RetrogeneDB ID: retro_dnov_767

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_105840:3156..4032(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AIFM1
• Ensembl ID: ENSDNOG00000018718
• Aliases: None
• Description: apoptosis-inducing factor, mitochondrion-associated, 1 [Source:HGNC Symbol;Acc:8768]

Sequence

>retro_dnov_767
AGTCATGTTCCTTTCCTGCTATTTAGCAGAGCACCGCTGCTTTTGCTGCAGCCAGATCACTCCGAGCTCAGGATCCTGGG
GCCAGGGTACTGAATGTCTCTGAAGATCCTGAGTTGCCATACATGCAGCCTCCACAAAAGAACTGTGGTTTTCAGATGAT
CCAAATGTCACAAAGACACTGCAATTAAGGCAGTGGAATGGAAAGAGAAGCATGTATTTCCAGCCGCCTTCTTTCTCTGC
TCAGGACCTGCTTAACATTGAGAATAGTGTTGTGGCTGTCCTCACTGGAAAGAAGGTGGTACAGCTGGATGTGAGAGGCA
ACACAGGGAAACTTCATGATGGCTCTCAAATAACCTATGAAAAGTGCTTGATTGCAACAGGAGGCACTCCAAGAAACTGT
CTACCATGGATAGGGCTAGAGCAGAGAAGAGTGTAACAAGGCTTTTCAGAAAAATTAGAGACTTTAGAGCCTTGGAGATT
TCACGGAAGTCAAGTTGATTACAATTATTGGTAGGCGCTTCCTTGGCAGCAAACTGGCCTGTACTCTTGGCAGAAAATTT
CAAGCCTTGGGCTCAGAAGTGATTTAACTCTTCCCTAAGAAAGGAAGCATGGGAAAGATCCTCCCTGAATACCTCAGCAA
CTGGACCATGGAAAAAGTCCGATGAGAGGAGGTAAACACAATTCCCAATGCTGTTGTGCAATCCATTGGGGTCAGCAGGG
GCAAGTTACTGATCAAGCTGAAAAGGTGACAGGAAGGTAGAAACTGGCCACACAGAGGCAGCTGTGGGCCTGGAGCCCAA
TGTCGAATTGGCCAAGACTGAGGGCATGGAAATAGGCTCAGATTTGGGTGGCTTCCAAGTTGCAAGTGTACTCCGG

Alignment

ORF - retro_dnov_767 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.66 %
• Parental protein coverage: 51.82 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  SHVPFLLIGGG-TAAFAAARSIRARDPGARVLIISEDPELPYMRPPLSKELWF-SDDPNVTKTLRFRQWN
          SHVPFLL.....TAAFAAARS.RA.DPGARVL..SEDPELPYM.PP..K...F.SDDPNVTKTL..RQWN
Retrocopy SHVPFLLFSRA<TAAFAAARSLRAQDPGARVLNVSEDPELPYMQPP-QKNCGF<SDDPNVTKTLQLRQWN

Parental  GKERSIYFQPPSFYVSAQDLPNIENGGVAVLTGKKVVQLDVRGNMVKLNDGSQITYEKCLIATGGTPRS-
          GK.RS.YFQPPSF..SAQDL.NIEN..VAVLTGKKVVQLDVRGN..KL.DGSQITYEKCLIATGGTPR..
Retrocopy GK-RSMYFQPPSF--SAQDLLNIENSVVAVLTGKKVVQLDVRGNTGKLHDGSQITYEKCLIATGGTPRN<

Parental  LSAIDRAGAEVKSRTTLFRKIGDFRALEKISR-EVKSITIIGGGFLGSELACALGRKARALGTEVIQLFP
          LS..DRA.AE.KS.T.LFRKI.DFRALE.ISR.EVK.ITIIG..FLGS.LAC.LGRK..ALG.EVI.LFP
Retrocopy LSTMDRARAE-KSVTRLFRKIRDFRALE-ISR<EVKLITIIGRRFLGSKLACTLGRKFQALGSEVI*LFP

Parental  EKGNMGKILPEYLSNWTTEKVRREGVNVMPSAIVQSVGVSGGKLLIKL-KDGRKVETDHIVAAVGLEPNV
          .KG.MGKILPEYLSNWT.EKVR.E.VN..P.A.VQS.GVS.GKLLIKL.K..RKVET.H..AAVGLEPNV
Retrocopy KKGSMGKILPEYLSNWTMEKVR*EEVNTIPNAVVQSIGVSRGKLLIKL>KGDRKVETGHTEAAVGLEPNV

Parental  ELAKTGGLEIDSDFGGFRVNAELQ
          ELAKT.G.EI.SD.GGF.V...L.
Retrocopy ELAKTEGMEIGSDLGGFQVASVLR

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	92.76 RPM
SRP012922_cerebellum	5.91 RPM	44.13 RPM
SRP012922_heart	0.00 RPM	69.84 RPM
SRP012922_kidney	0.00 RPM	222.32 RPM
SRP012922_liver	0.00 RPM	92.26 RPM
SRP012922_lung	0.00 RPM	36.65 RPM
SRP012922_quadricep_muscle	0.00 RPM	66.12 RPM
SRP012922_spleen	0.00 RPM	43.72 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_767 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 5 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000018718	1 retrocopy	retro_dnov_767 ,
Homo sapiens	ENSG00000156709	1 retrocopy	retro_hsap_546,
Gorilla gorilla	ENSGGOG00000007635	1 retrocopy	retro_ggor_497,
Microcebus murinus	ENSMICG00000016006	1 retrocopy	retro_mmur_492,
Tarsius syrichta	ENSTSYG00000000060	1 retrocopy	retro_tsyr_615,