RetrogeneDB ID: retro_dnov_1058

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_14169:56650..57404(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GINM1
• Ensembl ID: ENSDNOG00000000884
• Aliases: None
• Description: glycoprotein integral membrane 1 [Source:HGNC Symbol;Acc:21074]

Sequence

>retro_dnov_1058
CCGCAGGGCAGCATCACCATTAATCTTACTACCTTGAAAGATGACGGGGAGGTCTCTGAAGAACAGGTTGATCTTAACGT
AACTTATGGGAATGGACAGATGTATGTAAATGACTTCCCTGTACATGGTGTGACCCAAATAAGCTGTCAGACTTGAATAG
TGAAGAATGAAATTCTGGAAAATTTGGAGGAAAAGGGATATTTTGGAATTGTCAGCATAAGGATTTTAGTTCATGAATGG
CCTATGCCATTTGGCTCCAGTTTGCAACATACTGTCATTCAAGAAAAGGTAGTAGAAATTGATGGACAACAAACTCAACA
AAAGAATGTGACTCAAATGGATATTTTAGTTAAGAACGATGGAATACTCAGGCATTCAAACTGCACGCTTCCTTTGAAAG
AAAGCTTGCTGCACTCTGTTTCCCAAGACAGTGCATTTTGTTTACCCTCCCAACCTCTCCAAAAAGGTAAGAAGTGTCAT
TTCATCACAGACTACCCTCTAGGGTCTTGTCGGGAATGTGGAGACCACCATGGAGGAGGATGTGCTACCTGGCAAGTTAC
CCGAAACGCATCTCAGAGCAGAGCTGCCATCCTTGTATAAGGTCATGTGTCAGTGGATGGAACAGCTCAGAAAACGCCTT
TGCAGGTTCTGGAGAAGTGTTTCCCCAGTATTCTTTATGATTTTGAACATCATGGTTGTTAGAATTAGAGGAGTAGCTGT
GGAAATAACCGTCTTAAAGGTGCTTTTACGGGTT

Alignment

ORF - retro_dnov_1058 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.55 %
• Parental protein coverage: 77.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PQDSIRINVTVLQDGGEVSKEQVVLNITYENGQVYVNDFPVKSGVTRISCQTWIVKNENLENLEEKGYFG
          PQ.SI.IN.T.L.D.GEVS.EQV.LN.TY.NGQ.YVNDFPV..GVT.ISCQT.IVKNE.LENLEEKGYFG
Retrocopy PQGSITINLTTLKDDGEVSEEQVDLNVTYGNGQMYVNDFPVH-GVTQISCQT*IVKNEILENLEEKGYFG

Parental  IVSLRILVHEWPMTSGSSLQLIVIQEEVVEIDGQQAQQKDVTEIDILVKNQGILRHSNYTVPLEESMLYF
          IVS.RILVHEWPM..GSSLQ..VIQE.VVEIDGQQ.QQK.VT..DILVKN.GILRHSN.T.PL.ES.L..
Retrocopy IVSIRILVHEWPMPFGSSLQHTVIQEKVVEIDGQQTQQKNVTQMDILVKNDGILRHSNCTLPLKESLLHS

Parental  ISQDSD-IFFTL-PNLSKKV-GAGSLQTTSQALLRTVETTSEEDALPGKLPETPLRAEPPSSYKVMCQWM
          .SQDS..I.FTL.PNLSKKV....S.QTT...L...VETT.EED.LPGKLPET.LRAE.PS.YKVMCQWM
Retrocopy VSQDSA<ILFTL<PNLSKKVRSVISSQTTL*GLVGNVETTMEEDVLPGKLPETHLRAELPSLYKVMCQWM

Parental  EKLRKDLCRFWSSIVPVFFMFMNVMVVGIIGAAVLIAILKVLFPV
          E.LRK.LCRFW.S..PVFFM..N.MVV.I.G.AV.I..LKVL..V
Retrocopy EQLRKRLCRFWRSVSPVFFMILNIMVVRIRGVAVEITVLKVLLRV

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	43.95 RPM
SRP012922_cerebellum	0.41 RPM	15.12 RPM
SRP012922_heart	0.23 RPM	26.22 RPM
SRP012922_kidney	0.00 RPM	68.45 RPM
SRP012922_liver	0.15 RPM	60.37 RPM
SRP012922_lung	0.46 RPM	63.23 RPM
SRP012922_quadricep_muscle	0.17 RPM	41.37 RPM
SRP012922_spleen	0.00 RPM	82.53 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_1058 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000000884	1 retrocopy	retro_dnov_1058 ,
Monodelphis domestica	ENSMODG00000016822	1 retrocopy	retro_mdom_1159,