RetrogeneDB ID: retro_dnov_1035

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_138941:1..797(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UAP1
• Ensembl ID: ENSDNOG00000024661
• Aliases: None
• Description: UDP-N-acteylglucosamine pyrophosphorylase 1 [Source:HGNC Symbol;Acc:12457]

Sequence

>retro_dnov_1035
AAGGCCATTGAAGGATTTAACCAGTCCTCTTACCAAGAGAAAATGGATGCATGAATGAAACCTGTAGCTCGAGAGGTATT
GGGCAGTGCTACTAGGGATCAGGATCAACTCCAGGCCTGGGAAAGTGAAGGACTTTTCCAGATTTCTCAAAACAAAGTAG
CAGTTCTTCTTCTAGCTGGTGGTCAGGGGACAAGACTCGACGTTGCCTATCCTAAAGGGAATGTATGATGTTAGTTTGCC
ATCACACAAAACACTTTTTCAGATTCTAGCAGAGCGTATCGTGAAGCTACAACAGTTAGCAGAAAAATATCATGGCAAAA
AGTGTACCATACCATGGTATATAATGACCAGTGGCAGAACAATGGAATATACAAAGGAATTCTTCATAAAGCACAAGTAC
TTTGGGTTAAAAAAAGAGAATATAATCTTTTTTCAGCAAGGAATGCTGCCTGTTATGAAGTTTGATGGGAAAATTATTTT
AGAAGAGAAGAGCAAAGTTTCTATGGCTCCAGATGGGAATGGTGGTCTTTATCGGGCTCTTGCAGCCCAGAATATTGTGG
AAGATACAGAGCAAAGAGGCATTTGGAATATTCATGTCTATTGTGGTGATAGCATATTAGTTAAAGTGGTAGATCCACTG
TTCATTGGATTTTGCATTCAGAAAGGAGCAGACTGTGGAGCAAAGTTAGTAGAGAAAACAAACCCTATGGAACCAGTTGG
AGTGGTTTGCCGAGTGGATGGAGTGTACCAGGTGGTAGAATATAGCGAGATTTCCCTGGCAACAGCACACACAAAA

Alignment

ORF - retro_dnov_1035 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.35 %
• Parental protein coverage: 50.77 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KAIEGFNQSSYQEKVDARMEPVPREVLGSATRDQDQLQAWESEGLFQISQNKVAVLLLAGGQGTRLGVAY
          KAIEGFNQSSYQEK.DA.M.PV.REVLGSATRDQDQLQAWESEGLFQISQNKVAVLLLAGGQGTRL.VAY
Retrocopy KAIEGFNQSSYQEKMDA*MKPVAREVLGSATRDQDQLQAWESEGLFQISQNKVAVLLLAGGQGTRLDVAY

Parental  PKG-MYDVGLPSHKTLFQIQAERILKLQQLAEKYHGKKCTIPWYIMTSGRTMESTKEFFIKHKYFGLKKE
          PKG.MYDV.LPSHKTLFQI.AERI.KLQQLAEKYHGKKCTIPWYIMTSGRTME.TKEFFIKHKYFGLKKE
Retrocopy PKG>MYDVSLPSHKTLFQILAERIVKLQQLAEKYHGKKCTIPWYIMTSGRTMEYTKEFFIKHKYFGLKKE

Parental  NVIFFQQGMLPAMKFDGKIILEEKSKVSMAPDGNGGLYRALAAQNIVEDMEQRGIWSIHVYCVDNILVKV
          N.IFFQQGMLP.MKFDGKIILEEKSKVSMAPDGNGGLYRALAAQNIVED.EQRGIW.IHVYC.D.ILVKV
Retrocopy NIIFFQQGMLPVMKFDGKIILEEKSKVSMAPDGNGGLYRALAAQNIVEDTEQRGIWNIHVYCGDSILVKV

Parental  ADPRFIGFCIQKGADCGAKVVEKTNPTEPVGVVCRVDGVYQVVEYSEISLATAQKR
          .DP.FIGFCIQKGADCGAK.VEKTNP.EPVGVVCRVDGVYQVVEYSEISLATA...
Retrocopy VDPLFIGFCIQKGADCGAKLVEKTNPMEPVGVVCRVDGVYQVVEYSEISLATAHTK

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	2.53 RPM	183.58 RPM
SRP012922_cerebellum	0.41 RPM	31.07 RPM
SRP012922_heart	0.23 RPM	18.10 RPM
SRP012922_kidney	0.27 RPM	20.26 RPM
SRP012922_liver	0.31 RPM	29.41 RPM
SRP012922_lung	0.46 RPM	60.33 RPM
SRP012922_quadricep_muscle	1.21 RPM	27.87 RPM
SRP012922_spleen	0.57 RPM	29.19 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_1035 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 6 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000004264	1 retrocopy	retro_cjac_2537,
Cavia porcellus	ENSCPOG00000004568	5 retrocopies	retro_cpor_1186, retro_cpor_1187, retro_cpor_1188, retro_cpor_1189, retro_cpor_511,
Dasypus novemcinctus	ENSDNOG00000024661	1 retrocopy	retro_dnov_1035 ,
Macaca mulatta	ENSMMUG00000019514	1 retrocopy	retro_mmul_1238,
Rattus norvegicus	ENSRNOG00000002926	1 retrocopy	retro_rnor_2277,
Tarsius syrichta	ENSTSYG00000002725	3 retrocopies	retro_tsyr_121, retro_tsyr_390, retro_tsyr_582,