RetrogeneDB ID: retro_dnov_2319

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_63711:4782..5189(+)
• 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_2319
GGATTGGACGCTGCTGGCAAGAAGATCATTCTGTAGAAACTGAAGTTAGGGGAGGTAGTCACCACCATTGGTTTTAATGA
GGAAACAGTAGAATATAAGAACATTTGTTTCACAATATGGGGTGTTGGTGGTCAAGATAAAATTAGGCCTCTCTGGAGGC
ATTACTTCCAAAACACCCAGAGTCTTATTTTTGTGGTAGATAGCAAAGATCATGAAAGAATTCAAGAAGGAGCAGCAGAG
CTGCAGAAAATGCATCAGGAAGATGAGTTGTGAGATGCAGTGCTGCTGCTGTTTGCAAACAAACGTATTTGCCAAATGCT
ATGGTCATCAGTGAAATGACAGATAAATTAGGTCTTCAGTCCCTTCTTAACAGAACATGGTATGTTCAAGACTTGTGCTA
CACAAGG

Alignment

ORF - retro_dnov_2319 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.43 %
• Parental protein coverage: 88.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GLDAAGKTTILYKLKLGEIVTTIPTIGFNVETVEYKNICFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVD
          GLDAAGK..IL.KLKLGE.VT...TIGFN.ETVEYKNICFT.W.VGGQDKIRPLWRHYFQNTQ.LIFVVD
Retrocopy GLDAAGKKIIL*KLKLGEVVT---TIGFNEETVEYKNICFTIWGVGGQDKIRPLWRHYFQNTQSLIFVVD

Parental  SNDRERVQESADELQKMLQEDELRDAVLLVFANKQ-DMPNAMPVSELTDKLGLQHLRSRTWYVQATCATQ
          S.D.ER.QE.A.ELQKM.QEDEL.DAVLL.FANK....PNAM..SE.TDKLGLQ.L..RTWYVQ..C.T.
Retrocopy SKDHERIQEGAAELQKMHQEDEL*DAVLLLFANKR<YLPNAMVISEMTDKLGLQSLLNRTWYVQDLCYTR

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	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	0.17 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_2319 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,