RetrogeneDB ID: retro_dnov_786

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_107173:2872..3524(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYPLAL1
• Ensembl ID: ENSDNOG00000001461
• Aliases: None
• Description: lysophospholipase-like 1 [Source:HGNC Symbol;Acc:20440]

Sequence

>retro_dnov_786
CATCTTCCTGCATGGCTCAGAGCACATTAGTAAGGTGATACTGGACAAGGATTGAGAAAGTGGATCAAGCAAGTTTCTCA
TCAAGATTTAACATTCCAACACATAAAAATTATTTACCCAACACCTCCTTCCAGGCCCTCTACTCCTATGAAAGGAGCAA
TGTCCAACGTATGGTTTGACAGGTTTAAAATATCTGATGACTGCCCAGAACACCATGAATCAATTGATGAAATGTGTCAA
GTGCTTTACTGATTTAATTAATGATGAAGTAAAAAGTGGAATTAAGAACAACGGGATATTAATAGGAGGATTTTCGATGG
GAGGATGCATGGCAATGCATTTAGCATATAGAAATCATCAAGATGTGGCAGGAGTATTTGCTCTTTCTAGTTTTCTGAAT
AAAACATCTACTGTTTACCCAGCTCTTCAGAAAACTGATGGTACACTTCCTGAATTATTTCAGTGTCATGGAACTGCAGA
TGAGTTAGTTCTTCATTCTTGGGGTGAAGAGACAAACTTAAAGCTGAAATCTCTAGGTGTGAGCACATAGTTTTATAGTT
TCCCAGATGTTTATCATGAGCTAAGCAAAACTGAGCTAGAAAAATTGAAGTTGTGGATTCTTAAAAAGCTACCAGGAGAA
ATGGAAAGGCAA

Alignment

ORF - retro_dnov_786 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.65 %
• Parental protein coverage: 91.85 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  HSASVIYLHGSGDTGQGLRKWIKQVSHQDLAFQHIKIIYPTAPSRPYTPMKGAMSNVWFDRFKISDDCPE
          H.......H..GDTGQGLRKWIKQVSHQDL.FQHIKIIYPT.PSRP.TPMKGAMSNVWFDRFKISDDCPE
Retrocopy HLPAWLRAH**GDTGQGLRKWIKQVSHQDLTFQHIKIIYPTPPSRPSTPMKGAMSNVWFDRFKISDDCPE

Parental  HLESIDEMCQVL-TDLINDELKSGIKKNRILIEGLSMGGCRAMHLAYRHQQDVAGVFTLSSFPNKTSVVY
          H.ESIDEMCQVL.TDLINDE.KSGIK.N.ILI.G.SMGGC.AMHLAYR..QDVAGVF.LSSF.NKTS.VY
Retrocopy HHESIDEMCQVL>TDLINDEVKSGIKNNGILIGGFSMGGCMAMHLAYRNHQDVAGVFALSSFLNKTSTVY

Parental  PALQKTDGILP-LFQCHGTTDELVLHSWGEETNLMLKSLGMGTKFYSFPDVDAEISET--EKLKSWILKK
          PALQKTDG.LP.LFQCHGT.DELVLHSWGEETNL.LKSLG..T.FYSFPDV..E.S.T..EKLK.WILKK
Retrocopy PALQKTDGTLPELFQCHGTADELVLHSWGEETNLKLKSLGVST*FYSFPDVYHELSKTELEKLKLWILKK

Parental  LPTEMERQ
          LP.EMERQ
Retrocopy LPGEMERQ

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	3.50 RPM	2.53 RPM
SRP012922_cerebellum	9.21 RPM	3.85 RPM
SRP012922_heart	7.19 RPM	3.25 RPM
SRP012922_kidney	5.20 RPM	5.48 RPM
SRP012922_liver	2.79 RPM	2.94 RPM
SRP012922_lung	7.33 RPM	5.96 RPM
SRP012922_quadricep_muscle	3.46 RPM	0.35 RPM
SRP012922_spleen	4.12 RPM	4.35 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_786 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 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002210	1 retrocopy	retro_chof_1721,
Dasypus novemcinctus	ENSDNOG00000001461	1 retrocopy	retro_dnov_786 ,
Dasypus novemcinctus	ENSDNOG00000011285	2 retrocopies	retro_dnov_1186, retro_dnov_134,
Tursiops truncatus	ENSTTRG00000004004	1 retrocopy	retro_ttru_1267,