RetrogeneDB ID: retro_dnov_2354

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_66986:4114..4679(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000025615
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: HRAS
• Ensembl ID: ENSDNOG00000015293
• Aliases: None
• Description: Harvey rat sarcoma viral oncogene homolog [Source:HGNC Symbol;Acc:5173]

Sequence

>retro_dnov_2354
ATGACTGAGTACAAACTGGTAGTGGTTGAAGCAGGTGGTGTTGGGGAAAGTGCACTGGCAGTGCAGCTAATACAGAACCA
TTTTGTGGATGAGTATGATCCCACCATAGGGGATTCTTCCCCAAAACTGGTGTTTATAGGTGGTGAAACCTGTCTGCTAT
ACATACTGACAAGCCAGTACACAGCCAGACAAGAGGAGTACAGTGCCATGAGAGATCAATGCATGAGGACAGGCAAAGGG
TTCCCTTGTGTGTTTGCCATCCGTAATAGCAAATCATTTGCAGATATTAACCTCTACAGAGCAAAGTAGGCAAGTTAAAG
ATTCAGATGATGTACCTATGTTGCTGGTAGGAAACAAGTGTGATTTGTCAACAAGGACAGTTGACACAAAAGAAGCCCAT
GAACTGGCCAGGAGTTATGGGATTCCATTCATTGAAACCTCAGCCAAGACCAGAGAGAGTGTAGAAGACGCCTTTTACAC
ATTGGTAAGAGAAATATGTCAGTGCCGAATGAAAAAACTCAACAGCAGTCGTGATAGGACTCGAGGTTGCATGGGGTTGT
CATGT

Alignment

ORF - retro_dnov_2354 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.06 %
• Parental protein coverage: 98.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILD---TAGQEEYSAM
          MTEYKLVVV.AGGVG.SAL..QLIQNHFVDEYDPTI.DS..K.V.I.GETCLL.IL....TA.QEEYSAM
Retrocopy MTEYKLVVVEAGGVGESALAVQLIQNHFVDEYDPTIGDSSPKLVFIGGETCLLYILTSQYTARQEEYSAM

Parental  RDQYMRTGEGFLCVFAINNTKSFEDIHQYR-EQIKRVK-DSDDVPMVLVGNKCDLPARTVDARQAQELAC
          RDQ.MRTG.GF.CVFAI.N.KSF.DI..YR.......K.DSDDVPM.LVGNKCDL..RTVD...A.ELA.
Retrocopy RDQCMRTGKGFPCVFAIRNSKSFADINLYR<SKVGKLK<DSDDVPMLLVGNKCDLSTRTVDTKEAHELAR

Parental  SYGLPYVETSAKTRQGVEDAFYTLVREIRQHKLRKLNPPDESGPGCADCKC
          SYG.P..ETSAKTR..VEDAFYTLVREI.Q....KLN.......GC....C
Retrocopy SYGIPFIETSAKTRESVEDAFYTLVREICQCRMKKLNSSRDRTRGCMGLSC

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	11.67 RPM
SRP012922_cerebellum	0.00 RPM	17.73 RPM
SRP012922_heart	0.00 RPM	7.19 RPM
SRP012922_kidney	0.00 RPM	23.00 RPM
SRP012922_liver	0.00 RPM	8.20 RPM
SRP012922_lung	0.00 RPM	17.72 RPM
SRP012922_quadricep_muscle	0.00 RPM	37.73 RPM
SRP012922_spleen	0.00 RPM	9.39 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_2354 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 8 parental genes, and 32 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007809	5 retrocopies	retro_dnov_101, retro_dnov_1617, retro_dnov_1764, retro_dnov_628, retro_dnov_94,
Dasypus novemcinctus	ENSDNOG00000015293	3 retrocopies	retro_dnov_1358, retro_dnov_154, retro_dnov_2354 ,
Dasypus novemcinctus	ENSDNOG00000017413	1 retrocopy	retro_dnov_573,
Dasypus novemcinctus	ENSDNOG00000019724	18 retrocopies	retro_dnov_1243, retro_dnov_1249, retro_dnov_1323, retro_dnov_1395, retro_dnov_1574, retro_dnov_1710, retro_dnov_1763, retro_dnov_1841, retro_dnov_186, retro_dnov_1976, retro_dnov_2033, retro_dnov_217, retro_dnov_2679, retro_dnov_298, retro_dnov_318, retro_dnov_719, retro_dnov_761, retro_dnov_84,
Echinops telfairi	ENSETEG00000019899	2 retrocopies	retro_etel_1028, retro_etel_391,
Macropus eugenii	ENSMEUG00000008467	1 retrocopy	retro_meug_852,
Microcebus murinus	ENSMICG00000006472	1 retrocopy	retro_mmur_948,
Rattus norvegicus	ENSRNOG00000016611	1 retrocopy	retro_rnor_2941,