RetrogeneDB ID: retro_dnov_89

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1407:90404..90871(-)
• Located in intron of: ENSDNOG00000016937

Retrocopy information

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

Parental gene information

• Parental gene symbol: NDUFAB1
• Ensembl ID: ENSDNOG00000017122
• Aliases: None
• Description: NADH dehydrogenase (ubiquinone) 1, alpha/beta subcomplex, 1, 8kDa [Source:HGNC Symbol;Acc:7694]

Sequence

>retro_dnov_89
ATGGCGGTTCGTGTCCTTTCCGCTGTGTCCGCCGCCTGTCCGTGGCCTTTACGCCGCTGCCGCGGGCTCCTAGGCCGTGC
ACGGCTCAGCTGCTCAGCACTGCCTTGTGCCCCGCAGGGATCCGGACGGGGCTTGTAGCTCCACAGCTGGTCTCGGTGCT
CGTGCGGGTTCCAGGTGAAGTTACACAGTTATGCCGGCAGTATAGTGATGCACCCCCTTTGACATTAGAGGGAATTAAGG
ACCGTGTTCTTTACGACTTGAAACTCTATGATAAAATTGATCCTGAAAAGCTCTCAGTAAATTCGCATTTCATGAAAGAC
CTGGGCTTAGACAGTTTGGACCAAGTGGAGATTATCATGGCCATGGAGGATGACTTTGGGTTTGAAATTCCTGATATAGA
TGCAGAAAAGTTAATGGGCCCACAAGAAATTGTAGATTACATTGCAGATAAGAAGGATGTATATGAA

Alignment

ORF - retro_dnov_89 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.34 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAVRVLSA-CVRRLSVAFTPLPLAPRLFAARPLSIALCPAGIRTGLVVLQPVSVLTQVPGKVTQLCRQYS
          MAVRVLSA.CVRRLSVAFTPLP.APR...A..LS.ALCPAGIRTGLV..Q.VSVL..VPG.VTQLCRQYS
Retrocopy MAVRVLSA<CVRRLSVAFTPLPRAPRPCTAQLLSTALCPAGIRTGLVAPQLVSVLVRVPGEVTQLCRQYS

Parental  DAPPLTLEGIKDRVLYVLKLYDKIDPEKXXXXXHFMKDLGLDSLDXXXXXXXXXXXXXFEIPDIDAEKLM
          DAPPLTLEGIKDRVLY.LKLYDKIDPEK.....HFMKDLGLDSLD.............FEIPDIDAEKLM
Retrocopy DAPPLTLEGIKDRVLYDLKLYDKIDPEKLSVNSHFMKDLGLDSLDQVEIIMAMEDDFGFEIPDIDAEKLM

Parental  CPQEIVDYIADKKDVYE
          .PQEIVDYIADKKDVYE
Retrocopy GPQEIVDYIADKKDVYE

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	19.45 RPM	60.87 RPM
SRP012922_cerebellum	11.13 RPM	29.69 RPM
SRP012922_heart	46.87 RPM	119.03 RPM
SRP012922_kidney	26.01 RPM	61.60 RPM
SRP012922_liver	10.84 RPM	24.61 RPM
SRP012922_lung	6.26 RPM	22.60 RPM
SRP012922_quadricep_muscle	29.08 RPM	106.27 RPM
SRP012922_spleen	6.64 RPM	24.15 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_89 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 17 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000014304	1 retrocopy	retro_amel_1692,
Canis familiaris	ENSCAFG00000017667	3 retrocopies	retro_cfam_1738, retro_cfam_1821, retro_cfam_450,
Choloepus hoffmanni	ENSCHOG00000003558	2 retrocopies	retro_chof_1517, retro_chof_2498,
Callithrix jacchus	ENSCJAG00000020616	2 retrocopies	retro_cjac_2635, retro_cjac_3099,
Cavia porcellus	ENSCPOG00000012038	2 retrocopies	retro_cpor_728, retro_cpor_767,
Dasypus novemcinctus	ENSDNOG00000017122	5 retrocopies	retro_dnov_1450, retro_dnov_1733, retro_dnov_2024, retro_dnov_89 , retro_dnov_911,
Felis catus	ENSFCAG00000013241	3 retrocopies	retro_fcat_1104, retro_fcat_1181, retro_fcat_2012,
Loxodonta africana	ENSLAFG00000001032	1 retrocopy	retro_lafr_330,
Macropus eugenii	ENSMEUG00000012681	3 retrocopies	retro_meug_1780, retro_meug_303, retro_meug_830,
Macaca mulatta	ENSMMUG00000020522	1 retrocopy	retro_mmul_101,
Monodelphis domestica	ENSMODG00000016352	1 retrocopy	retro_mdom_389,
Mustela putorius furo	ENSMPUG00000012142	2 retrocopies	retro_mputfur_1135, retro_mputfur_466,
Mus musculus	ENSMUSG00000030869	6 retrocopies	retro_mmus_1724, retro_mmus_2073, retro_mmus_2188, retro_mmus_2947, retro_mmus_3094, retro_mmus_3332,
Otolemur garnettii	ENSOGAG00000005562	2 retrocopies	retro_ogar_2916, retro_ogar_325,
Rattus norvegicus	ENSRNOG00000018129	2 retrocopies	retro_rnor_1353, retro_rnor_2058,
Sus scrofa	ENSSSCG00000010795	1 retrocopy	retro_sscr_1017,
Tursiops truncatus	ENSTTRG00000005258	2 retrocopies	retro_ttru_1229, retro_ttru_989,