RetrogeneDB ID: retro_dnov_1407

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_197826:996..1242(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ARF5
• Ensembl ID: ENSDNOG00000013387
• Aliases: None
• Description: ADP-ribosylation factor 5 (Predicted) [Source:UniProtKB/TrEMBL;Acc:C0RW27]

Sequence

>retro_dnov_1407
GAAAATTCAAGAAGGAGCAGAAGAGCTGCAGAAAATGCTTCAAGAAAAGATTAGTTGTGAGATGCAGTACTGCTCCTGTT
TGCAAACAAACAGGATTTGCCAAATGCTATGGACATCAGTGAAATGACAGATAAATTAAGTCTTCAGTCCTCTCAAAACA
AAACATAGTATATTCAAGCTACTTATGCTACACAAGGAACTCGTCTATATGAGGAATTTGACTGACTGTCAAACGACCTT
TCAAAA

Alignment

ORF - retro_dnov_1407 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.88 %
• Parental protein coverage: 52.23 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ERVQESADELQKMLQEDELRDAVLLVFANKQDMPNAMPVSELTDKLGLQHLRSRTWYVQATCATQGTGLY
          E....S..........D.L.DAVLL.FANKQD.PNAM..SE.TDKL.LQ.....T.Y.QAT.ATQGT.LY
Retrocopy ENSRRSRRAAENASRKD*L*DAVLLLFANKQDLPNAMDISEMTDKLSLQSSQNKT*YIQATYATQGTRLY

Parental  DGLDWLSHELSK
          ...D.LS..LSK
Retrocopy EEFD*LSNDLSK

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	1.75 RPM
SRP012922_cerebellum	0.00 RPM	48.94 RPM
SRP012922_heart	0.00 RPM	1.16 RPM
SRP012922_kidney	0.00 RPM	3.56 RPM
SRP012922_liver	0.00 RPM	0.77 RPM
SRP012922_lung	0.00 RPM	3.67 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.35 RPM
SRP012922_spleen	0.00 RPM	5.84 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_1407 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Ciona intestinalis	ENSCING00000021790	1 retrocopy	retro_cint_10,
Dasypus novemcinctus	ENSDNOG00000010454	3 retrocopies	retro_dnov_2375, retro_dnov_2459, retro_dnov_26,
Dasypus novemcinctus	ENSDNOG00000013387	5 retrocopies	retro_dnov_1132, retro_dnov_1251, retro_dnov_1260, retro_dnov_1407 , retro_dnov_2319,
Gorilla gorilla	ENSGGOG00000016749	1 retrocopy	retro_ggor_1016,
Monodelphis domestica	ENSMODG00000015229	1 retrocopy	retro_mdom_905,
Otolemur garnettii	ENSOGAG00000013336	1 retrocopy	retro_ogar_378,
Tursiops truncatus	ENSTTRG00000006043	1 retrocopy	retro_ttru_493,