAAAGTTGG
ATTGTCTGAAGAGCCCGGATCTGTTTAACTATGAGGTCACCAACCTGAACGACTATGGCGAGAGCATCTTCAGGGTCCTG
CCGCAGCTGACCTATCTGGATGGCTATGACCAAGAGGACCAGGAGCCCCCAAATACT

Alignment

ORF - retro_dnov_956 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.28 %
• Parental protein coverage: 70.05 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IHLELRNRTPSDVKELVLDNCRSNEGKIEGLTDEFEELEFLSTINVGLTSVANLPKLNKLKKLELSDNRI
          .HLELR.RT...V.ELVL.NC.SN.GKIEGLT.EF..LEFLS.INVGL.SV..LPKL.KLK.L.LSDN.I
Retrocopy LHLELRHRTLAAVPELVLHNCKSNDGKIEGLTAEFVNLEFLSLINVGLISVSKLPKLPKLKELDLSDNTI

Parental  SGGLEVLAEKCP-NLTHLNLSGNKIKDLSTIEPLKKLENLKSLDLFNCEVTNLNDYRENVFKLLPQLTYL
          .G.L...AEK...NLTHLNL.GNK.KD.ST.EPLKKL..LKS.DLFN.EVTNLNDY.E..F..LPQLTYL
Retrocopy FGSLDMFAEKTS>NLTHLNLNGNKLKDISTLEPLKKLDCLKSPDLFNYEVTNLNDYGESIFRVLPQLTYL

Parental  DGYDRDDKEAPDS
          DGYD..D.E.P..
Retrocopy DGYDQEDQEPPNT

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	1.75 RPM	60.09 RPM
SRP012922_cerebellum	0.41 RPM	53.89 RPM
SRP012922_heart	0.46 RPM	31.56 RPM
SRP012922_kidney	1.10 RPM	56.40 RPM
SRP012922_liver	1.24 RPM	30.19 RPM
SRP012922_lung	1.37 RPM	40.62 RPM
SRP012922_quadricep_muscle	1.04 RPM	27.69 RPM
SRP012922_spleen	6.75 RPM	56.77 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_956 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 11 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002339	2 retrocopies	retro_cjac_3305, retro_cjac_3799,
Dasypus novemcinctus	ENSDNOG00000015360	5 retrocopies	retro_dnov_1199, retro_dnov_1250, retro_dnov_1696, retro_dnov_836, retro_dnov_956 ,
Felis catus	ENSFCAG00000015773	1 retrocopy	retro_fcat_1188,
Homo sapiens	ENSG00000140350	3 retrocopies	retro_hsap_1479, retro_hsap_3117, retro_hsap_48,
Gorilla gorilla	ENSGGOG00000015417	1 retrocopy	retro_ggor_1134,
Nomascus leucogenys	ENSNLEG00000013347	2 retrocopies	retro_nleu_15, retro_nleu_2383,
Pongo abelii	ENSPPYG00000006595	2 retrocopies	retro_pabe_210, retro_pabe_2575,
Pan troglodytes	ENSPTRG00000007219	2 retrocopies	retro_ptro_2108, retro_ptro_758,
Rattus norvegicus	ENSRNOG00000045651	1 retrocopy	retro_rnor_1043,
Sarcophilus harrisii	ENSSHAG00000010906	1 retrocopy	retro_shar_540,
Tupaia belangeri	ENSTBEG00000016417	2 retrocopies	retro_tbel_4078, retro_tbel_4595,