RetrogeneDB ID: retro_dnov_2304

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_62352:8204..8759(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: APOPT1
• Ensembl ID: ENSDNOG00000019553
• Aliases: None
• Description: apoptogenic 1, mitochondrial [Source:HGNC Symbol;Acc:20492]

Sequence

>retro_dnov_2304
TTGGTGGCCTTTCGGCTCGCGAGTAGGACTCTTCTCTCACTTCTGTGCCGCGTTTTCGTCTGCCCGGCCGCCAGCTGGCT
CCAGAGCATGGCGCCGAGTACAGGGAGGCAGCGTCAAGCCCGGTCTCGAGTTCCCACCATGATTGGATAGGACCCCCAGA
TAAATATTCAAACCTTCAACCTGTGCAGTTTTACGTCCCTGAAAAAAAATCACCACCGGAACAAAAGCTGAGAGAGCTGA
GATAAGAAACACAAGAATGGAATCAACAATTCTGGGCAAACCAGAATTTGACTTTCAGTAAGGAAAAAGAATTCATTCAT
TCACTTGAGACTGAAGGCCAGAGGCTTGGTAGTGAGAGCTGGATCAGGTCAAAAAGCAACACTGAATGCAGAGGAAATGG
CTGAGTTTTACAAGGAATTTTTAAATAAAAATATCCAGGAGCTTATGTATTTCAACAGAGACTGGTACACGCGTAAATTT
TCCCTCACATTCTTCATGGGATAAGTGGCCCTGGAGAGGATTTGGAAAAGGCTTGGGCTCAACCAGGAGACGACC

Alignment

ORF - retro_dnov_2304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.52 %
• Parental protein coverage: 98.93 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAAWRPRRRLLLPLLGRAFAGR-GRQPAPERGAERREAAPSRVSSSHHDWIGPPDKYSNLRPVQFYIPEN
          ..A.R...R.LL.LL.R.F....GRQ.APE.GAE.REAA.S.VSSSHHDWIGPPDKYSNL.PVQFY.P..
Retrocopy LVAFRLASRTLLSLLCRVFVCP<GRQLAPEHGAEYREAASSPVSSSHHDWIGPPDKYSNLQPVQFYVPXX

Parental  ESPLERKLRELRQETQEWNQRFWTNQNLTFSKEKE-EFIHSRLKARGLGGSAGSGQKPTLNAEEMAEFYK
          .SP.E.KLRELR.ETQEWNQ.FW.NQNLTFSKEKE..FIH.RLKARGL...AGSGQK.TLNAEEMAEFYK
Retrocopy XSPPEQKLRELR*ETQEWNQQFWANQNLTFSKEKE>SFIHLRLKARGLVVRAGSGQKATLNAEEMAEFYK

Parental  EFLNKNFQKHMYYNRGWYKHNFAVTFFLGKLTPKRIWKKFGLKQKKT
          EFLNKN.Q..MY.NR.WY...F..TFF.G.....RIWK..GL.Q..T
Retrocopy EFLNKNIQELMYFNRDWYTRKFSLTFFMG*VALERIWKRLGLNQETT

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	6.61 RPM
SRP012922_cerebellum	0.00 RPM	8.39 RPM
SRP012922_heart	0.00 RPM	4.64 RPM
SRP012922_kidney	0.00 RPM	4.38 RPM
SRP012922_liver	0.00 RPM	2.01 RPM
SRP012922_lung	0.00 RPM	3.82 RPM
SRP012922_quadricep_muscle	0.00 RPM	8.48 RPM
SRP012922_spleen	0.00 RPM	4.24 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_2304 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000030884	2 retrocopies	retro_cfam_1514, retro_cfam_396,
Dasypus novemcinctus	ENSDNOG00000019553	5 retrocopies	retro_dnov_1003, retro_dnov_2304 , retro_dnov_2391, retro_dnov_441, retro_dnov_777,
Erinaceus europaeus	ENSEEUG00000011728	1 retrocopy	retro_eeur_107,
Felis catus	ENSFCAG00000027939	3 retrocopies	retro_fcat_482, retro_fcat_549, retro_fcat_649,
Microcebus murinus	ENSMICG00000009792	1 retrocopy	retro_mmur_744,
Mustela putorius furo	ENSMPUG00000002350	2 retrocopies	retro_mputfur_1406, retro_mputfur_166,
Otolemur garnettii	ENSOGAG00000015416	1 retrocopy	retro_ogar_1394,