RetrogeneDB ID: retro_dnov_1317

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_18076:12589..12936(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PFDN6
• Ensembl ID: ENSDNOG00000011211
• Aliases: None
• Description: prefoldin subunit 6 [Source:HGNC Symbol;Acc:4926]

Sequence

>retro_dnov_1317
GTGGAAAAATATCAGCAGCTATAGAAGGACTTGAGCAAGTCCAAGTCAGGGAGGCAGAAGTTAGAGGCACAACTAACAGA
AAATAATATCGCGAAGGAGGAATTGGCCCTGCTGGATGGATCCAATGTGGTCTTTAAACTCCTGGGTCTGGTATTGCTCA
AAAAGGAGCTGCAGGAGGCCCAAGCCACAGTGGGGACAAGGCTGGACCATATTACAGCTGAAATTAAATGATACAAGTCC
CAGTTCCGGGACCTTGAGCGGCAGTCCGAGCAACAGAGGGAGATGCTTGCTCAGCTGAGCAGGAAATCCAGCAGGCCCTG
GCAGCAAAAGCAGGGGCTCCTAAGAAG

Alignment

ORF - retro_dnov_1317 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.91 %
• Parental protein coverage: 89.92 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  VEKYQQLQKDLSKSMSGRQKLEAQLTENNIVKEELALLDGSNVVFKLLGPVLVKQELGEAQATVGKRLDY
          VEKYQQL.KDLSKS.SGRQKLEAQLTENNI.KEELALLDGSNVVFKLLG.VL.K.EL.EAQATVG.RLD.
Retrocopy VEKYQQL*KDLSKSKSGRQKLEAQLTENNIAKEELALLDGSNVVFKLLGLVLLKKELQEAQATVGTRLDH

Parental  ITAEIKRYESQLRDLERQSERQRETLAQL-QQEFQRAQAAKAGAPEK
          ITAEIK.Y.SQ.RDLERQSE.QRE.LAQL..QE.Q.A.AAKAGAP.K
Retrocopy ITAEIK*YKSQFRDLERQSEQQREMLAQL<EQEIQQALAAKAGAPKK

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	30.53 RPM
SRP012922_cerebellum	0.00 RPM	35.74 RPM
SRP012922_heart	0.00 RPM	30.63 RPM
SRP012922_kidney	0.00 RPM	55.31 RPM
SRP012922_liver	0.00 RPM	21.36 RPM
SRP012922_lung	0.00 RPM	32.68 RPM
SRP012922_quadricep_muscle	0.00 RPM	24.23 RPM
SRP012922_spleen	0.00 RPM	27.47 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_1317 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 6 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000011211	2 retrocopies	retro_dnov_1317 , retro_dnov_2064,
Loxodonta africana	ENSLAFG00000012967	1 retrocopy	retro_lafr_363,
Macropus eugenii	ENSMEUG00000016778	1 retrocopy	retro_meug_1930,
Otolemur garnettii	ENSOGAG00000028341	4 retrocopies	retro_ogar_1185, retro_ogar_2023, retro_ogar_3508, retro_ogar_85,
Ochotona princeps	ENSOPRG00000000983	1 retrocopy	retro_opri_12,
Procavia capensis	ENSPCAG00000006019	1 retrocopy	retro_pcap_226,