RetrogeneDB ID: retro_dnov_521

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_5632:2450..3050(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000006702
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: C8orf33
• Ensembl ID: ENSDNOG00000015805
• Aliases: None
• Description: chromosome 8 open reading frame 33 [Source:HGNC Symbol;Acc:26104]

Sequence

>retro_dnov_521
ATGGCAGTCCCTGGACACCCTGCTCGGGAGACTTCGGCGGCCGCAGCCCCAGGTGCGGCCCGCGTGCCTCACACCGGCCC
CCTGGCCCGGCTCTCAGCGCCCCGACTCTTTCCTCTGTAACATCATCCAGCGCATCTCTGCCCCGGGCACCCACCTGTAA
TGACGCTGTCCCCAGGGTGCTCCCCGTAGGCGATGACGGTGATGCAGCCTCTAAGAAGCAAAAGAAGAATAAGAAGAAAA
CCGGGAACGGGGCGTCTGTGGCAAATGGAGGCGGGAAGGCCTCAGAAAAGCTGGCCCCAGAGGAGCCCTAAGTGCTGAGG
CCCAGGCAGAGCAGCTGGCCCAGGAACTGGCTTGGTGTGTGGAGCAGCTCCATCTGGATCTCAGGACCCAGAGACCCAGC
CCAAAACAGAAAGAGCAGGCTACTGGAGCAATCCGGACCCTCGTCAGCGAACCCCCCTGCCCCGGAAGAGGCAGCTCATG
CATTCCTTATTTGGGGACTACAGGACTCAGATGGAAGCAGAATGGAGAGGGGCCCTGCAGGCTCTCAGGGCTGCAGCCCA
TTCATCCCAGGTGAAGCCTGTAAGACCACCAGAAAGAAGA

Alignment

ORF - retro_dnov_521 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.43 %
• Parental protein coverage: 87.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MAVSGHPARETAAAAAPGAARAPHAPRPPGPALSAPTLSSATSPPARLCPGRP-TCKDAVPRVLPAGDDG
          MAV.GHPARET.AAAAPGAAR.PH....P...LSAP.L......PA.LCPG.P.TC.DAVPRVLP.GDDG
Retrocopy MAVPGHPARETSAAAAPGAARVPHTG--PLARLSAPRLFPL*HHPAHLCPGHP<TCNDAVPRVLPVGDDG

Parental  D-AASKKQKKKKKTRDGASVADGGGKASEKLVPEEP-LSAEAQAEQLAQELAWCVEQLQLGLRTQRPSPK
          D.A.............GASVA.GGGKASEKL.PEEP.LSAEAQAEQLAQELAWCVEQL.L.LRTQRPSPK
Retrocopy DAASXXXXXXXXXXGNGASVANGGGKASEKLAPEEP<LSAEAQAEQLAQELAWCVEQLHLDLRTQRPSPK

Parental  QKEQATGAIRTLLSERTPLP-RKRQLMRSLFGDYRTQMEAERRETLQALRAAAHSSQVKPVSKAARK
          QKEQATGAIRTL.SE..P.P.RKRQLM.SLFGDYRTQMEAE.R..LQALRAAAHSSQVKPV....R.
Retrocopy QKEQATGAIRTLVSE-PPCP<RKRQLMHSLFGDYRTQMEAEWRGALQALRAAAHSSQVKPVRPPERR

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	12.64 RPM
SRP012922_cerebellum	0.69 RPM	6.05 RPM
SRP012922_heart	0.00 RPM	5.10 RPM
SRP012922_kidney	0.27 RPM	18.34 RPM
SRP012922_liver	0.00 RPM	4.95 RPM
SRP012922_lung	0.00 RPM	15.27 RPM
SRP012922_quadricep_muscle	0.00 RPM	6.23 RPM
SRP012922_spleen	0.11 RPM	13.96 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_521 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000015805	3 retrocopies	retro_dnov_1578, retro_dnov_406, retro_dnov_521 ,
Macaca mulatta	ENSMMUG00000016084	1 retrocopy	retro_mmul_1436,
Monodelphis domestica	ENSMODG00000028791	2 retrocopies	retro_mdom_1056, retro_mdom_388,
Mustela putorius furo	ENSMPUG00000005972	1 retrocopy	retro_mputfur_1096,
Rattus norvegicus	ENSRNOG00000034107	1 retrocopy	retro_rnor_436,