RetrogeneDB ID: retro_dnov_1195

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_1620:72827..73299(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS24
• Ensembl ID: ENSDNOG00000016853
• Aliases: None
• Description: mitochondrial ribosomal protein S24 [Source:HGNC Symbol;Acc:14510]

Sequence

>retro_dnov_1195
GGGCTCCAGGACCGTGTCCTTGCCGCGGCCTTGAGCTGCTGTGCATCCGCCGTGCCCTGCATGTCTCCCCAGCCTGGCAC
CAAGAACCGGGCAGCCAGCATCTGTATGGGAAAGGGGGACAAGCCCGTGACCTACGAGGAGGCATACGCGCCGCACTACA
TCGCCCACTGCAAGGGCTGACTGTCACTGCACACGGGTAACCTGGGTCTGGAGGAACAGGCTGCGGATGAACGGTGGAGA
ATGTTTTCCTGCTCAAGTTCACGCTGGGTACCTTCCCAGGCTGCCTGCTGACCAGGTGGTCCCAAAGCGCCAGGCTAACC
TGGTGGAGATCTGTGCCTTGATGCTGAGACAGCACCCTCCCCACAAGTTCTACTGCCTTGTGGGCTACAGTGAAACGCTA
CTGTCCCACTTCTTCAGGTGTCCTGTGTGACTGCACCTCCAAATTGTACCCTCAAATGCTGTGTATAAGTAC

Alignment

ORF - retro_dnov_1195 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.69 %
• Parental protein coverage: 94.61 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GIAARVLAGSRGP-LCAGRALHVSAAC-AKNRAARIRVGKGDKPVTYEEAHAPHYIAHRKGWLSLHTGNL
          G...RVLA......LC..RALHVS.A...KNRAA.I..GKGDKPVTYEEA.APHYIAH.KG.LSLHTGNL
Retrocopy GLQDRVLAAALSC<LCIRRALHVSPAW>TKNRAASICMGKGDKPVTYEEAYAPHYIAHCKG*LSLHTGNL

Parental  DGEEHAAER-TVEDVFLRKFMLGTFPGCL-ADQVVLKRRANLVEICALMLRQLPPHKFYFLVGYSETLLS
          ..EE.AA...TVE.VFL.KF.LGTFPGCL.ADQVV.KR.ANLVEICALMLRQ.PPHKFY.LVGYSETLLS
Retrocopy GLEEQAADE<TVENVFLLKFTLGTFPGCL<ADQVVPKRQANLVEICALMLRQHPPHKFYCLVGYSETLLS

Parental  HFYKCPVRLHLQTVPSKVVYKY
          HF..CPV.LHLQ.VPS..VYKY
Retrocopy HFFRCPV*LHLQIVPSNAVYKY

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	17.31 RPM
SRP012922_cerebellum	0.00 RPM	13.33 RPM
SRP012922_heart	0.00 RPM	12.53 RPM
SRP012922_kidney	0.00 RPM	16.98 RPM
SRP012922_liver	0.00 RPM	14.86 RPM
SRP012922_lung	0.00 RPM	16.49 RPM
SRP012922_quadricep_muscle	0.00 RPM	20.25 RPM
SRP012922_spleen	0.00 RPM	16.94 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_1195 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 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017491	1 retrocopy	retro_amel_1126,
Bos taurus	ENSBTAG00000007398	1 retrocopy	retro_btau_411,
Choloepus hoffmanni	ENSCHOG00000003106	1 retrocopy	retro_chof_2334,
Dasypus novemcinctus	ENSDNOG00000016853	3 retrocopies	retro_dnov_1195 , retro_dnov_153, retro_dnov_2049,
Echinops telfairi	ENSETEG00000016782	1 retrocopy	retro_etel_1350,
Homo sapiens	ENSG00000062582	1 retrocopy	retro_hsap_836,
Gorilla gorilla	ENSGGOG00000005692	1 retrocopy	retro_ggor_687,
Loxodonta africana	ENSLAFG00000011905	1 retrocopy	retro_lafr_426,
Macaca mulatta	ENSMMUG00000002405	1 retrocopy	retro_mmul_1089,
Monodelphis domestica	ENSMODG00000013889	1 retrocopy	retro_mdom_1785,
Pan troglodytes	ENSPTRG00000019127	1 retrocopy	retro_ptro_583,
Pteropus vampyrus	ENSPVAG00000015911	4 retrocopies	retro_pvam_1129, retro_pvam_1360, retro_pvam_180, retro_pvam_978,
Tursiops truncatus	ENSTTRG00000002938	1 retrocopy	retro_ttru_1860,