RetrogeneDB ID: retro_dnov_2361

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_67398:5307..6668(-)
• 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_2361
TATTACAGTTCAGGATTAGATATGTCAAATCCAGGAAACTTCTGTGATCTTAGTAAACCCATTGGAGCACTAAACAAGGA
AAGGCTGGATAAATTACTGACAGCTATTGGGAAGTGCCAGAGCCAAAAGTCACATATGGAAGTCACTCTTCTTCCCCACG
TTATGTGCTGCTTTATCATGGTAGGATTGCACCTGAGTATATCCTATTGCCTTCAGAATGGAAGATTTGATAATGCAGAT
AGAATGTTCAACCATATTGCAGAAACTTGGAAAAACTGTATGGATGTTGCAACTGATTTTAAAGAGTTGATTCCAGAATT
CTAGGGTGATGATGTTGGCTTTTTAGTCAATAGTCTGAAATTGGATTTGGAAAAGAGACAAGGAGGGAAAATGGTGGATG
ATGTAAAACTTCCTCATGGGCCATCACGTCCTGAGGATTTTCTCCAGAAGAGTAAAGAGGCATTGGAGAGAAATCATGTG
TCAGAGCATCTTCATGAGTGGATCAATATCATATTTGGCTACACTCAAAAAGGGAGTGATGCTGATGAGGCCATGATGCA
TTTTACTCCCTGTCCTATGAAGGAGGCATGGACTTGAACAGCATTGAGGGTCCTGATGAGGAAGTAGCCATGCTGACCCA
AATTTTGTAATTTGGGCAGATACCATAACAGCTGTTCATGACACCAGACCCTCAAAGGATCGCCCCAAAGTTTAAAAGTG
TGTCTCAAAACTGCAATAATAATGCTTCTGTAGCAGATTCCCCAGGCTCCCCAGGTGATGATCTTTTGAAGACCTGATCA
AAGAAAGCAAAACTCTCACCTAGAGTAACATCACCCAACTGCAGTTACTTGAGCACTATAAAATGCACAAAGAGGCAGTT
ACTGGAGTCATAGTCTCTCGCAATGGGTCTTCAGGCTTTACAACATCATTTTCTTTGAAGATGTTTTCCAAAGAATCCAA
AATGCTACAAAGAAGTACATCATTTCTGAATATGGCTTTATCATCTTGTTTATGTTTTACTAGGAGATACCACTTTTACA
GGTTCTTTATGGTATAATAACATCTATTTTTATTCCATAGCATTTGGAAGATGCCAAGACACAATTATGGGATGTGATGA
TGCTGTTAATAATATCTTTTGGCATGAAAACAGGTTATATTCTGCATCATGGGACTCGACAGTGAAGGTGTGGTCTGGTC
TTCCTGTGGACATGCCAGACACCAAAAGACATCAGTGTGACTTGCTGGCTGAGCTAGAACATAATGTCAGTGTAGACACA
TTCAATTTAAATGCTGCCAGCCCAGTTCTGGCTTCAGGCACCAAAGAAGGTATAGTTAATATTTGGAATCTCATTAATGC
T

Alignment

ORF - retro_dnov_2361 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.23 %
• Parental protein coverage: 50.5 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  YYSAELDLSNPGTFRDLSKPVGALNQERLERLLTR-YREMPEPKFMYGSHYSSPGYVLFYLVRIAPEYML
          YYS..LD.SNPG.F.DLSKP.GALN.ERL..LLT..Y.E.PEPK..YGSH.SSP.YVL.Y..RIAPEY.L
Retrocopy YYSSGLDMSNPGNFCDLSKPIGALNKERLDKLLTA<YWEVPEPKVTYGSHSSSPRYVLLYHGRIAPEYIL

Parental  -CLQNGRFDNADRMFNSIAETWKNCLDGATDFKELIPEFYGDDISSSVNSLKLDL-KRQGGKMVDDVELP
          .CLQNGRFDNADRMFN.IAETWKNC.D.ATDFKELIPEF.GDD....VNSLKLDL.KRQGGKMVDDV.LP
Retrocopy >CLQNGRFDNADRMFNHIAETWKNCMDVATDFKELIPEF*GDDVGFLVNSLKLDLEKRQGGKMVDDVKLP

Parental  RWASSPGDFLQKSKEALESSYVSEHLHEWIDLIFGYKQKGSEAVGA-HNVFHPLTYEGGVDLNSIEGPDE
          ...S.P.DFLQKSKEALE...VSEHLHEWI..IFGY.QKGS.A..A.H..F..L.YEGG.DLNSIEGPDE
Retrocopy HGPSRPEDFLQKSKEALERNHVSEHLHEWINIIFGYTQKGSDADEA<HDAFYSLSYEGGMDLNSIEGPDE

Parental  KVAMQT-VLEFGQTPKQLFITPHPQRITPKFKTVSHTSSNSAPIAD---SPGEE-SFEDLTEESKTLAWS
          .VAM.T..L.FGQ.P.QLF.TP.PQRI.PKFK.VS....N.A..AD...SPG...SFEDL..ESKTL..S
Retrocopy EVAMLTQIL*FGQIP*QLFMTPDPQRIAPKFKSVSQNCNNNASVADSPGSPGDD<SFEDLIKESKTLT*S

Parental  NITKLQLQEHYKIHKEAVTGIAVSCNGSSVFTTSQDSTLKMFSKESKTLQRSISFSNMALSSCL-LLPGD
          NIT.LQL.EHYK.HKEAVTG..VS.NGSS.FTTS....LKMFSKESK.LQRS.SF.NMALSSCL..L.GD
Retrocopy NITQLQLLEHYKMHKEAVTGVIVSRNGSSGFTTS--FSLKMFSKESKMLQRSTSFLNMALSSCL>VLLGD

Parental  TTVISSSWDNNVYFYSIAFGRRQDTLMGHDDAVSKICWHDNRLYSASWDSTVKVWSGVPADMPGTKRHHF
          TT...S.W.NN.YFYSIAFGR.QDT.MG.DDAV..I.WH.NRLYSASWDSTVKVWSG.P.DMP.TKRH..
Retrocopy TTFTGSLWYNNIYFYSIAFGRCQDTIMGCDDAVNNIFWHENRLYSASWDSTVKVWSGLPVDMPDTKRHQC

Parental  DLLAELEHDVSVDTISLNTASTLLVSGTKEGTVSIWDLTTA
          DLLAELEH.VSVDT..LN.AS..L.SGTKEG.V.IW.L..A
Retrocopy DLLAELEHNVSVDTFNLNAASPVLASGTKEGIVNIWNLINA

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_2361 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,