RetrogeneDB ID: retro_dnov_72

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1265:265589..266064(-)
• Located in intron of: ENSDNOG00000017875

Retrocopy information

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

Parental gene information

• Parental gene symbol: VIM
• Ensembl ID: ENSDNOG00000011305
• Aliases: None
• Description: vimentin [Source:HGNC Symbol;Acc:12692]

Sequence

>retro_dnov_72
GATGTAGATGCAGCCACTCTAGTTCGTATTGACCTGGGGCTCAGAATCGAGTCTCTCAAGGAGATGATCGCTTTCCTTAA
GAAAGTGCACGAAGAGAACAGAGAGCTGCAGGTCCAACTCCAGGTGGAGATGGACATGTTCATGCCAGACCTCACCTCCG
CCCTCAGGGACATCCAGGCTCAGTACGCGACCATCACTGCTCGGAACATCTCTAAGGCGAGGAGTAGAGCAAGTCGAAAG
TGTCCCACCTGACCCAGGCAGCCAACAAGAACAGTGAGCGCTGCGTCAAGTAGGAGGTGGTGGAGTACCGGCACCAGATC
CAGTCCTACACCTGTGAGGTCCACCCCCCAAGGGCACTAAAGATTCCCTGATGAGGCAGACATGGGAGCTGGAGCACCGT
TCTGCCAGTGAGGCCAGCAGTTACCAGGACAACATTGCAGGCCTGGAGGAGGAGATCTGGCACCTCAAGCATGAG

Alignment

ORF - retro_dnov_72 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.3 %
• Parental protein coverage: 66.53 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DVDNASLARLDLERKVESLQEEIAFLKKLHEEEIQELQAQIQEQHVQIDMDVSKPDLTAALRDVRQQYES
          DVD.A.L.R.DL....ESL.E.IAFLKK.HEE...ELQ.Q.Q...V..DM....PDLT.ALRD...QY..
Retrocopy DVDAATLVRIDLGLRIESLKEMIAFLKKVHEEN-RELQVQLQ---VEMDMFM--PDLTSALRDIQAQYAT

Parental  VAAKNLQEA-EEWYKSKFADLSEAANRNNDALRQAKQESNEYRRQVQSLTCEV-DALKGTNESLERQMRE
          ..A.N...A.EE..KSK...L..AAN.N....R..K.E..EYR.Q.QS.TCEV....KGT..SL.RQ..E
Retrocopy ITARNISKA<EE*SKSKVSHLTQAANKNSE--RCVK*EVVEYRHQIQSYTCEV<PPPKGTKDSLMRQTWE

Parental  MEENFAVEAANYQDTIGRLQDEIQNMLRE
          .E...A.EA..YQD.I..L..EI.....E
Retrocopy LEHRSASEASSYQDNIAGLEEEIWHLKHE

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	180.47 RPM
SRP012922_cerebellum	0.00 RPM	30.66 RPM
SRP012922_heart	0.00 RPM	130.17 RPM
SRP012922_kidney	0.00 RPM	120.20 RPM
SRP012922_liver	0.00 RPM	31.89 RPM
SRP012922_lung	0.00 RPM	897.41 RPM
SRP012922_quadricep_muscle	0.00 RPM	195.93 RPM
SRP012922_spleen	0.11 RPM	903.33 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_72 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000004529	2 retrocopies	retro_cfam_1902, retro_cfam_2022,
Callithrix jacchus	ENSCJAG00000008688	2 retrocopies	retro_cjac_1026, retro_cjac_1456,
Dasypus novemcinctus	ENSDNOG00000011305	1 retrocopy	retro_dnov_72 ,
Tarsius syrichta	ENSTSYG00000004937	2 retrocopies	retro_tsyr_1756, retro_tsyr_564,