RetrogeneDB ID: retro_dnov_1590

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_241891:902..1335(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATXN7L3
• Ensembl ID: ENSDNOG00000003379
• Aliases: None
• Description: ataxin 7-like 3 [Source:HGNC Symbol;Acc:25416]

Sequence

>retro_dnov_1590
AATTTTGAGATTGTGCACCAAATGGAGTTTGGACATCTTTGGAGATGATTTCAACCAATGGACTAGGAAAGAAGTGTGTT
TGCCCATTTGAAGATGCAGCATCACTGCCTCCAGCTTTGCTCCCCATCTGGAGAAATGCTGGGAATGGGTGAACAACAGC
TGCATTGCAGCCTCCAGTTTGCCAATAGCAACAGTAGGAACAAGTCTGAAAGTGACCATGTGGACGATGATGGCATCAAT
GGCAATGATGGGTCCTGTGGCTCGAGAAGAAAGCTAAGAAGAGAAAGTCAGTAAGAACCCCAATTCCTCTTGATCTAAGT
CTTTAGAACACAAAAACATTGAGTTTAGCAATCCAGGTTCTTTTAAGCATCATAACTCCACTGGGATGAGCTATGAGACC
ATGGGGCCAGAGGAACTGTGATGCCTGCTTACC

Alignment

ORF - retro_dnov_1590 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 62.25 %
• Parental protein coverage: 80.33 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  DFEIVDQP-GLDIFGQVFNQWKSKECVCPNCSRSIAASRFAPHLEKC-LGMGRNSSRIANRRIANSNNMN
          .FEIV.Q...LDIFG..FNQW..KE...P....SI.AS.FAPHLEKC.LGMG...........ANSN..N
Retrocopy NFEIVHQM>SLDIFGDDFNQWTRKEVCLPI*RCSITASSFAPHLEKC<LGMGEQQLH-CSLQFANSNSRN

Parental  KSESDQEDNDDINDNDWSYGS-EKKAKKRKS-DKNPNSPRRSKSLKHKNGELSNSDPFKYNNSTGISYET
          KSESD..D.D.IN.ND.S.GS.EKKAKKRKS..KNPNS...SKSL.HKN.E.SN...FK..NSTG.SYET
Retrocopy KSESDHVDDDGINGNDGSCGS<EKKAKKRKS<SKNPNS-S*SKSLEHKNIEFSNPGSFKHHNSTGMSYET

Parental  LGPEELRSLLT
          .GPEEL..LLT
Retrocopy MGPEEL*CLLT

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	6.22 RPM
SRP012922_cerebellum	0.00 RPM	10.59 RPM
SRP012922_heart	0.00 RPM	2.32 RPM
SRP012922_kidney	0.00 RPM	2.46 RPM
SRP012922_liver	0.00 RPM	3.41 RPM
SRP012922_lung	0.00 RPM	5.65 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.21 RPM
SRP012922_spleen	0.00 RPM	4.92 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_1590 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 5 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000003379	13 retrocopies	retro_dnov_1026, retro_dnov_1144, retro_dnov_1211, retro_dnov_1590 , retro_dnov_1902, retro_dnov_2325, retro_dnov_2448, retro_dnov_2497, retro_dnov_2600, retro_dnov_516, retro_dnov_86, retro_dnov_867, retro_dnov_961,
Homo sapiens	ENSG00000087152	1 retrocopy	retro_hsap_4847,
Gorilla gorilla	ENSGGOG00000010959	1 retrocopy	retro_ggor_3023,
Myotis lucifugus	ENSMLUG00000006416	1 retrocopy	retro_mluc_41,
Macaca mulatta	ENSMMUG00000029935	1 retrocopy	retro_mmul_820,