RetrogeneDB ID: retro_dnov_2654

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_95025:3585..4016(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: KDELR2
• Ensembl ID: ENSDNOG00000009897
• Aliases: None
• Description: KDEL (Lys-Asp-Glu-Leu) endoplasmic reticulum protein retention receptor 2 [Source:HGNC Symbol;Acc:6305]

Sequence

>retro_dnov_2654
TTATGCCCCTATGTCACAATGTACCTCATCTACATGAAATTTAAACCAAACTATGATGGCAATCATAATACCTTCTGAGT
GGAGTTCTGGAGGTCCCTGTGGGAGTCCTCTCATTTCAAGTTAATCATGATTTCTCTCCTCTTGAGATTCTGTGGATCTT
GTGCATCTACCTTGAGTCAACAACTATCCTCGCACAGCTCTTTATGATCAGCATGTCGGGCAAGGTAGAGATCATCACCA
CCCACTACCTGTTCTTCCTGGGCCTCTACCATGTTCTATACCTTTTCAACTGGATCTGGCACTTGCACTTTGAGGACTTC
TCTGAACTCATGCCTGTGGTGGCCAGTGTAGTACAGATCATTCTGTATTGTGACCTCTTCTATCTGTACATCACAAAAGT
ACTCAAGAGGAAGTAGCTCAGCTTGCCAGCA

Alignment

ORF - retro_dnov_2654 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.79 %
• Parental protein coverage: 67.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VCSYATVYLIYMKFKATYDGNHDTFRVEF-LVVPVGGLSFLVNHDFSPLEILWTFSIYLESVTILPQLFM
          .C.Y.T.YLIYMKFK..YDGNH.TF.VEF.L.VPVG.LSF.VNHDFSPLEILW...IYLES.TIL.QLFM
Retrocopy LCPYVTMYLIYMKFKPNYDGNHNTF*VEF<LEVPVGVLSFQVNHDFSPLEILWILCIYLESTTILAQLFM

Parental  ISKTGEAETITTHYLFFLGLYRALYLVNWIWRFYFEGFFDLIAVVAGVVQTILYCDFFYLYITKVLKGKK
          IS..G..E.ITTHYLFFLGLY..LYL.NWIW...FE.F..L..VVA.VVQ.ILYCD.FYLYITKVLK.K.
Retrocopy ISMSGKVEIITTHYLFFLGLYHVLYLFNWIWHLHFEDFSELMPVVASVVQIILYCDLFYLYITKVLKRK*

Parental  LSLPA
          LSLPA
Retrocopy LSLPA

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	107.74 RPM
SRP012922_cerebellum	0.00 RPM	16.08 RPM
SRP012922_heart	0.00 RPM	6.26 RPM
SRP012922_kidney	0.00 RPM	16.70 RPM
SRP012922_liver	0.00 RPM	42.26 RPM
SRP012922_lung	0.00 RPM	42.76 RPM
SRP012922_quadricep_muscle	0.00 RPM	10.21 RPM
SRP012922_spleen	0.00 RPM	43.50 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_2654 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000015746	2 retrocopies	retro_cfam_1944, retro_cfam_318,
Choloepus hoffmanni	ENSCHOG00000000125	1 retrocopy	retro_chof_2624,
Dasypus novemcinctus	ENSDNOG00000009897	1 retrocopy	retro_dnov_2654 ,
Echinops telfairi	ENSETEG00000016544	1 retrocopy	retro_etel_1867,
Monodelphis domestica	ENSMODG00000007832	1 retrocopy	retro_mdom_1547,