RetrogeneDB ID: retro_dnov_1254

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_17007:57774..58095(-)
• 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_1254
GAGATTTTTTATGAAACTGTAACCACTGAATTGAAGAATGGAACATATTTCCATGGAACCACCACAGGTGTGCTCGTCAG
CATGAATACACGTCTTAAAGCTGTGAAAATGACCCTGAAGAACAGAGAACATGTACAGCTACATATACTGAGGATTTGAG
GAAATAATATTCGATCATTTATTCTGCCAGACAGCTTTCCTCTGGTTACACTACTTGTGGATGTTGAACCTAAGGTGAAA
TCCAAGAAAAGGGAAGCTGTTGCAGGAAAAGGAAGAGGCCAAGGTAGAGGAAGAGGAAGAGGATGTGGCTTTGGTAGAGG
A

Alignment

ORF - retro_dnov_1254 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.29 %
• Parental protein coverage: 93.86 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KLSHETVTIELKNGTQVHGTITGVDVSMNTHLKAVKMTLKNREPVQLETLSIRGNNIRYFILPDSLPLDT
          ....ETVT.ELKNGT..HGT.TGV.VSMNT.LKAVKMTLKNRE.VQL..L.I.GNNIR.FILPDS.PL.T
Retrocopy EIFYETVTTELKNGTYFHGTTTGVLVSMNTRLKAVKMTLKNREHVQLHILRI*GNNIRSFILPDSFPLVT

Parental  LLVDVEPKVKSKKREAXAGRGRGRGRGRGRGRGRGRG
          LLVDVEPKVKSKKREA................G.GRG
Retrocopy LLVDVEPKVKSKKREAVXXXXXXXXXXXXXXCGFGRG

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	1.17 RPM	39.48 RPM
SRP012922_cerebellum	0.82 RPM	21.31 RPM
SRP012922_heart	0.46 RPM	9.28 RPM
SRP012922_kidney	0.82 RPM	20.26 RPM
SRP012922_liver	0.31 RPM	8.51 RPM
SRP012922_lung	0.76 RPM	26.57 RPM
SRP012922_quadricep_muscle	0.35 RPM	8.13 RPM
SRP012922_spleen	0.57 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_1254 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.

---

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,