RetrogeneDB ID: retro_dnov_78

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1314:495909..496592(-)
• Located in intron of: ENSDNOG00000002653

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMX1
• Ensembl ID: ENSDNOG00000016496
• Aliases: None
• Description: thioredoxin-related transmembrane protein 1 [Source:HGNC Symbol;Acc:15487]

Sequence

>retro_dnov_78
ATGGCACCTTCCAGGAGTCTCATGTTTCCCTTGGCAGTCCTGGTGTTGTTACTCTTGGGGGCTCCCTGGATCCATGGGCA
GCATAGCAACATGTACATCATGACAGATGCAAACTGGAAAGAGTTACTGGAAGGAGAGTGGATGATAGAATTTTATGCTC
TGTGATGTCCTGCTTGTCAGAATCTTCAGCCAGAAAGGGAAAGTTTTGCTGAATGGGGAGAAGATCTTGAGATTAATGTT
GCAAAAATAGATGTCACAGAGCAGCCAGGACTGAGTAGACAATTTATCATAACTGCTTTTCCTACTATTTATCATTGTAA
GGATGGTGAATTTAGGTGCTATCAAGGCCTGAGAGCTAAGAAGGACTTCATAAACTTTATAAATGAAAAAGAGTAGAAGA
GTACTGAACCTGTTTCATCATGGCTTGGTCAGGTTTTGTGATGATGAGTAGTATGTCAGCACTCTTCCAGCTGTCTGTGT
AGATCAGGACTTGCCATAACTATTTTATTGAAGACCTTGGATTACCAGTTTGGGGATCATGCACAGTTTTTGCTTTAGCA
ACTCTGCTTTTAGGACTATTATTAGAATTTTGTATGCTATTTGTAGCAGATTGCCTTTGTCCTTCAAAAAGGCATAGATC
GCGACCAAACCCTTCAAAAAAATTACTACCAGAATCTTCTCAA

Alignment

ORF - retro_dnov_78 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.42 %
• Parental protein coverage: 82.01 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAPSGSLVVPLAVLVLLLWGAPWIHGRRSDVRIITDANWKELLEGEWMIEFYAPWCPACQNLQPEWESFA
          MAPS.SL..PLAVLVLLL.GAPWIHG..S...I.TDANWKELLEGEWMIEFYA..CPACQNLQPE.ESFA
Retrocopy MAPSRSLMFPLAVLVLLLLGAPWIHGQHSNMYIMTDANWKELLEGEWMIEFYAL*CPACQNLQPERESFA

Parental  EWGEDLEINVAKVDVTEQPXXXXXXXXXXXXXXXXCRDGEFRRYQGPRTKKDFINFINEREWKSIEPVSS
          EWGEDLEINVAK.DVTEQP................C.DGEFR.YQG.R.KKDFINFINE.E.KS.EPVSS
Retrocopy EWGEDLEINVAKIDVTEQPGLSRQFIITAFPTIYHCKDGEFRCYQGLRAKKDFINFINEKE*KSTEPVSS

Parental  WLG-PGSVLMSSMSALFQLSMWIRTCHNYFIEDLGLPVWGSYAVFALATLLSGLLLGLCMIFVADCLCPS
          WLG..G.V.MSSMSALFQLS..IRTCHNYFIEDLGLPVWGS..VFALATLL.GLLL..CM.FVADCLCPS
Retrocopy WLG<SGFVMMSSMSALFQLSV*IRTCHNYFIEDLGLPVWGSCTVFALATLLLGLLLEFCMLFVADCLCPS

Parental  KRRRPQPYPPKKLLPESSQ
          KR.R..P.P.KKLLPESSQ
Retrocopy KRHRSRPNPSKKLLPESSQ

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	0.58 RPM	34.81 RPM
SRP012922_cerebellum	0.14 RPM	11.68 RPM
SRP012922_heart	0.00 RPM	4.87 RPM
SRP012922_kidney	0.00 RPM	9.58 RPM
SRP012922_liver	0.00 RPM	9.44 RPM
SRP012922_lung	0.46 RPM	26.12 RPM
SRP012922_quadricep_muscle	0.00 RPM	5.19 RPM
SRP012922_spleen	0.46 RPM	43.61 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_78 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 14 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015041	1 retrocopy	retro_amel_719,
Canis familiaris	ENSCAFG00000014626	1 retrocopy	retro_cfam_796,
Choloepus hoffmanni	ENSCHOG00000011305	1 retrocopy	retro_chof_1249,
Callithrix jacchus	ENSCJAG00000006893	1 retrocopy	retro_cjac_1453,
Dasypus novemcinctus	ENSDNOG00000016496	1 retrocopy	retro_dnov_78 ,
Felis catus	ENSFCAG00000002780	1 retrocopy	retro_fcat_333,
Homo sapiens	ENSG00000139921	2 retrocopies	retro_hsap_3840, retro_hsap_3970,
Gorilla gorilla	ENSGGOG00000009768	1 retrocopy	retro_ggor_2587,
Loxodonta africana	ENSLAFG00000013251	1 retrocopy	retro_lafr_1214,
Macaca mulatta	ENSMMUG00000001901	1 retrocopy	retro_mmul_1618,
Nomascus leucogenys	ENSNLEG00000012362	2 retrocopies	retro_nleu_1976, retro_nleu_2524,
Oryctolagus cuniculus	ENSOCUG00000003980	1 retrocopy	retro_ocun_571,
Pongo abelii	ENSPPYG00000005810	2 retrocopies	retro_pabe_3058, retro_pabe_3264,
Pan troglodytes	ENSPTRG00000006339	2 retrocopies	retro_ptro_2522, retro_ptro_2695,