RetrogeneDB ID: retro_dnov_2048

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_44423:4715..5586(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NIPAL1
• Ensembl ID: ENSDNOG00000002047
• Aliases: None
• Description: NIPA-like domain containing 1 [Source:HGNC Symbol;Acc:27194]

Sequence

>retro_dnov_2048
GGCCTCCTGCGACTTGCCAGAAAAGGCTCCATGAGAGCAGGTCAAGGTGGCCATGCATATCTTAAAGAATGGCTGTGGTG
GGCTGCACTGCAATCAATGGGAGCTGGTGAGGTGGCCAACTTTGCAGCATATGCATTTGCTGCAGCCACATTAGTGACTC
CTTTGGGAGCTCTTGGTGTCTTAGAGAGTGCCATTCTTTCTTCATATTTTCTAAATGAAAGACTTAAATCTTCATGGGAA
AATTGTATGTTTGTTAAGTATTTTAGGGTCTACAGTTATGGTCATCCATGCTCCAAAAGAAGAGGAGATAGAGACCTTAA
ATGAAATGTTTCACAAACTAGGTGATCCAGGTTTTGTGGTCTTTGCAACACTTGTGGTCATTGTGTCTTTGATATTAATT
TTCGTGGTGGGACCTCGCCATGGACAGACAAACGTTCTTGTGTACCTAACAATCTGCTCCGTGATTGGAGTGTTTTCCGT
CTCCTGTGTGAAAGGCCTGGGCATCGCTATTAAAGAACTGTTTGCTGGAAAGCCTGTTCTGCGACACCCCCTGGCCTGGA
TTCTCCTGCTGAGCCTGATAGTATGTGTGAGCACACAGATTAATTATCTGAACAGGGCCTTGGACATATTCAACACTTCC
ATCATGACACCAATATATTATGTATTATTCACAACATCAGTTTTAACTTGTTCAGCTACTCTTTTTAAGGAGTGGCAAGA
CATGCCTGTTGATGATATCATTGGTACTTTGAGCGGCTTCCTTACCATCATTGTGGGGATATTTTTATTGCATGCTTTTA
AAGATGTCAGTTTTAGTCTAGCGAGTCTGCCATTGTCTTTTCGAAAAGATGAGAAAGCAACAAATGGTAAT

Alignment

ORF - retro_dnov_2048 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 71.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLLQLAQRGVTRAGEGGHSYLKEWLWWAGLLLMGAGEAVNFAAYAFAPATLVTPLGALSVLISAILSSYF
          GLL.LA..G..RAG.GGH.YLKEWLWWA.L..MGAGE..NFAAYAFA.ATLVTPLGAL.VL.SAILSSYF
Retrocopy GLLRLARKGSMRAGQGGHAYLKEWLWWAALQSMGAGEVANFAAYAFAAATLVTPLGALGVLESAILSSYF

Parental  LNEHL-NIHGKIGCILSILGSTVMAIHAPREEEVTSLHEMEMKLRDPEFISFAVIIIVISLVLILVVAPK
          LNE.L.N.HGKI.C.LSILGSTVM.IHAP.EEE...L.EM..KL.DP.F..FA......SL.LI.VV.P.
Retrocopy LNERL>NLHGKIVCLLSILGSTVMVIHAPKEEEIETLNEMFHKLGDPGFVVFATLVVIVSLILIFVVGPR

Parental  KGQTNILVYISICSLIGAFSVSSVKGLGIAIKELLEWKPVYKHPLVFVLLAVLVLSVSTQINYLNKALDT
          .GQTN.LVY..ICS.IG.FSVS.VKGLGIAIKEL...KPV..HPL...LL..L...VSTQINYLN.ALD.
Retrocopy HGQTNVLVYLTICSVIGVFSVSCVKGLGIAIKELFAGKPVLRHPLAWILLLSLIVCVSTQINYLNRALDI

Parental  FNTSLVTPIYYVFFTSMVVTCSAILFQEWYGMKAEDIIGTLSGFFTIISGIFLLHAFKNTDITWSQLTST
          FNTS..TPIYYV.FT..V.TCSA.LF.EW..M...DIIGTLSGF.TII.GIFLLHAFK........L...
Retrocopy FNTSIMTPIYYVLFTTSVLTCSATLFKEWQDMPVDDIIGTLSGFLTIIVGIFLLHAFKDVSFSLASLPLS

Parental  AKKDMITLNGH
          ..KD....NG.
Retrocopy FRKDEKATNGN

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	10.70 RPM	6.61 RPM
SRP012922_cerebellum	6.60 RPM	0.14 RPM
SRP012922_heart	2.55 RPM	9.51 RPM
SRP012922_kidney	3.83 RPM	0.00 RPM
SRP012922_liver	3.56 RPM	0.00 RPM
SRP012922_lung	10.54 RPM	1.83 RPM
SRP012922_quadricep_muscle	6.58 RPM	0.00 RPM
SRP012922_spleen	6.98 RPM	1.14 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_2048 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000002047	1 retrocopy	retro_dnov_2048 ,
Homo sapiens	ENSG00000163293	1 retrocopy	retro_hsap_2463,
Gorilla gorilla	ENSGGOG00000009006	1 retrocopy	retro_ggor_1533,
Macaca mulatta	ENSMMUG00000018625	1 retrocopy	retro_mmul_638,
Nomascus leucogenys	ENSNLEG00000017377	1 retrocopy	retro_nleu_2814,
Pongo abelii	ENSPPYG00000014714	1 retrocopy	retro_pabe_1810,
Pan troglodytes	ENSPTRG00000016038	1 retrocopy	retro_ptro_1422,