RetrogeneDB ID: retro_dnov_172

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2305:299185..299721(+)
• Located in intron of: ENSDNOG00000013535

Retrocopy information

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

Parental gene information

• Parental gene symbol: PLA2G12A
• Ensembl ID: ENSDNOG00000016573
• Aliases: None
• Description: phospholipase A2, group XIIA [Source:HGNC Symbol;Acc:18554]

Sequence

>retro_dnov_172
TCACTGAGGCTCCTCCTCCTGGCTGTAGCTCTCAGGTGACAGGAGGAGGCCAAACCATCCACTGGAGGGCCACCTTTAAG
ACTATTTGGAACAGACCTCACAAGACAGACACATACCTGAATGCCACCTTGGACCTCCAGGGAGAGAGGATGGGCTGTGC
CCGTACAAGAGCAGTGTTGGATTTAAGTCCTTGCCACATTATGTTTATAAACCCTTGCCACAAAATGGATATGTCCTCTG
CTGTTTGGTGTTCTCACCTTAACACTGGCATCCCTTCCCTAAAAAAGTGCTGCAACCAACATGACAGGTGCTATGAGACC
TGTGGCAAAAGCAAGAATAACTGCGATGAGGAGTTCCAGTACTGCCACTCCAAGATCTGCCGAGATGCGCAGAAAACATT
AGGACTAGCTCAGCATGTTCAGGCATGTGAAACAATAGTAGAGCTCTTGTTTGACACTGTTACACATTTAAGCTGTAAAC
CATATTTGGATAGCCAAAGAGCCACATGCAGGTGTTGTTATGAGGAAAAACTGGAT

Alignment

ORF - retro_dnov_172 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.53 %
• Parental protein coverage: 95.72 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ALALLLLAAALSCQGEA-QTTDWRTTLKTIRNGVHKIDTYLNAALDLLGG-EDGLCQYKCSDGSKPFPHY
          .L.LLLLA.AL..Q.EA.QT..WR.T.KTI.N..HK.DTYLNA.LDL.G..EDGLC.YK.S.G.K..PHY
Retrocopy SLRLLLLAVALR*QEEA<QTIHWRATFKTIWNRPHKTDTYLNATLDLQGE<EDGLCPYKSSVGFKSLPHY

Parental  DYKPSPPNG-CGSPMFGVHLNIGIPSLTKCCNQHDRCYETCGKSKNDCDEEFQYCLSKICRNVQKTLGLA
          .YKP.P.NG...S.....HLN.GIPSL.KCCNQHDRCYETCGKSKN.CDEEFQYC.SKICR..QKTLGLA
Retrocopy VYKPLPQNG>MSSAVWCSHLNTGIPSLKKCCNQHDRCYETCGKSKNNCDEEFQYCHSKICRDAQKTLGLA

Parental  QHVQACETTVELLFGSVIHLGCKPYLDSQRAACRCRYEEKTD
          QHVQACET.VELLF..V.HL.CKPYLDSQRA.CRC.YEEK.D
Retrocopy QHVQACETIVELLFDTVTHLSCKPYLDSQRATCRCCYEEKLD

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	14.59 RPM
SRP012922_cerebellum	0.00 RPM	14.30 RPM
SRP012922_heart	0.00 RPM	3.94 RPM
SRP012922_kidney	0.00 RPM	12.87 RPM
SRP012922_liver	0.15 RPM	18.73 RPM
SRP012922_lung	0.00 RPM	9.77 RPM
SRP012922_quadricep_muscle	0.00 RPM	10.56 RPM
SRP012922_spleen	0.00 RPM	13.39 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_172 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 14 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000015230	1 retrocopy	retro_btau_1557,
Callithrix jacchus	ENSCJAG00000016169	2 retrocopies	retro_cjac_1992, retro_cjac_3936,
Dasypus novemcinctus	ENSDNOG00000016573	7 retrocopies	retro_dnov_1694, retro_dnov_172 , retro_dnov_1856, retro_dnov_1930, retro_dnov_2286, retro_dnov_2572, retro_dnov_434,
Homo sapiens	ENSG00000123739	1 retrocopy	retro_hsap_153,
Gorilla gorilla	ENSGGOG00000001082	2 retrocopies	retro_ggor_242, retro_ggor_929,
Loxodonta africana	ENSLAFG00000000852	2 retrocopies	retro_lafr_402, retro_lafr_718,
Mustela putorius furo	ENSMPUG00000008637	1 retrocopy	retro_mputfur_964,
Mus musculus	ENSMUSG00000027999	1 retrocopy	retro_mmus_2368,
Otolemur garnettii	ENSOGAG00000004686	1 retrocopy	retro_ogar_670,
Ochotona princeps	ENSOPRG00000014505	2 retrocopies	retro_opri_30, retro_opri_921,
Pan troglodytes	ENSPTRG00000016362	1 retrocopy	retro_ptro_817,
Sus scrofa	ENSSSCG00000009139	3 retrocopies	retro_sscr_622, retro_sscr_623, retro_sscr_670,
Tarsius syrichta	ENSTSYG00000004756	4 retrocopies	retro_tsyr_1366, retro_tsyr_376, retro_tsyr_487, retro_tsyr_493,
Vicugna pacos	ENSVPAG00000009842	1 retrocopy	retro_vpac_466,