RetrogeneDB ID: retro_dnov_2290

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_61300:6874..8394(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NSMAF
• Ensembl ID: ENSDNOG00000010583
• Aliases: None
• Description: neutral sphingomyelinase (N-SMase) activation associated factor [Source:HGNC Symbol;Acc:8017]

Sequence

>retro_dnov_2290
CTCTATTTTTATATTGCCAAGCATAGGTCCAAGAGCTTCATGCTCCAGTGGCAGCATGGGCTTCTCTCTTACTGCCAGTA
CCTCCTGCCCCTCAACCACCTGGCTGACCAAAGCTGCAATGACATCTCCCAGTATCCTGTGTTTCCACGGATAATAACCA
ATTATTACAGTTCAGGATTAGATATGTCAAATCCAGGAAACTTCTGTGATCTTAGTAAAGCCGTTGGAGCAATAAACAAA
AAGGCTGGATAAATTACTGACAGCTATTGGGAAGTGCCAGAGCCAAAAGTCACATATGGAAGCCACTCTTCTTCCCCACG
TTATGTGCTGCTTTATCATGGTAGGATTGCACCTGAGTATATCCTATTGCCTTCAGAATGGAAGATTTGATAATGCAGAT
AGAATGTTCAACCATATTGCAGAAACTTGGAAAAACTGTATGGATGTTGCAACTGATTTTAAAGAGTTGATTCCAGAATT
CTAGGGTGATGATGTTGGCTTTTTAGTCAATAGTCTGAAATTGGATTTGGAAAAGAGACAAGGAGGGAAAATGGTGGATG
ATGTAAAACTTCCTCATGGGCCATCACGTCCTGAGGATTTTCTCCAGAAGAGTAAAGAGGCATTGGAGAGAAATCATGTG
TCAGAGCATCTTCATGAGTGGATCAATATCATATTTGGCTACACTCAAAAAGGGAGTGATGCTGATGAGGCCATGATGCA
TTTTACTCCCTGTCCTATGAAGGAGGCATGGACTTGAACAGCATTGAGGGTCCTGATGAGGAAGTAGCCATGCTGACCCA
AATTTTGTAATTTGGGCAGATACCATAACAGCTGTTCATGACACCAGACCCTCAAAGGATCACCCCAAAGTTTAAAAGTG
TGTCTCAAAACTGCAATAATAATGCTTCTGTAGCAGATTCCACAGGCTCCCCAGGTGATGATCTTTTAAGACCTGATCAA
AGAAAGCAAAACTCTCACCTGGAGTAACATCAGCCAACTGCAGTTACTTGAGCACTATAAAATGCACAAAGAGGCAGTTA
CTGGAGTCATAGTCTCTTGCAATGGGTCTTCAGGCTTTACAACATCATTTTCTTTGAAGATGTTTTCCAAAGAATCCATA
ATGCTACAAAGAAGTATATCATTTCTGAATATGACTTTATCATCTTGTTTATGTTTTACTAGGAGATACCACTGTTATAG
GTTCTTTATGGTATAATAACATCTATTTTTATTCCATAGCATTTGGAAGATGCCAAGACACATTAATGGGATGTGATGAT
GTTGTTAATAATATCTTTTGGCATGAAAACAGGTTATATTCTGCATCATGGGACTCGACAGTGAAGGTGTGGTCTGGTCT
TCCTGTGGACATGCCAGACACCAAAAGACATCAGTGTGACTTGCTGGCTGAGCTAGAACATAATGTCAGTGTAGACACAA
TCAATTTAAATGCTGCCAGCACAGTTCTGGCTTCAGGCACCAAAGAAGGTATAGTTAATATTTGTGATCTCACTACTGCT

Alignment

ORF - retro_dnov_2290 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.49 %
• Parental protein coverage: 56.55 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  LEHHVAEHTAESYMLQWQRGLLSNYQYLLHLNNLADRSCNDLSQYPVFPWIINDYYSAELDLSNPGTFRD
          L....A.H...S.MLQWQ.GLLS..QYLL.LN.LAD.SCND.SQYPVFP.II..YYS..LD.SNPG.F.D
Retrocopy LYFYIAKHRSKSFMLQWQHGLLSYCQYLLPLNHLADQSCNDISQYPVFPRIITNYYSSGLDMSNPGNFCD

