RetrogeneDB ID: retro_dnov_1749

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_28668:13864..14598(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TDG
• Ensembl ID: ENSDNOG00000013722
• Aliases: None
• Description: thymine-DNA glycosylase [Source:HGNC Symbol;Acc:11700]

Sequence

>retro_dnov_1749
ATGACAGGGCTGAGTGAAGTCCAGTTGAATCATATGAATGATCATACTTTACCAGGGACGTATGGTATTGGATTTATCAA
CATGATGGAAAGGACAACACCAGGCAGTCGAGATCTTTCTAGTAAAGAATTTCATGAAAGAGAATGTATTCTGGTGCAGA
AATTACAGAAATAGCCACAAATTGCGGTGTTTAATAGAAAATGTATTTATGAAATTTTTAGTAAAGAAGTTCTTGGAGTA
AAGGTTAAGAACTTAGAATTTGGGCGTCAACCCCATGAGATCCCAGACACAGAAACACTGCTATGTTATGCCATCATACA
GCACAAGATGTGCTCAGTTTCCCAAGCCCAGGACAAAGTTCATTACTACATGAAGCTGAAGGACTTAAGGGGTCAGTGGA
AAGGCATTGACCAATATGCAGACATTCAGGAGGTGTAATATGTATTTGACTTACAGCTTGCCCAAGAGATGCAAAGAAGA
TGGTGGTTAAGGAAGAAAACTATGACCTGGGTCGTGAAGCAGCATATGGTGGTGCCTATGGCGAGAATCCATGCAATAGT
GAACCTTGCACTTCTCTTCACATGTACTGACAGCTAACAGTGCGCAGTTAAGTAGAGGAGCTCCTTTCAGGGACATTCCA
AATGGGCAGCAGATGACCCAGCCGTTTACAGACCAGATTCCAGCCTTTCATAATCCTTGTGGGATGCCAGAACAGGAAGA
AGGGAAGCCATGCT

Alignment

ORF - retro_dnov_1749 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.19 %
• Parental protein coverage: 52.56 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  MSGLSEVQLNHMDDHTLPGKYGIGFTNMVERTTPGSKDLSSKEFREGGRILVQKLQKYQPRIAVFNGKCI
          M.GLSEVQLNHM.DHTLPG.YGIGF.NM.ERTTPGS.DLSSKEF.E...ILVQKLQK..P.IAVFN.KCI
Retrocopy MTGLSEVQLNHMNDHTLPGTYGIGFINMMERTTPGSRDLSSKEFHERECILVQKLQK*-PQIAVFNRKCI

Parental  YEIFSKEVFGVKVKNLEF-GLQPHKIPDTETLCYVMPSSSARCAQFPR-AQDKVHYYIKLKDLRDQLKGI
          YEIFSKEV.GVKVKNLEF.G..P.....T...CYVMPS.S.RCAQFP..AQDKVHYY.KLKDLR.Q.KGI
Retrocopy YEIFSKEVLGVKVKNLEF>GVNPMR-SQTQKHCYVMPSYSTRCAQFPK<AQDKVHYYMKLKDLRGQWKGI

Parental  ERNTDVQEVQYTFDLQLAQE-DAKKMAVKEEKYDPGYEAAYGGAYGENPCNSEPCS-FSSNGLT-DSAQL
          ....D.QEV.Y.FDLQLAQE.DAKKM.VKEE.YD.G.EAAYGGAYGENPCNSEPC..FSS..LT..SAQL
Retrocopy DQYADIQEV*YVFDLQLAQE<DAKKMVVKEENYDLGREAAYGGAYGENPCNSEPCT<FSSHVLTANSAQL

Parental  SRESTFSDIPNGQWMTQPFTDQIPAFNNHCGTPEQEE-GSHA
          SR...F.DIPNGQ.MTQPFTDQIPAF.N.CG.PEQEE.GSHA
Retrocopy SRGAPFRDIPNGQQMTQPFTDQIPAFHNPCGMPEQEE>GSHA

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	36.56 RPM
SRP012922_cerebellum	0.00 RPM	30.93 RPM
SRP012922_heart	0.00 RPM	15.08 RPM
SRP012922_kidney	0.00 RPM	9.58 RPM
SRP012922_liver	0.00 RPM	40.87 RPM
SRP012922_lung	0.00 RPM	50.70 RPM
SRP012922_quadricep_muscle	0.00 RPM	28.56 RPM
SRP012922_spleen	0.00 RPM	46.93 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_1749 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 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013722	1 retrocopy	retro_dnov_1749 ,
Echinops telfairi	ENSETEG00000019930	1 retrocopy	retro_etel_2184,
Homo sapiens	ENSG00000139372	1 retrocopy	retro_hsap_980,
Loxodonta africana	ENSLAFG00000003813	1 retrocopy	retro_lafr_460,
Mus musculus	ENSMUSG00000034674	4 retrocopies	retro_mmus_1125, retro_mmus_1363, retro_mmus_3040, retro_mmus_637,
Oryctolagus cuniculus	ENSOCUG00000016313	1 retrocopy	retro_ocun_1289,
Rattus norvegicus	ENSRNOG00000027124	1 retrocopy	retro_rnor_2286,