RetrogeneDB ID: retro_dnov_1085

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_144477:2..562(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KHDRBS3
• Ensembl ID: ENSDNOG00000010878
• Aliases: None
• Description: KH domain containing, RNA binding, signal transduction associated 3 [Source:HGNC Symbol;Acc:18117]

Sequence

>retro_dnov_1085
ATTCCTGACTACAATGATAAAATCAGGCCCAGCACAGCTGCAGGAATTAACATATTTGAATGATGGTTCAGAAAATGCAG
ATGTCCTAGTGGTTTGAGGTAGTCCCCTATGCATACAAGCAGTGTACCACCCACAGCAATAACCACATGGAAGGAAAAGC
ATCTCATTCTTGCTGGTTAGAGTTGGGGTGCTTCGAGGGACACAAGTTTCCAGGGACATCCTTCCTAACCAAGGGCCAGT
GAGCTGTGGAAGAGGGCTTCTCACTCCCAGAGGCATCCCGTCAAATGGGTACTGACCTCCATCCCTACTGCCTTCAAAAG
AGAGCTATGGAGATTCTGACTATGTGGACGGCTATGGTACTACTTATGACCAACAGAGTTAAGTTTCCTGTGATAACAGC
TACAACATCCAGCTCAAAGTGGTGCTGATGACTATAATTATGGACATGGACTTTGTGAGGATACTTAAGATTCTTATGAG
CAAGAAGAGTGGACTAACTCAGACACAAGGCCTTTTCCACAAGGACAAGGAAGGGAGTCTACTGAAACCAGTCAAATGGC

Alignment

ORF - retro_dnov_1085 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.95 %
• Parental protein coverage: 54.94 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  IPDYNDEIRQ-AQLQELTYLNGGSENADVPVVRGKP-PLRTRGVPSTAVT-RGRGGVSARPVGVGVPRGT
          IPDYND.IR..AQLQELTYLN.GSENADV.VV.G.P.P..T..VP.TA.T..GR...S...V.VGV.RGT
Retrocopy IPDYNDKIRP>AQLQELTYLNDGSENADVLVV*GSP<PMHTSSVPPTAIT>HGRKSISFLLVRVGVLRGT

Parental  PASRGVLPSRGPGSRGRGLLTPRARGVPSTGYRPPPPPPAQEAYGDYDYEDGYGTAYDEQSYESYDNSYS
          ..SR..LP..GP.S.GRGLLTPR..G.PS.GY.PP...P..E.YGD.DY.DGYGT.YD.QS..S.DNSY.
Retrocopy QVSRDILPNQGPVSCGRGLLTPR--GIPSNGY*PPSLLPSKESYGDSDYVDGYGTTYDQQS*VSCDNSYN

Parental  T-PAQSGADYYDYGHGLNEETYDSYGQEEWTNS-RHKAPSARTTKGAYRDQPYG
          ..PAQSGAD.Y.YGHGL.E.T.DSY.QEEWTNS.RHKA.S.RT.KG.Y..Q..G
Retrocopy I<PAQSGADDYNYGHGLCEDT*DSYEQEEWTNS<RHKAFSTRTRKGVY*NQSNG

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	105.21 RPM
SRP012922_cerebellum	0.00 RPM	37.94 RPM
SRP012922_heart	0.00 RPM	46.87 RPM
SRP012922_kidney	0.00 RPM	43.53 RPM
SRP012922_liver	0.00 RPM	58.67 RPM
SRP012922_lung	0.00 RPM	67.66 RPM
SRP012922_quadricep_muscle	0.00 RPM	35.31 RPM
SRP012922_spleen	0.00 RPM	112.40 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_1085 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 7 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003761	1 retrocopy	retro_dnov_2549,
Dasypus novemcinctus	ENSDNOG00000010878	2 retrocopies	retro_dnov_1085 , retro_dnov_1131,
Dipodomys ordii	ENSDORG00000014595	1 retrocopy	retro_dord_689,
Equus caballus	ENSECAG00000010194	1 retrocopy	retro_ecab_460,
Otolemur garnettii	ENSOGAG00000005150	3 retrocopies	retro_ogar_2456, retro_ogar_3114, retro_ogar_550,
Sarcophilus harrisii	ENSSHAG00000000632	1 retrocopy	retro_shar_179,
Tursiops truncatus	ENSTTRG00000001270	2 retrocopies	retro_ttru_1633, retro_ttru_1929,