Parental  LSKPVGALNQERLERLLTRYREMPEPKFMYGSHYSSPGYVLFYLVRIAPEYML-CLQNGRFDNADRMFNS
          LSK.VGA.N..........Y.E.PEPK..YGSH.SSP.YVL.Y..RIAPEY.L.CLQNGRFDNADRMFN.
Retrocopy LSKAVGAIN-KKAG*ITDSYWEVPEPKVTYGSHSSSPRYVLLYHGRIAPEYIL>CLQNGRFDNADRMFNH

Parental  IAETWKNCLDGATDFKELIPEFYGDDISSSVNSLKLDL-KRQGGKMVDDVELPRWASSPGDFLQKSKEAL
          IAETWKNC.D.ATDFKELIPEF.GDD....VNSLKLDL.KRQGGKMVDDV.LP...S.P.DFLQKSKEAL
Retrocopy IAETWKNCMDVATDFKELIPEF*GDDVGFLVNSLKLDLEKRQGGKMVDDVKLPHGPSRPEDFLQKSKEAL

Parental  ESSYVSEHLHEWIDLIFGYKQKGSEAVGA-HNVFHPLTYEGGVDLNSIEGPDEKVAMQT-VLEFGQTPKQ
          E...VSEHLHEWI..IFGY.QKGS.A..A.H..F..L.YEGG.DLNSIEGPDE.VAM.T..L.FGQ.P.Q
Retrocopy ERNHVSEHLHEWINIIFGYTQKGSDADEA<HDAFYSLSYEGGMDLNSIEGPDEEVAMLTQIL*FGQIP*Q

Parental  LFITPHPQRITPKFKTVSHTSSNSAPIADS---PGEE-SFEDLTEESK-TLAWSNITKLQLQEHYKIHKE
          LF.TP.PQRITPKFK.VS....N.A..ADS...PG...SF.......K.TL.WSNI..LQL.EHYK.HKE
Retrocopy LFMTPDPQRITPKFKSVSQNCNNNASVADSTGSPGDD<SFKT*SKKAK<TLTWSNISQLQLLEHYKMHKE

Parental  AVTGIAVSCNGSSVFTTSQDSTLKMFSKESKTLQRSISFSNMALSSCL-LLPGDTTVISSSWDNNVYFYS
          AVTG..VSCNGSS.FTTS....LKMFSKES..LQRSISF.NM.LSSCL..L.GDTTVI.S.W.NN.YFYS
Retrocopy AVTGVIVSCNGSSGFTTS--FSLKMFSKESIMLQRSISFLNMTLSSCL>VLLGDTTVIGSLWYNNIYFYS

Parental  IAFGRRQDTLMGHDDAVSKICWHDNRLYSASWDSTVKVWSGVPADMPGTKRHHFDLLAELEHDVSVDTIS
          IAFGR.QDTLMG.DD.V..I.WH.NRLYSASWDSTVKVWSG.P.DMP.TKRH..DLLAELEH.VSVDTI.
Retrocopy IAFGRCQDTLMGCDDVVNNIFWHENRLYSASWDSTVKVWSGLPVDMPDTKRHQCDLLAELEHNVSVDTIN

Parental  LNTASTLLVSGTKEGTVSIWDLTTA
          LN.AST.L.SGTKEG.V.I.DLTTA
Retrocopy LNAASTVLASGTKEGIVNICDLTTA

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	17.50 RPM
SRP012922_cerebellum	0.00 RPM	38.77 RPM
SRP012922_heart	0.00 RPM	12.07 RPM
SRP012922_kidney	0.00 RPM	12.32 RPM
SRP012922_liver	0.00 RPM	7.90 RPM
SRP012922_lung	0.00 RPM	21.99 RPM
SRP012922_quadricep_muscle	0.00 RPM	16.44 RPM
SRP012922_spleen	0.00 RPM	27.13 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_2290 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000010583	3 retrocopies	retro_dnov_2269, retro_dnov_2290 , retro_dnov_2361,
Macaca mulatta	ENSMMUG00000017297	1 retrocopy	retro_mmul_949,