RetrogeneDB ID: retro_dnov_2406

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_72069:42982..43254(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TIMM17B
• Ensembl ID: ENSDNOG00000025897
• Aliases: None
• Description: translocase of inner mitochondrial membrane 17 homolog B (yeast) [Source:HGNC Symbol;Acc:17310]

Sequence

>retro_dnov_2406
AGCCTCGCTGTGTGGGGTGGCCTGATCCCCACCACTGACTGCAGCCTGGTGCAGCTGCGGGGCAAGGAGGATCCCTGGAA
CTCCACCACCAGTGGAGCTCTGACCGGGCTATGCTGGCTGTCCGCAGCGGCCCACTGGGCATGGTTGGGCTCAGCAATGA
TGGGGACATCTGGTTGGTCTATTTCTAGTGATGTCAGCATCCTTCTCACAGCTTATACCGGCCCAACATTTCACATGGCA
CCCTGTTTCTGGAGGACCCAGCCCTCTGCCCC

Alignment

ORF - retro_dnov_2406 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.89 %
• Parental protein coverage: 52.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SFAVWGGLFSTIDCGLVRLRGKEDPWNSITSGALTG-AVLAARSGPLAMV-GSAMMGGILLALIEGVGIL
          S.AVWGGL..T.DC.LV.LRGKEDPWNS.TSGALTG.A.LA.RSGPL.MV.GSAMMG.........V.IL
Retrocopy SLAVWGGLIPTTDCSLVQLRGKEDPWNSTTSGALTG<AMLAVRSGPLGMV>GSAMMGTSGWSISSDVSIL

Parental  LTRYTAQQFRNAP-PFLEDPSQLP
          LT.YT...F..AP..FLEDP...P
Retrocopy LTAYTGPTFHMAP<LFLEDPALCP

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	20.42 RPM
SRP012922_cerebellum	0.55 RPM	10.17 RPM
SRP012922_heart	0.00 RPM	24.60 RPM
SRP012922_kidney	1.10 RPM	50.10 RPM
SRP012922_liver	0.31 RPM	20.74 RPM
SRP012922_lung	0.00 RPM	19.85 RPM
SRP012922_quadricep_muscle	0.00 RPM	37.39 RPM
SRP012922_spleen	0.00 RPM	21.29 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_2406 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 19 parental genes, and 35 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012474	1 retrocopy	retro_amel_717,
Bos taurus	ENSBTAG00000018496	4 retrocopies	retro_btau_1022, retro_btau_1550, retro_btau_1552, retro_btau_882,
Cavia porcellus	ENSCPOG00000008768	2 retrocopies	retro_cpor_867, retro_cpor_893,
Dasypus novemcinctus	ENSDNOG00000006389	7 retrocopies	retro_dnov_1113, retro_dnov_1420, retro_dnov_1806, retro_dnov_2586, retro_dnov_273, retro_dnov_274, retro_dnov_814,
Dasypus novemcinctus	ENSDNOG00000025897	2 retrocopies	retro_dnov_2282, retro_dnov_2406 ,
Felis catus	ENSFCAG00000002569	2 retrocopies	retro_fcat_1429, retro_fcat_1654,
Gorilla gorilla	ENSGGOG00000011427	1 retrocopy	retro_ggor_779,
Macropus eugenii	ENSMEUG00000004174	1 retrocopy	retro_meug_2071,
Microcebus murinus	ENSMICG00000005971	3 retrocopies	retro_mmur_1128, retro_mmur_1272, retro_mmur_232,
Myotis lucifugus	ENSMLUG00000009148	1 retrocopy	retro_mluc_148,
Macaca mulatta	ENSMMUG00000004547	1 retrocopy	retro_mmul_796,
Mustela putorius furo	ENSMPUG00000013675	1 retrocopy	retro_mputfur_1232,
Mus musculus	ENSMUSG00000031158	1 retrocopy	retro_mmus_1509,
Nomascus leucogenys	ENSNLEG00000007902	1 retrocopy	retro_nleu_1616,
Oryctolagus cuniculus	ENSOCUG00000027418	2 retrocopies	retro_ocun_121, retro_ocun_1451,
Pteropus vampyrus	ENSPVAG00000007643	1 retrocopy	retro_pvam_470,
Ictidomys tridecemlineatus	ENSSTOG00000014173	1 retrocopy	retro_itri_83,
Tarsius syrichta	ENSTSYG00000010396	2 retrocopies	retro_tsyr_1132, retro_tsyr_1703,
Vicugna pacos	ENSVPAG00000009578	1 retrocopy	retro_vpac_92,