RetrogeneDB ID: retro_dnov_350

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_3899:424137..424466(+)
• Located in intron of: ENSDNOG00000006976

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB5B
• Ensembl ID: ENSDNOG00000016952
• Aliases: None
• Description: RAB5B, member RAS oncogene family [Source:HGNC Symbol;Acc:9784]

Sequence

>retro_dnov_350
GAAACCTTTGCCAGAGTAAAGACATGGGTGAAGAAACCACAGTGACAGGCGAGCCCTAGCATTGTTATTGCCCTAGAGGG
AATAAAGCTCACCTGGCCAACAATCACATGGTAGAATATAAAGAGGCCCAGGTGTATGCAGATGACAACAGCTTATTGTT
TATGGACACTTCAGCCAACATAGCTATGAATGTGAATGATTTCCTCCTGGCAATAACTAAGAAGTTAACAAAGAGTGAAC
CCCAGATTCTGGAGGGTGCAGTAGGCCAAAGCCAAGGTGTGGATCTCCGTGAGCAGTCCCAGCAGAACATGAGCCATTGT
TGTAGCAAC

Alignment

ORF - retro_dnov_350 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.77 %
• Parental protein coverage: 51.4 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ETFARAKTWVKELQRQASPSIVIALAG-NKADLANKRMVEYEEAQAYADDNSLLFMETSAKTAMNVNDLF
          ETFAR.KTWVK..Q.QASPSIVIAL.G.NKA.LAN..MVEY.EAQ.YADDNSLLFM.TSA..AMNVND..
Retrocopy ETFARVKTWVKKPQ*QASPSIVIALEG<NKAHLANNHMVEYKEAQVYADDNSLLFMDTSANIAMNVNDFL

Parental  LAIAKKLPKSEPQNLGGTACRSRGVDLHEQSQQNKSQCCSN
          LAI.KKL.KSEPQ.L.G....S.GVDL.EQSQQN.S.CCSN
Retrocopy LAITKKLTKSEPQILEGAVGQSQGVDLREQSQQNMSHCCSN

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	32.87 RPM
SRP012922_cerebellum	0.00 RPM	36.57 RPM
SRP012922_heart	0.00 RPM	11.60 RPM
SRP012922_kidney	0.00 RPM	17.52 RPM
SRP012922_liver	0.00 RPM	15.17 RPM
SRP012922_lung	0.00 RPM	35.43 RPM
SRP012922_quadricep_muscle	0.17 RPM	30.29 RPM
SRP012922_spleen	0.00 RPM	30.79 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_350 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007527	2 retrocopies	retro_cjac_1215, retro_cjac_1879,
Dasypus novemcinctus	ENSDNOG00000016952	1 retrocopy	retro_dnov_350 ,
Equus caballus	ENSECAG00000023306	1 retrocopy	retro_ecab_280,
Echinops telfairi	ENSETEG00000009603	2 retrocopies	retro_etel_617, retro_etel_698,
Mus musculus	ENSMUSG00000000711	1 retrocopy	retro_mmus_2081,
Nomascus leucogenys	ENSNLEG00000017570	1 retrocopy	retro_nleu_2531,
Oryctolagus cuniculus	ENSOCUG00000013895	1 retrocopy	retro_ocun_1193,
Ochotona princeps	ENSOPRG00000007883	3 retrocopies	retro_opri_1061, retro_opri_1116, retro_opri_299,
Procavia capensis	ENSPCAG00000010486	1 retrocopy	retro_pcap_380,