RetrogeneDB ID: retro_dnov_213

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_2665:162272..162619(+)
• Located in intron of: ENSDNOG00000015236

Retrocopy information

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

Parental gene information

• Parental gene symbol: RBM3
• Ensembl ID: ENSDNOG00000010420
• Aliases: None
• Description: RNA binding motif (RNP1, RRM) protein 3 [Source:HGNC Symbol;Acc:9900]

Sequence

>retro_dnov_213
GTTGTCACCAAAGAATGGGAGATTCAGCAATCCCAGGGTTTTGGCTTCATCACCTTCACAAACACAGAGCATACTTCAGA
TGCCATACAAGCCATGAATGGAGAATCCCTGGGTGGCCACCAGATTCATGTGGATGAGTCGGCCCAAGGAACCAGAAGGG
GTGCTTTTGGGAGTCATGGACATGGTCACAGCTACTCTAGAGGTGGTGGGACCAGGGATATAGGAGCAGCCAGTATGACA
ATTAGTCTAGAGGATATGGATATGGATTTGGAAGGTCCAGAGACTACGGTGGCAGCAGTCAGGATGATTATGACCACTGC
TCTAGAGGGAATTACAGAGACAATTAC

Alignment

ORF - retro_dnov_213 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.33 %
• Parental protein coverage: 98.32 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VVVKDRETQRSRG-GFITFTNPEHASDAMQAM-GESLDGRQIRVDHAGKSARGTRGGAFGGHGRGRSYSR
          VV.K..E.Q.S.G.GFITFTN.EH.SDA.QAM.GESL.G.QI.VD....SA.GTR.GAFG.HG.G.SYSR
Retrocopy VVTKEWEIQQSQGFGFITFTNTEHTSDAIQAMNGESLGGHQIHVD---ESAQGTRRGAFGSHGHGHSYSR

Parental  GGG-DQGYGSSRYDSRPGGYGYGYGRSRDYGGRNQGGYDRYSGGNYRDNY
          GGG.DQGY.SS.YD....GYGYG.GRSRDYGG..Q..YD..S.GNYRDNY
Retrocopy GGG<DQGYRSSQYDN*SRGYGYGFGRSRDYGGSSQDDYDHCSRGNYRDNY

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	0.19 RPM	56.40 RPM
SRP012922_cerebellum	0.14 RPM	29.42 RPM
SRP012922_heart	0.00 RPM	22.28 RPM
SRP012922_kidney	0.00 RPM	38.06 RPM
SRP012922_liver	0.00 RPM	23.53 RPM
SRP012922_lung	0.00 RPM	50.86 RPM
SRP012922_quadricep_muscle	0.00 RPM	14.02 RPM
SRP012922_spleen	0.00 RPM	71.19 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_213 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 11 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000013718	1 retrocopy	retro_acar_197,
Bos taurus	ENSBTAG00000025848	1 retrocopy	retro_btau_1144,
Canis familiaris	ENSCAFG00000015485	2 retrocopies	retro_cfam_1475, retro_cfam_259,
Cavia porcellus	ENSCPOG00000003553	1 retrocopy	retro_cpor_950,
Dasypus novemcinctus	ENSDNOG00000010420	16 retrocopies	retro_dnov_1343, retro_dnov_1380, retro_dnov_1463, retro_dnov_151, retro_dnov_1718, retro_dnov_180, retro_dnov_2034, retro_dnov_2076, retro_dnov_212, retro_dnov_213 , retro_dnov_2217, retro_dnov_2367, retro_dnov_2581, retro_dnov_733, retro_dnov_778, retro_dnov_974,
Dasypus novemcinctus	ENSDNOG00000017199	3 retrocopies	retro_dnov_1436, retro_dnov_2205, retro_dnov_696,
Gadus morhua	ENSGMOG00000012137	1 retrocopy	retro_gmor_4,
Loxodonta africana	ENSLAFG00000007003	1 retrocopy	retro_lafr_1091,
Pongo abelii	ENSPPYG00000020314	1 retrocopy	retro_pabe_40,
Sus scrofa	ENSSSCG00000021591	1 retrocopy	retro_sscr_842,
Ictidomys tridecemlineatus	ENSSTOG00000027493	1 retrocopy	retro_itri_142,