RetrogeneDB ID: retro_dnov_946

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_125606:3194..3762(-)
• 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_946
TCCCTTGTTGAAATGCAGCAGGATTTAGGGCATTTCCCGCTGTCCACAGTGGTTCGGGTAAAGATAGTCTCTGCGAATTT
CCAGACTGCTGAGGGACTCTTGGAGGTTAAACCCCCAGAGCTCAGCAAAGAAGTTGGGCTATCTAAAGGGGAAGCCTTAG
AAACTCCACATATTGTGAGAAGAGAATGTCTCTTAAAGATAACAAGACATGCTGGGACACCTGACACAGACAAGAAGTGT
ACAGCACTGGGACTTCTTGAGCAGGAGTATACCCAGGGCTCCGTATTTACCTTCTGTTCAGCCCTAGATAATATTCTTGG
GGGTGAAGTACCTTCAACCTAAACAACAGAAAGCTGTGGTGCACCTGGAGTTGGAAACACACTATTATGTATGGAATTGG
CAATAGATGCAGTAGATGTGCAGATACCAGAATGTTTTGGAGGAGTGGCAGCTGAAGCAGTTTTTATCGATACAGAGGAA
AGTTTTCTGGTTGACAGAGTGGTAGACCTGCCACTACCTGTGTTCAGCAGCTCATCTTATAACAGACATACATGGGACAG
AGCACAAA

Alignment

ORF - retro_dnov_946 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.09 %
• Parental protein coverage: 50.54 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SCVEMQRDLGSFPLSTAVRVKLVSAGFQTAEELLEVKPSELSKEVGISKEEALETLHIIRRECLLNIPRH
          S.VEMQ.DLG.FPLST.VRVK.VSA.FQTAE.LLEVKP.ELSKEVG.SK.EALET.HI.RRECLL.I.RH
Retrocopy SLVEMQQDLGHFPLSTVVRVKIVSANFQTAEGLLEVKPPELSKEVGLSKGEALETPHIVRRECLLKITRH

Parental  ANTSETGKKCTALELLEQEHTQGFIITFCSALDNILGGGVPLTKTTEICGAPGVGKTQLCMQLAADE---
          A.T..T.KKCTAL.LLEQE.TQG...TFCSALDNILGG.VP.T.TTE.CGAPGVG.T.LCM.LA.D....
Retrocopy AGTPDTDKKCTALGLLEQEYTQGSVFTFCSALDNILGGEVPST*TTESCGAPGVGNTLLCMELAIDAVDV

Parental  QIPECFGGVAGEAVFIDTEGSFMVDRVVDL-ATACIQHL-HLIAGTHMGEKHQ
          QIPECFGGVA.EAVFIDTE.SF.VDRVVDL.AT.C.Q.L.HLI...H.G..H.
Retrocopy QIPECFGGVAAEAVFIDTEESFLVDRVVDL<ATTCVQQL<HLITDIH-GTEHK

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	6.22 RPM
SRP012922_cerebellum	0.00 RPM	9.21 RPM
SRP012922_heart	0.00 RPM	3.71 RPM
SRP012922_kidney	0.00 RPM	7.39 RPM
SRP012922_liver	0.00 RPM	3.10 RPM
SRP012922_lung	0.00 RPM	9.01 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.38 RPM
SRP012922_spleen	0.00 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_946 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.

---

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 ,