RetrogeneDB ID: retro_dnov_605

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_6739:261..559(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL11
• Ensembl ID: ENSDNOG00000011230
• Aliases: None
• Description: ribosomal protein L11 [Source:HGNC Symbol;Acc:10301]

Sequence

>retro_dnov_605
CTAACCCAGGGTGCAGGTCAGAAGGAGCACCCCGTGCGGGAATCTCATAGCCACAAGCTGTGTCTCAGCATCTATGTGGG
GTGGAACTGGATGAAGACAGACTGACGGGGCAGCTAAGGTGCTGGAGCAGCTCAAATGGTGGACCCTCATGTTTTCCAAA
GCTAGATACACTGGGAGATCCTTTGGCCTCAGGAGAAAGGAGAAGATTGGCATCCACTGCACAGACCTCAGGGCCAAGAC
CAAGGAAATCTTGATGGAAGGTCTCAAGGTGTGGGAGTTTGCATTAAGAAAAAATAAC

Alignment

ORF - retro_dnov_605 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.0 %
• Parental protein coverage: 55.06 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAQDQGEKENPMRELRIRKLCLNICV-GESGDRLTR-AAKVLEQLTGQTPVFSKARYTVRSFGIRRNEKI
          ..Q..G.KE.P.RE....KLCL.I.V.G..G.R.T..AAKVLEQL...T..FSKARYT.RSFG.RR.EKI
Retrocopy LTQGAGQKEHPVRESHSHKLCLSIYV>GGTG*RQTDGAAKVLEQLKWWTLMFSKARYTGRSFGLRRKEKI

Parental  AVHCTVRGAKAEEILEKGLKVREYELRKNN
          ..HCT...AK..EIL..GLKV.E..LRKNN
Retrocopy GIHCTDLRAKTKEILMEGLKVWEFALRKNN

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	632.60 RPM
SRP012922_cerebellum	0.00 RPM	326.08 RPM
SRP012922_heart	0.00 RPM	315.79 RPM
SRP012922_kidney	0.00 RPM	785.52 RPM
SRP012922_liver	0.00 RPM	351.41 RPM
SRP012922_lung	0.00 RPM	975.76 RPM
SRP012922_quadricep_muscle	0.00 RPM	429.08 RPM
SRP012922_spleen	0.00 RPM	1140.03 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_605 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 20 parental genes, and 67 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020905	1 retrocopy	retro_btau_267,
Canis familiaris	ENSCAFG00000013232	2 retrocopies	retro_cfam_1059, retro_cfam_543,
Callithrix jacchus	ENSCJAG00000020953	1 retrocopy	retro_cjac_790,
Dasypus novemcinctus	ENSDNOG00000011230	2 retrocopies	retro_dnov_1453, retro_dnov_605 ,
Dipodomys ordii	ENSDORG00000012496	1 retrocopy	retro_dord_143,
Echinops telfairi	ENSETEG00000014825	8 retrocopies	retro_etel_1054, retro_etel_136, retro_etel_1452, retro_etel_1893, retro_etel_2018, retro_etel_500, retro_etel_62, retro_etel_948,
Homo sapiens	ENSG00000142676	6 retrocopies	retro_hsap_1159, retro_hsap_1801, retro_hsap_2272, retro_hsap_3238, retro_hsap_606, retro_hsap_712,
Gorilla gorilla	ENSGGOG00000014628	6 retrocopies	retro_ggor_1192, retro_ggor_1325, retro_ggor_1690, retro_ggor_2204, retro_ggor_533, retro_ggor_603,
Loxodonta africana	ENSLAFG00000030853	2 retrocopies	retro_lafr_371, retro_lafr_434,
Macropus eugenii	ENSMEUG00000013738	3 retrocopies	retro_meug_488, retro_meug_517, retro_meug_633,
Macaca mulatta	ENSMMUG00000002445	3 retrocopies	retro_mmul_2039, retro_mmul_2415, retro_mmul_2462,
Monodelphis domestica	ENSMODG00000012828	1 retrocopy	retro_mdom_641,
Mus musculus	ENSMUSG00000059291	3 retrocopies	retro_mmus_144, retro_mmus_146, retro_mmus_78,
Ornithorhynchus anatinus	ENSOANG00000000321	1 retrocopy	retro_oana_49,
Oryctolagus cuniculus	ENSOCUG00000022928	1 retrocopy	retro_ocun_1387,
Pongo abelii	ENSPPYG00000001736	6 retrocopies	retro_pabe_1478, retro_pabe_1946, retro_pabe_2686, retro_pabe_612, retro_pabe_615, retro_pabe_964,
Pteropus vampyrus	ENSPVAG00000004282	1 retrocopy	retro_pvam_1068,
Rattus norvegicus	ENSRNOG00000026260	9 retrocopies	retro_rnor_1735, retro_rnor_2287, retro_rnor_2314, retro_rnor_2690, retro_rnor_271, retro_rnor_2725, retro_rnor_668, retro_rnor_795, retro_rnor_919,
Sus scrofa	ENSSSCG00000024260	4 retrocopies	retro_sscr_1048, retro_sscr_1049, retro_sscr_1074, retro_sscr_819,
Tarsius syrichta	ENSTSYG00000001349	6 retrocopies	retro_tsyr_1138, retro_tsyr_127, retro_tsyr_1583, retro_tsyr_1605, retro_tsyr_516, retro_tsyr_520,