RetrogeneDB ID: retro_dnov_1704

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_270915:4..443(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSDNOG00000024423
• Aliases: None
• Description: None

Sequence

>retro_dnov_1704
GAGGTAGTGGAAGCAGAGCTATTTGCTCGTTATGACCGCCTTCTCCTCCAGTCTACCTTGGACCTGATGGCCGATGTGGT
ATACTGCCCCGGCCCATGCTGCCAACTGCCTGTGATGCAGGAGCCAGGTGGTACCATGGGCATCTGCTCCAGCTGCAATT
TTGCCTTCTGTATCTTGTGCAGATTGACCTACCATGGAGTCTCTCCATGTAAGGCCAGCGCAGAGAAGTTAATGGACTTA
CGAAATGAGTACTCGCAAGCAGATGAGGCCAATAAAAGATTTTTGGAACAGAGATATGGTAAGAGGGTGATTCAGAAGGC
ACTGGAAGACACAGAAAAGAACTCAAAGAGCTGTCTATGTTGTGGGACTAGGGGTAAAGAAATTAGAGAAATTAGATGGA
TGTAACCAGCCTATCGCATGTACTGGCTGCATGCAGTAT

Alignment

ORF - retro_dnov_1704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76. %
• Parental protein coverage: 61.16 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ELVEAELFARYDRLLLQYTLDLMADVVYCPRPCCQLPVMQEPGETMGICSSCSFAFCTLCRLTYHGVSPC
          E.VEAELFARYDRLLLQ.TLDLMADVVYCP.PCCQLPVMQEPG.TMGICSSC.FAFC.LCRLTYHGVSPC
Retrocopy EVVEAELFARYDRLLLQSTLDLMADVVYCPGPCCQLPVMQEPGGTMGICSSCNFAFCILCRLTYHGVSPC

Parental  NVTSEKLMDLRNEYLQADEANKRFLEQRYGKRVIQKALEEMKSKKWLKKNSKSCPCCGTPI-EKLDGCNK
          ....EKLMDLRNEY.QADEANKRFLEQRYGKRVIQKALE.........K....C...G..I.EKLDGCN.
Retrocopy KASAEKLMDLRNEYSQADEANKRFLEQRYGKRVIQKALEDTEKN---SKSCLCCGTRGKEI>EKLDGCNQ

Parental  -MTCTACKQY
          ...CT.C.QY
Retrocopy PIACTGCMQY

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	2.53 RPM
SRP012922_cerebellum	0.41 RPM	2.06 RPM
SRP012922_heart	0.46 RPM	1.62 RPM
SRP012922_kidney	0.27 RPM	2.74 RPM
SRP012922_liver	0.15 RPM	1.55 RPM
SRP012922_lung	0.31 RPM	1.53 RPM
SRP012922_quadricep_muscle	0.35 RPM	2.94 RPM
SRP012922_spleen	0.23 RPM	3.43 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_1704 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000007803	1 retrocopy	retro_dnov_332,
Dasypus novemcinctus	ENSDNOG00000024423	1 retrocopy	retro_dnov_1704 ,
Homo sapiens	ENSG00000013561	2 retrocopies	retro_hsap_3790, retro_hsap_3881,
Gorilla gorilla	ENSGGOG00000008542	1 retrocopy	retro_ggor_2612,
Macaca mulatta	ENSMMUG00000009768	2 retrocopies	retro_mmul_1647, retro_mmul_934,
Oryctolagus cuniculus	ENSOCUG00000016953	1 retrocopy	retro_ocun_340,
Pongo abelii	ENSPPYG00000015894	2 retrocopies	retro_pabe_3095, retro_pabe_3115,
Pan troglodytes	ENSPTRG00000017356	2 retrocopies	retro_ptro_2571, retro_ptro_2643,