RetrogeneDB ID: retro_dnov_1119

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_149866:4452..4955(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PDLIM1
• Ensembl ID: ENSDNOG00000012381
• Aliases: None
• Description: PDZ and LIM domain 1 [Source:HGNC Symbol;Acc:2067]

Sequence

>retro_dnov_1119
ACCACCCAGCAGATCCTCCAGAGCCCGAAGCTGTGGAGCTTCCGCCCTTGTGAGGAGCAAGGACTTAGAGCAGCCTCTTG
CCATTTCCCGAGTCACTCCTGGAAGCAAGGCTGCTATAGTTAATTTATGTATTGGAGATGTGATCACAGCCGTCAATGGG
GAAAACACTAGCCATATGACACACTTGGAAGCTCAGAATAAAATCAAGGTTTGCACAGACAGCGTGACTCTCATGGTAGC
CAGACCTAAACATAAGATCTGGTCTCCTCTGATGGCCGAGGAAGGGAAGCATCATCCATACAAGATGAATTTAGCTTCCA
AACCCCAAAAAGTCCTGCACATGGGAAGTGCCCATAACTGAAGCGCCATGCCCTTTACTGAGTCACCCGCCTCTAGTACT
GCCCCCCAGGGTCATCACAAACCAGTACAATAACCCAGCTGGCCTCTACTCTTCTGAAAACATCTCCAACTTCAACAGAG
CTGTAGAGTCAAAGACTGTGGCA

Alignment

ORF - retro_dnov_1119 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.53 %
• Parental protein coverage: 51.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TTQQIVLQGPGPWGFR-LVGGKDFEQPLAISRVTPGSKAAIANLCIGDVITAIDGENTSHMTHLEAQNKI
          TTQQI.LQ.P..W.FR.LV..KD.EQPLAISRVTPGSKAAI.NLCIGDVITA..GENTSHMTHLEAQNKI
Retrocopy TTQQI-LQSPKLWSFR>LVRSKDLEQPLAISRVTPGSKAAIVNLCIGDVITAVNGENTSHMTHLEAQNKI

Parental  KGCTDSMTLTVARPEHKIWSPLATEEGKRHPYKMNLASEPQEVLHIGSAHNRSAMPFTASPASSTA-PRV
          K.CTDS.TL.VARP.HKIWSPL..EEGK.HPYKMNLAS.PQ.VLH.GSAHN.SAMPFT.SPASSTA.PRV
Retrocopy KVCTDSVTLMVARPKHKIWSPLMAEEGKHHPYKMNLASKPQKVLHMGSAHN*SAMPFTESPASSTA>PRV

Parental  ITNQYNNPAGLYSSENISNFNSAIESKTAA
          ITNQYNNPAGLYSSENISNFN.A.ESKT.A
Retrocopy ITNQYNNPAGLYSSENISNFNRAVESKTVA

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	218.78 RPM
SRP012922_cerebellum	0.00 RPM	59.80 RPM
SRP012922_heart	0.00 RPM	168.45 RPM
SRP012922_kidney	0.00 RPM	14.51 RPM
SRP012922_liver	0.00 RPM	95.21 RPM
SRP012922_lung	0.00 RPM	168.00 RPM
SRP012922_quadricep_muscle	0.00 RPM	187.97 RPM
SRP012922_spleen	0.00 RPM	108.05 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_1119 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 12 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011182	1 retrocopy	retro_btau_690,
Canis familiaris	ENSCAFG00000028553	1 retrocopy	retro_cfam_2080,
Dasypus novemcinctus	ENSDNOG00000012381	1 retrocopy	retro_dnov_1119 ,
Homo sapiens	ENSG00000107438	2 retrocopies	retro_hsap_1815, retro_hsap_2681,
Macaca mulatta	ENSMMUG00000000454	2 retrocopies	retro_mmul_1250, retro_mmul_1419,
Mus musculus	ENSMUSG00000055044	2 retrocopies	retro_mmus_2558, retro_mmus_779,
Nomascus leucogenys	ENSNLEG00000013055	3 retrocopies	retro_nleu_1819, retro_nleu_2767, retro_nleu_2970,
Oryctolagus cuniculus	ENSOCUG00000013643	1 retrocopy	retro_ocun_417,
Pongo abelii	ENSPPYG00000002507	2 retrocopies	retro_pabe_1109, retro_pabe_1485,
Pan troglodytes	ENSPTRG00000002783	1 retrocopy	retro_ptro_912,
Tarsius syrichta	ENSTSYG00000000834	2 retrocopies	retro_tsyr_1056, retro_tsyr_1224,
Tursiops truncatus	ENSTTRG00000012118	2 retrocopies	retro_ttru_1777, retro_ttru_976,