RetrogeneDB ID: retro_dnov_1716

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_27393:7020..7336(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPD1
• Ensembl ID: ENSDNOG00000018773
• Aliases: None
• Description: small nuclear ribonucleoprotein D1 polypeptide 16kDa [Source:HGNC Symbol;Acc:11158]

Sequence

>retro_dnov_1716
TTTTGGGTGAAAGTGAGTCATGAAACCGTAACCCTTGAATTGAACAATGGAACTCAGGTCTGTGGAACCACCACAGGCAT
GGACGTCAGCATGAAAACACATCTGAAAGCCACGAAAATGACCCTGAAGAGCAGAGAAACTGTATAGCTGGAAACACTAA
GTATTGGAGGAAGTGATCATCGATATCTTATTCTGCTAGATGGCTTGCCTCTGATTATACTACTTGTAGATGTTGAACCT
AAGGTGAAATTCAAGAAAAGGGAAGTTGTTGGCAGGAAGAAGAAGAGGCTGTGGTAGAGAAAGAGGGGGTCCTAGG

Alignment

ORF - retro_dnov_1716 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.75 %
• Parental protein coverage: 92.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  FLMKLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLP
          F..K.SHETVT.EL.NGTQV.GT.TG.DVSM.THLKA.KMTLK.RE.V.LETLSI.G...RY.IL.D.LP
Retrocopy FWVKVSHETVTLELNNGTQVCGTTTGMDVSMKTHLKATKMTLKSRETV*LETLSIGGSDHRYLILLDGLP

Parental  LDTLLVDVEPKVKSKKREA-XAGRGRGRGRGRGRGR
          L..LLVDVEPKVK.KKRE...AGR.RG.GR.RG..R
Retrocopy LIILLVDVEPKVKFKKREV>LAGRRRGCGRERGGPR

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	39.48 RPM
SRP012922_cerebellum	0.00 RPM	21.31 RPM
SRP012922_heart	0.00 RPM	9.28 RPM
SRP012922_kidney	0.00 RPM	20.26 RPM
SRP012922_liver	0.00 RPM	8.51 RPM
SRP012922_lung	0.00 RPM	26.57 RPM
SRP012922_quadricep_muscle	0.00 RPM	8.13 RPM
SRP012922_spleen	0.00 RPM	32.51 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_1716 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 13 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000006364	1 retrocopy	retro_acar_129,
Bos taurus	ENSBTAG00000008292	3 retrocopies	retro_btau_144, retro_btau_706, retro_btau_84,
Canis familiaris	ENSCAFG00000018247	1 retrocopy	retro_cfam_373,
Dasypus novemcinctus	ENSDNOG00000018773	4 retrocopies	retro_dnov_1254, retro_dnov_1716 , retro_dnov_1832, retro_dnov_2403,
Felis catus	ENSFCAG00000012352	1 retrocopy	retro_fcat_1885,
Macaca mulatta	ENSMMUG00000003992	2 retrocopies	retro_mmul_887, retro_mmul_891,
Mustela putorius furo	ENSMPUG00000005567	1 retrocopy	retro_mputfur_185,
Oryctolagus cuniculus	ENSOCUG00000023761	1 retrocopy	retro_ocun_224,
Pongo abelii	ENSPPYG00000025874	3 retrocopies	retro_pabe_254, retro_pabe_948, retro_pabe_952,
Pan troglodytes	ENSPTRG00000009909	2 retrocopies	retro_ptro_291, retro_ptro_781,
Pteropus vampyrus	ENSPVAG00000005511	1 retrocopy	retro_pvam_450,
Rattus norvegicus	ENSRNOG00000013714	2 retrocopies	retro_rnor_2671, retro_rnor_2729,
Tursiops truncatus	ENSTTRG00000002654	2 retrocopies	retro_ttru_1566, retro_ttru_1890,