RetrogeneDB ID: retro_dnov_253

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_306:45219..45668(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MEMO1
• Ensembl ID: ENSDNOG00000001254
• Aliases: None
• Description: mediator of cell motility 1 [Source:HGNC Symbol;Acc:14014]

Sequence

>retro_dnov_253
GAGTTTACCATTATTCCTGTACTGGTTGGAGCTCTGAGTGACTCAAAAGAACAGGAATTTGGAAAACTCTTCAGTAAATA
TCTAGTGGACCCTAGTACTCGCTTTGTGGTTTCTTCTGATTTCTGTCATTGGATCAAAGGTTCCATTACAGTTACTATGA
TGAATCCCAGGGGGAGATTTACAGATCCACTGAACATCTAAACAAATGGGCATGAGTTTTATAGAACAATGAGACCCTGT
ATCTTGTAGCAATTACTTGAAGAAATGCCATAATAAAATTTATGGAAGACATCCCATTGGGATGCTTCCTGTTGGGATTA
AATGCTATCACAGAGCTCCAGAAGAATGGAATGAATATGAACTTTTCCTTATTGAATTATGCCCAGTCAAGCCAGTGCAG
AAACTGGCAGGACAGTTCAGTGAGCTGTGCAGCTGGAGCACTTGCCGTC

Alignment

ORF - retro_dnov_253 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.7 %
• Parental protein coverage: 52.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  EFTIIPVLV-ALSESKEQEFGKLFSKYLADPSNLFVVSSDFCHW-GQRFRYSYYDESQGEIYRSIEHLDK
          EFTIIPVLV.ALS.SKEQEFGKLFSKYL.DPS..FVVSSDFCHW..QRF.YSYYDESQGEIYRS.EHL.K
Retrocopy EFTIIPVLVGALSDSKEQEFGKLFSKYLVDPSTRFVVSSDFCHW<DQRFHYSYYDESQGEIYRSTEHLNK

Parental  -MGMS-IEQLDPVSFSNYLKKYHNTICGRH-PIGVL---LNAITELQKNGMNMSFSFLNYAQSSQCRNWQ
          .MGMS.IEQ.DPVS.SNYLKK.HN.I.GRH.P.G.....LNAITELQKNGMNM.FS.LNYAQSSQCRNWQ
Retrocopy <MGMSFIEQ*DPVSCSNYLKKCHNKIYGRH>PLGCFLLGLNAITELQKNGMNMNFSLLNYAQSSQCRNWQ

Parental  DSSVSYAAGALTV
          DSSVS.AAGAL.V
Retrocopy DSSVSCAAGALAV

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	10.70 RPM
SRP012922_cerebellum	0.00 RPM	3.30 RPM
SRP012922_heart	0.00 RPM	9.51 RPM
SRP012922_kidney	0.00 RPM	11.50 RPM
SRP012922_liver	0.00 RPM	2.32 RPM
SRP012922_lung	0.00 RPM	7.03 RPM
SRP012922_quadricep_muscle	0.00 RPM	24.58 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_253 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000012339	2 retrocopies	retro_chof_2257, retro_chof_2552,
Cavia porcellus	ENSCPOG00000012278	1 retrocopy	retro_cpor_1159,
Dasypus novemcinctus	ENSDNOG00000001254	1 retrocopy	retro_dnov_253 ,
Oryctolagus cuniculus	ENSOCUG00000005878	3 retrocopies	retro_ocun_1441, retro_ocun_1663, retro_ocun_928,
Pteropus vampyrus	ENSPVAG00000011427	1 retrocopy	retro_pvam_184,