RetrogeneDB ID: retro_dnov_962

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_12761:10831..11253(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBE2W
• Ensembl ID: ENSDNOG00000012909
• Aliases: None
• Description: ubiquitin-conjugating enzyme E2W (putative) [Source:HGNC Symbol;Acc:25616]

Sequence

>retro_dnov_962
AAATGACTACAGAAAGAACTGTTGGCTTTGCGAAATGACACATCTCCTGGGATGACTTTAAATGAAAAGAGTGTTCAGAA
TTCAATCACACAGGGGATCCTGAACATGAAAGGCACACCAGGTACTTTATATGAAGGGGAAACTTTTCAGCTTCTATTTA
AGTTTAGCAGTCAATATCCTTTGGCTTTCCTCAGGTCGTATTTACTGGTGAAATTACTGCTGTTCATGTTTATGGCAATG
GTCATATCTGTTTATCCATTATAACAGAAGACTGGTCCCCCATGCTCTCAGTCTAGTCATTTTGTCTTAGCACTATTAGC
ATGCTTTCCAGCTGCAAAGAAAAGAGATGACCACCAGATAATCCTTTTTATGTTTGAACATGTAACAAGAATTCAAAGAA
AACAAAGTGGTGGTATCATGAT

Alignment

ORF - retro_dnov_962 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.17 %
• Parental protein coverage: 99.31 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KRLQKELLALQNDPPPGMTLNEKSVQNSITQWIVDMEGAPGTLYEGEKFQLLFKFSSRYP-FDSPQVMFT
          K.LQKELLAL.ND..PGMTLNEKSVQNSITQ.I..M.G.PGTLYEGE.FQLLFKFSS.YP.F..PQV.FT
Retrocopy K*LQKELLALRNDTSPGMTLNEKSVQNSITQGILNMKGTPGTLYEGETFQLLFKFSSQYP<FGFPQVVFT

Parental  GENIPVHPHVYSNGHICLSILTEDWSPALSVQSVCLSIISMLSSCKEKRRPPDNSFYVRTCNKNPKKTKW
          GE...VH..VY.NGHICLSI.TEDWSP.LSV.S.CLS.ISMLSSCKEKR.PPDN.FYV.TCNKN.KKTKW
Retrocopy GEITAVH--VYGNGHICLSIITEDWSPMLSV*SFCLSTISMLSSCKEKR*PPDNPFYV*TCNKNSKKTKW

Parental  WYHD
          WYHD
Retrocopy WYHD

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	3.50 RPM
SRP012922_cerebellum	1.37 RPM	1.51 RPM
SRP012922_heart	0.00 RPM	0.70 RPM
SRP012922_kidney	0.00 RPM	2.46 RPM
SRP012922_liver	0.00 RPM	2.94 RPM
SRP012922_lung	0.00 RPM	1.83 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.87 RPM
SRP012922_spleen	0.00 RPM	1.83 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_962 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 7 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005910	4 retrocopies	retro_chof_1114, retro_chof_1974, retro_chof_889, retro_chof_957,
Dasypus novemcinctus	ENSDNOG00000012909	2 retrocopies	retro_dnov_1378, retro_dnov_962 ,
Erinaceus europaeus	ENSEEUG00000011886	1 retrocopy	retro_eeur_41,
Myotis lucifugus	ENSMLUG00000027009	3 retrocopies	retro_mluc_1510, retro_mluc_1900, retro_mluc_619,
Sorex araneus	ENSSARG00000007886	2 retrocopies	retro_sara_306, retro_sara_464,
Tupaia belangeri	ENSTBEG00000011410	3 retrocopies	retro_tbel_1929, retro_tbel_4440, retro_tbel_682,
Vicugna pacos	ENSVPAG00000001527	2 retrocopies	retro_vpac_115, retro_vpac_227,