RetrogeneDB ID: retro_dnov_280

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3248:294686..295227(-)
• Located in intron of: ENSDNOG00000000516

Retrocopy information

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

Parental gene information

• Parental gene symbol: PRPSAP1
• Ensembl ID: ENSDNOG00000003550
• Aliases: None
• Description: phosphoribosyl pyrophosphate synthetase-associated protein 1 [Source:HGNC Symbol;Acc:9466]

Sequence

>retro_dnov_280
AAAATTCAAGAATCTGTGAGGGGAAAAACATTTTCATTAACCAAACTGCTTCAAAGGATGTGAAGACCACCATCACGGGG
CTCCTGATCATGGTGTATGTCCCTAAAACCTCTTGTGCCAAGACCATTGTCAGCATGATTCCCTACTTTCCTTACAATAA
ATAGTACAAGATGAGGAAAAGACACTCCATTGTCTCTAAATTGATGGCTTCAATGATATGCAAAGCTGGTCTAACTCATC
TTATTATTATGGATTTACACAAGAAAGAAATTCAGGGCTTCATAAATATTCCTGTTATCTTTTAAGAGCATCACCCTTCC
TATTACAGAATATTCAAGAAGAGATCCTGGATTACAGGAATGAGTGATCATGGCCAAATCTCCAGCTTCTACCAAGAGGG
CACAGTCTTTCACTAAGCAACTTTGACTGGGCATTGCAGTGATTCACTGTGAAGTGCAGGACGCCAAGTCCAACTTGGTG
GACAGAAGTCATTCCCCACCTGGTCAGAAATGTGGCTGCCATCCACTCCAGCCTGGAGATC

Alignment

ORF - retro_dnov_280 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.92 %
• Parental protein coverage: 50.84 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  EIKESVRGQ-DIFIIQTIPRDVNTAVMELLIMAYALKTACARNIIGVIPYFPYSKQSKMRKRGSIVCKLL
          .I.ESVRG...IFI.QT...DV.T....LLIM.Y..KT.CA..I...IPYFPY.K..KMRKR.SIV.KL.
Retrocopy KIQESVRGK<NIFINQTASKDVKTTITGLLIMVYVPKTSCAKTIVSMIPYFPYNK*YKMRKRHSIVSKLM

Parental  ASMLAKAGLTHIITMDLHQKEIQGFFS-FPVDNLRASPFLLQYIQEEIPNYRNA-VIVAKSPDAAKRAQS
          ASM..KAGLTH.I.MDLH.KEIQGF........LRASPFLLQ.IQEEI..YRN..VI.AKSP...KRAQS
Retrocopy ASMICKAGLTHLIIMDLHKKEIQGFIN<YSCYLLRASPFLLQNIQEEILDYRNE<VIMAKSPASTKRAQS

Parental  YAERLRLGLAVIHGEAQCAELDMDDGRHSPPMVK-NATVHPGLEL
          ....L.LG.AVIH.E.Q.A.....D..HSPP..K..A..H..LE.
Retrocopy FTKQL*LGIAVIHCEVQDAKSNLVDRSHSPPGQK>VAAIHSSLEI

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	75.84 RPM
SRP012922_cerebellum	0.00 RPM	23.09 RPM
SRP012922_heart	0.00 RPM	7.19 RPM
SRP012922_kidney	0.00 RPM	35.59 RPM
SRP012922_liver	0.00 RPM	33.44 RPM
SRP012922_lung	0.00 RPM	78.96 RPM
SRP012922_quadricep_muscle	0.00 RPM	5.54 RPM
SRP012922_spleen	0.00 RPM	30.79 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_280 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002028	2 retrocopies	retro_dnov_2677, retro_dnov_947,
Dasypus novemcinctus	ENSDNOG00000003550	1 retrocopy	retro_dnov_280 ,
Monodelphis domestica	ENSMODG00000009171	1 retrocopy	retro_mdom_1440,