RetrogeneDB ID: retro_dnov_2577

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_87042:41390..42067(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAD51C
• Ensembl ID: ENSDNOG00000004696
• Aliases: None
• Description: RAD51 paralog C [Source:HGNC Symbol;Acc:9820]

Sequence

>retro_dnov_2577
TCCTGTGTTGAAATGCAGCGAATTTAGGGAGTTTCCGGCTGTCCAAAGTGGCACGGGTGAAATTAGTCTCTGCGGGTTTC
CAGACTGCTGAGGAGCTCCTGGTGGTGAAAGCTTAAGAGCTCAGAAAAGAAATTGGGATATCTAAAGAGGAAGATTTAGA
AACTCTACATATTATAAGAAGAGAATGTCTCTTAAATATACCAATGCATGCTGGTACATCTGAGACAGGCAAAAATAAAT
GTACAGCAGTGGAACTTCTTGAGCACGAGCATACCCAGGGCTTCATAATTACCTTTTGCTCAGCACTAGATAATATTCTT
GGGGGTGAAGTACCCTTAACCAAAACAACAGAAATCTGTGGTTCACCTGGTGTTGGAAAAACACAATTATGTATGCAATT
GGCAGTAGATGTGCCGATACCATAATGTTTTGGAGGAGTGACAGGGGAAACAGTTTTTATTGATACAGAGGGAAGTTTTA
TGGTGGACGGAGTTGTAGCCCTTGCCACTGCCTGAATTCAGTGTCTTCATCTTATAGCACGAACACACATGGGAGAGGAG
CACCAAAAGGCTTTGGAAGATTTCACTCTTGAAAATATTCTTTCCCATATTTATTATTTTCGTTGTCATGATTACATACA
TAGAACTCTTAGCACAAATTTATCTCCTTCCAGACTT

Alignment

ORF - retro_dnov_2577 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.5 %
• Parental protein coverage: 60.48 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SCVEMQR-DLGSFPLSTAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKEEALETLHIIRRECLLNIPR
          SCVEMQR..LGSF.LS...RVKLVSAGFQTAEELL.VK..EL.KE.GISKEE.LETLHIIRRECLLNIP.
Retrocopy SCVEMQR<NLGSFRLSKVARVKLVSAGFQTAEELLVVKA*ELRKEIGISKEEDLETLHIIRRECLLNIPM

Parental  HANTSETGK-KCTALELLEQEHTQGFIITFCSALDNILGGGVPLTKTTEICGAPGVGKTQLCMQLAADEQ
          HA.TSETGK.KCTA.ELLE.EHTQGFIITFCSALDNILGG.VPLTKTTEICG.PGVGKTQLCMQLA.D..
Retrocopy HAGTSETGKNKCTAVELLEHEHTQGFIITFCSALDNILGGEVPLTKTTEICGSPGVGKTQLCMQLAVDVP

Parental  IPECFGGVAGEAVFIDTEGSFMVDRVVDLATACIQHLHLIAGTHMGEKHQKALEDFTLENILSHIYYFRC
          IP.CFGGV.GE.VFIDTEGSFMVD.VV.LATA.IQ.LHLIA.THMGE.HQKALEDFTLENILSHIYYFRC
Retrocopy IP*CFGGVTGETVFIDTEGSFMVDGVVALATA*IQCLHLIARTHMGEEHQKALEDFTLENILSHIYYFRC

Parental  HDYTELLAQIYLLPDFL
          HDY........L.P..L
Retrocopy HDYIHRTLSTNLSPSRL

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	6.22 RPM
SRP012922_cerebellum	0.14 RPM	9.21 RPM
SRP012922_heart	0.23 RPM	3.71 RPM
SRP012922_kidney	0.00 RPM	7.39 RPM
SRP012922_liver	0.00 RPM	3.10 RPM
SRP012922_lung	0.15 RPM	9.01 RPM
SRP012922_quadricep_muscle	0.17 RPM	1.38 RPM
SRP012922_spleen	0.69 RPM	22.32 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_2577 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 1 parental gene, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000004696	3 retrocopies	retro_dnov_239, retro_dnov_2577 , retro_dnov_946,