RetrogeneDB ID: retro_dnov_2549

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_8494:52803..53597(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KHDRBS1
• Ensembl ID: ENSDNOG00000003761
• Aliases: None
• Description: KH domain containing, RNA binding, signal transduction associated 1 [Source:HGNC Symbol;Acc:18116]

Sequence

>retro_dnov_2549
TTTAATTTTGTGGCGAAGATTCTTGACTCACAAGGGAATCCAATCAAAAGACTGCAAGAAGGGACTGGTGCAGAGATCTC
TGTGTTGGCAAAGAGTTCCAAGAGCAACAAAGCCAAGAAGGAAGAGCTGCACAAGGGTGGAGACCTCCAAATATGCCCAC
TTGAATAGGAATCTACACGTTTTCATTGAAGTCTCTGGACCGCCATGTGAGGCCTTAGGCTTTCATGGTCCATGCCATGG
AGAAAGTCAAGAAGTTTCCGGTAGCAGAAATGATGGATGATACCTGCCAGAAACAGTTTCTGTTCTACTTGAATGGAGTA
GCTGAACCCACTTGCTAATGTGGGGTGCCAGTGAAAGCCTGAGGAACTGCCTTTCCACCTCCATCTGTTCCCAGGGGTCA
TGATGTTGGGCCACCTGGAGGGCCTTTGCTGGGTGGTACACCAGGAAGAGGAGCCATCATCAGAGGTACCACCATGACTC
AAGGAGTGCCACCCTCTATGTACTGTGTGGGGTGCTCCAGCACCAAGAGCAGGCACAACAGCTATCCAGAGACTATCTCT
GCTACCACTCCCTGCATCAGAAACATATAAAGAATATAGATATAATGATACATACGCCCAATAGTAGAAGGGTATTTATT
ACAGCCTGAGCCAAGGGGACTCAGAATACTATAACTTCACACATGGGGAAATTCAAGATTCTTACCAAGCTTATGGCTAA
GGCAACTGGAATGGGACCAGCCCACTGTTGAAGACTCTCCAACTCCGCCAGTGAAGGGAGGACTCTATGGGCAT

Alignment

ORF - retro_dnov_2549 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.64 %
• Parental protein coverage: 60.86 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  FNFVGKILGPQGNTIKRLQEETGAKISVLGKGSMRDKAKEEELRKGGD-PKYAHLNMDLHVFIEVFGPPC
          FNFV.KIL..QGN.IKRLQE.TGA.ISVL.K.S...KAK.EEL.KGGD..KYAHLN..LHVFIEV.GPPC
Retrocopy FNFVAKILDSQGNPIKRLQEGTGAEISVLAKSSKSNKAKKEELHKGGD>SKYAHLNRNLHVFIEVSGPPC

Parental  EAY-ALMAHAMEEVKKFLVPDMMDDICQEQFLELSYLNGVPEPPRGRGVPVRGRGTAPPPPPVPRGRGVG
          EA..A.M.HAME.VKKF.V..MMDD.CQ.QFL...YLNGV.EP....GVPV...GTA.PPP.VPRG..VG
Retrocopy EAL>AFMVHAMEKVKKFPVAEMMDDTCQKQFL--FYLNGVAEPTC*CGVPVKA*GTAFPPPSVPRGHDVG

Parental  PPRGALVRGTPVRGAITRGTTVTRGVPPPP-TVRGAPAPRARTTGIQRIPLPPPPAPETYEEYGYDDTYA
          PP.G.L..GTP.RGAI.RGTT.T.GVPP...TV.GAPAPRA.TT.IQR..L.P.PA.ETY.EY.Y.DTYA
Retrocopy PPGGPLLGGTPGRGAIIRGTTMTQGVPPSM>TVWGAPAPRAGTTAIQRLSLLPLPASETYKEYRYNDTYA

Parental  EQSYEGYEGYYSQSQGDSEYYDYGHGEVQDSYEAYGQDDWNGTRPSLKA-PPARPVKGAYREH
          .Q...G.....SQ..........G..E.QDSY.AYG...WNGT.P.LK...P..PVKG....H
Retrocopy -Q**KGIYYSLSQGDSEYYNFTHG--EIQDSYQAYG*GNWNGTSPLLKT<SPTPPVKGGLYGH

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	92.57 RPM
SRP012922_cerebellum	0.00 RPM	83.03 RPM
SRP012922_heart	0.00 RPM	20.19 RPM
SRP012922_kidney	0.00 RPM	30.94 RPM
SRP012922_liver	0.00 RPM	26.32 RPM
SRP012922_lung	0.00 RPM	78.96 RPM
SRP012922_quadricep_muscle	0.00 RPM	25.10 RPM
SRP012922_spleen	0.00 RPM	94.66 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_2549 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006973	1 retrocopy	retro_chof_314,
Callithrix jacchus	ENSCJAG00000006580	1 retrocopy	retro_cjac_1185,
Dasypus novemcinctus	ENSDNOG00000003761	1 retrocopy	retro_dnov_2549 ,
Dasypus novemcinctus	ENSDNOG00000010878	2 retrocopies	retro_dnov_1085, retro_dnov_1131,