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 summary: | ||
| Parental gene symbol: | NSMAF | ||
| Ensembl ID: | ENSDNOG00000010583 | ||
| Aliases: | None | ||
| Description: | neutral sphingomyelinase (N-SMase) activation associated factor [Source:HGNC Symbol;Acc:8017] |
Retrocopy-Parental alignment summary:
>retro_dnov_2361
TATTACAGTTCAGGATTAGATATGTCAAATCCAGGAAACTTCTGTGATCTTAGTAAACCCATTGGAGCACTAAACAAGGA
AAGGCTGGATAAATTACTGACAGCTATTGGGAAGTGCCAGAGCCAAAAGTCACATATGGAAGTCACTCTTCTTCCCCACG
TTATGTGCTGCTTTATCATGGTAGGATTGCACCTGAGTATATCCTATTGCCTTCAGAATGGAAGATTTGATAATGCAGAT
AGAATGTTCAACCATATTGCAGAAACTTGGAAAAACTGTATGGATGTTGCAACTGATTTTAAAGAGTTGATTCCAGAATT
CTAGGGTGATGATGTTGGCTTTTTAGTCAATAGTCTGAAATTGGATTTGGAAAAGAGACAAGGAGGGAAAATGGTGGATG
ATGTAAAACTTCCTCATGGGCCATCACGTCCTGAGGATTTTCTCCAGAAGAGTAAAGAGGCATTGGAGAGAAATCATGTG
TCAGAGCATCTTCATGAGTGGATCAATATCATATTTGGCTACACTCAAAAAGGGAGTGATGCTGATGAGGCCATGATGCA
TTTTACTCCCTGTCCTATGAAGGAGGCATGGACTTGAACAGCATTGAGGGTCCTGATGAGGAAGTAGCCATGCTGACCCA
AATTTTGTAATTTGGGCAGATACCATAACAGCTGTTCATGACACCAGACCCTCAAAGGATCGCCCCAAAGTTTAAAAGTG
TGTCTCAAAACTGCAATAATAATGCTTCTGTAGCAGATTCCCCAGGCTCCCCAGGTGATGATCTTTTGAAGACCTGATCA
AAGAAAGCAAAACTCTCACCTAGAGTAACATCACCCAACTGCAGTTACTTGAGCACTATAAAATGCACAAAGAGGCAGTT
ACTGGAGTCATAGTCTCTCGCAATGGGTCTTCAGGCTTTACAACATCATTTTCTTTGAAGATGTTTTCCAAAGAATCCAA
AATGCTACAAAGAAGTACATCATTTCTGAATATGGCTTTATCATCTTGTTTATGTTTTACTAGGAGATACCACTTTTACA
GGTTCTTTATGGTATAATAACATCTATTTTTATTCCATAGCATTTGGAAGATGCCAAGACACAATTATGGGATGTGATGA
TGCTGTTAATAATATCTTTTGGCATGAAAACAGGTTATATTCTGCATCATGGGACTCGACAGTGAAGGTGTGGTCTGGTC
TTCCTGTGGACATGCCAGACACCAAAAGACATCAGTGTGACTTGCTGGCTGAGCTAGAACATAATGTCAGTGTAGACACA
TTCAATTTAAATGCTGCCAGCCCAGTTCTGGCTTCAGGCACCAAAGAAGGTATAGTTAATATTTGGAATCTCATTAATGC
T
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 |
(Hint: click retrocopy or parental gene accession number on the plot's legend, to show / hide expression level values)
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 |
Dasypus novemcinctus was not studied using ChIP-Seq data.
Dasypus novemcinctus was not studied using EST data.
Dasypus novemcinctus was not studied using FANTOM5 data.
retro_dnov_2361 was not experimentally validated.
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.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 |