RetrogeneDB ID: retro_dnov_645

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_717:112538..112827(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBD2
• Ensembl ID: ENSDNOG00000019125
• Aliases: None
• Description: pterin-4 alpha-carbinolamine dehydratase/dimerization cofactor of hepatocyte nuclear factor 1 alpha (TCF1) 2 [Source:HGNC Symbol;Acc:24474]

Sequence

>retro_dnov_645
GCGGCAGCAGTGGGGGTGTACAGGGCAACGCGGCGCCTGTTGGGGGCGCTGCAGGGGGGGACCCAAGCCTTGCAGCCGTG
TCAGCAGATGCTCAGTAGTTGACAGCAGAGGAGAGAAACCAAGTTATACTTGACCTTAAAGCAGCAGAATGGTCGGAATT
AAGTGAGAGAGATGCCATTTACAAAGAATTCTCATTTAAAAATTTTAATCAGGCATTGGTTTTATGTCCTGAGTTGCCCT
ACAAGCAGAAAAGATGAATTGTCACCCAGAATGGTTCAGTGTATACAAC

Alignment

ORF - retro_dnov_645 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.77 %
• Parental protein coverage: 75.78 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  AAALRARGATLRLFGALRRE-DTRLAAMSADAHWLTAEERNQVILDLKAAGWSELSERNAIYKEFSFKNF
          AAA.....AT.RL.GAL....D..LAA.SADA..LTAEERNQVILDLKAA.WSELSER.AIYKEFSFKNF
Retrocopy AAAVGVYRATRRLLGALQGG<DPSLAAVSADAQ*LTAEERNQVILDLKAAEWSELSERDAIYKEFSFKNF

Parental  NQA-FGFMSRVALQAEKMNHHPEWFNVYN
          NQA..GFMS.VALQAEKMN.HPEWF.VYN
Retrocopy NQA<IGFMS*VALQAEKMNCHPEWFSVYN

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	0.19 RPM	5.64 RPM
SRP012922_cerebellum	0.00 RPM	3.71 RPM
SRP012922_heart	0.00 RPM	2.78 RPM
SRP012922_kidney	0.00 RPM	4.65 RPM
SRP012922_liver	0.00 RPM	4.02 RPM
SRP012922_lung	0.00 RPM	8.25 RPM
SRP012922_quadricep_muscle	0.00 RPM	8.31 RPM
SRP012922_spleen	0.00 RPM	6.98 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_645 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000019125	2 retrocopies	retro_dnov_645 , retro_dnov_660,
Equus caballus	ENSECAG00000015810	2 retrocopies	retro_ecab_489, retro_ecab_871,
Erinaceus europaeus	ENSEEUG00000007051	1 retrocopy	retro_eeur_190,
Echinops telfairi	ENSETEG00000016658	2 retrocopies	retro_etel_1252, retro_etel_75,
Macropus eugenii	ENSMEUG00000003784	1 retrocopy	retro_meug_1185,
Myotis lucifugus	ENSMLUG00000012638	1 retrocopy	retro_mluc_1445,
Monodelphis domestica	ENSMODG00000014351	1 retrocopy	retro_mdom_1369,
Pteropus vampyrus	ENSPVAG00000000384	2 retrocopies	retro_pvam_63, retro_pvam_750,
Tursiops truncatus	ENSTTRG00000016874	3 retrocopies	retro_ttru_1135, retro_ttru_359, retro_ttru_511,