RetrogeneDB ID: retro_dnov_1562

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_23506:42977..43441(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000005174
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SYS1-DBNDD2
• Ensembl ID: ENSDNOG00000011943
• Aliases: None
• Description: SYS1-DBNDD2 readthrough (NMD candidate) [Source:HGNC Symbol;Acc:33535]

Sequence

>retro_dnov_1562
ATGGCAGGCCAGTTCCGCAGCTACGTATGGGATCCGTTGCTGATCATGTCGCAGATCATCCTCATGCAGACCGTCTATTT
TGGCTCACTGGGCCTGTGGCTGGTGCTGGTGGATGGGCTGGTGCGCAGCGGCCCTTCGCTGGACCAGATGTTCAACGCTG
AGATCCTGGGCTTCTCCACCCCTCCAGGCCGGCTCTCCATGATGTCCTTCATCCTCAATGCCCTCACCTGTGCCCTGGGC
TTGCTGTACTTCATCCAGCGAGGGAAGCAGTGTCTGGATTTCACTGTCAATGTCCATTTCTTTCACCTGGCCTGCTGGTT
CTACAGCTCCCGTTTCCCTCGGTGCTGACCTGGTGGCTTGTCCAAGCTGTGTGCATTGCACTCATGGCTGTCATCAGGGA
GTACCTGTGCATGCAGATGGAGCTCAAGGAGATCCCCCTCAACTCAGCCCCTAAATCCAATGTC

Alignment

ORF - retro_dnov_1562 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 91.08 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MAGQFRSYVWDPLLIMSQIVLMQTVYYGSLGLWLALVDGLVRSSPSLDQMFDAEILGFSTPPGRLSMMSF
          MAGQFRSYVWDPLLIMSQI.LMQTVY.GSLGLWL.LVDGLVRS.PSLDQMF.AEILGFSTPPGRLSMMSF
Retrocopy MAGQFRSYVWDPLLIMSQIILMQTVYFGSLGLWLVLVDGLVRSGPSLDQMFNAEILGFSTPPGRLSMMSF

Parental  ILNALTCALGLLYFIRRGKQCLDFTVTVHFFHLLGCWFYSSR-FPSALTWWLVQAVCIALMAVIGEYLCM
          ILNALTCALGLLYFI.RGKQCLDFTV.VHFFH.L.CWFYSSR.FPS.LTWWLVQAVCIALMAVI.EYLCM
Retrocopy ILNALTCALGLLYFIQRGKQCLDFTVNVHFFH-LACWFYSSR<FPSVLTWWLVQAVCIALMAVIREYLCM

Parental  RTELKEIPLNSAPKSNV
          ..ELKEIPLNSAPKSNV
Retrocopy QMELKEIPLNSAPKSNV

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	21.59 RPM
SRP012922_cerebellum	0.14 RPM	24.47 RPM
SRP012922_heart	0.00 RPM	12.99 RPM
SRP012922_kidney	0.00 RPM	17.80 RPM
SRP012922_liver	0.00 RPM	60.37 RPM
SRP012922_lung	0.00 RPM	26.12 RPM
SRP012922_quadricep_muscle	0.00 RPM	13.85 RPM
SRP012922_spleen	0.00 RPM	28.84 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_1562 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 3 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011943	2 retrocopies	retro_dnov_1417, retro_dnov_1562 ,
Echinops telfairi	ENSETEG00000014613	2 retrocopies	retro_etel_1084, retro_etel_710,
Loxodonta africana	ENSLAFG00000008154	2 retrocopies	retro_lafr_230, retro_lafr_360,