RetrogeneDB ID: retro_dnov_2375

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_68815:8134..8517(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000015266
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ARF1
• Ensembl ID: ENSDNOG00000010454
• Aliases: None
• Description: ADP-ribosylation factor 1 [Source:HGNC Symbol;Acc:652]

Sequence

>retro_dnov_2375
TCAGTGTGGAAACTGGAGTACAAAAACAGCCTCACTGTGCGAGACATGGGTGGCCAGTACAAGATCCAGCCTCTGTGGCG
CCACTATTTCCAGAACACACCAGGTCTCGTCTTTGTGGTCGACAGCAGTGACCAAGAGTGTGTGAACGAGGCCCACAGGG
AGCTCCTGAGGGTGCTGGCAGAAGATGAGCTCAGGGGCAGTGTCACTGTGTTCCCTAACAAGCAGGATCTTCCCAGTGCC
CTGAATGCTGCTGACGTTGCTGGTGAACTGGGATTGCATCCTCTGTGCCACAGGAACTGGTACACTGAGGCCATGTGTGC
CACCAGCAGAGACAGGCTTTACAAGGACTGGACTGGTTGTCCATTAAGCTCCGGAACCAGAAG

Alignment

ORF - retro_dnov_2375 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.94 %
• Parental protein coverage: 71.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NVETVEYKNISFTVWDVGGQDKIRPLWRHYFQNTQGLIFVVDSNDRERVNEAREELMRMLAEDELRDAVL
          .V...EYKN.S.TV.D.GGQ.KI.PLWRHYFQNT.GL.FVVDS.D.E.VNEA..EL.R.LAEDELR..V.
Retrocopy SVWKLEYKN-SLTVRDMGGQYKIQPLWRHYFQNTPGLVFVVDSSDQECVNEAHRELLRVLAEDELRGSV-

Parental  LVFANKQDLPNAMNAAEITDKLGLHSLRHRNWYIQATCATSGDGLY-EGLDWLSNQLRNQK
          .VF.NKQDLP.A.NAA.....LGLH.L.HRNWY..A.CATS.D.LY..GLDWLS..LRNQK
Retrocopy TVFPNKQDLPSALNAADVAGELGLHPLCHRNWYTEAMCATSRDRLY<QGLDWLSIKLRNQK

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	138.27 RPM
SRP012922_cerebellum	0.00 RPM	67.63 RPM
SRP012922_heart	0.00 RPM	28.77 RPM
SRP012922_kidney	0.00 RPM	52.57 RPM
SRP012922_liver	0.00 RPM	38.24 RPM
SRP012922_lung	0.00 RPM	83.85 RPM
SRP012922_quadricep_muscle	0.00 RPM	34.96 RPM
SRP012922_spleen	0.00 RPM	85.50 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_2375 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.

---

Parental genes homology:

Parental genes homology involve 14 parental genes, and 42 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000004509	1 retrocopy	retro_apla_4,
Callithrix jacchus	ENSCJAG00000016671	10 retrocopies	retro_cjac_1295, retro_cjac_1691, retro_cjac_1719, retro_cjac_2189, retro_cjac_2896, retro_cjac_300, retro_cjac_3181, retro_cjac_3311, retro_cjac_3335, retro_cjac_390,
Ciona savignyi	ENSCSAVG00000007011	1 retrocopy	retro_csav_2,
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,
Erinaceus europaeus	ENSEEUG00000004638	4 retrocopies	retro_eeur_328, retro_eeur_660, retro_eeur_684, retro_eeur_76,
Gallus gallus	ENSGALG00000005393	1 retrocopy	retro_ggal_7,
Latimeria chalumnae	ENSLACG00000019009	1 retrocopy	retro_lcha_10,
Myotis lucifugus	ENSMLUG00000007020	6 retrocopies	retro_mluc_1631, retro_mluc_242, retro_mluc_2605, retro_mluc_428, retro_mluc_511, retro_mluc_876,
Macaca mulatta	ENSMMUG00000002792	3 retrocopies	retro_mmul_237, retro_mmul_541, retro_mmul_810,
Oryctolagus cuniculus	ENSOCUG00000023645	2 retrocopies	retro_ocun_1137, retro_ocun_247,
Procavia capensis	ENSPCAG00000014202	2 retrocopies	retro_pcap_15, retro_pcap_23,
Pan troglodytes	ENSPTRG00000002066	2 retrocopies	retro_ptro_112, retro_ptro_5,
Tetraodon nigroviridis	ENSTNIG00000011685	1 retrocopy	retro_tnig_19,