RetrogeneDB ID: retro_dnov_1108

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_148309:1201..1697(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000025273
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NUP62CL
• Ensembl ID: ENSDNOG00000001467
• Aliases: None
• Description: nucleoporin 62kDa C-terminal like [Source:HGNC Symbol;Acc:25960]

Sequence

>retro_dnov_1108
AGTCCCGCGATGACCTACGCCCAGCTGGAGAGTCTGATCAACAAGTGGAGCCTGGAGCTGGAGGACCAAGAGCGGCACTT
CCTGCAGCAGGCCACGCAGGTGAACGCCTGGGACCGCACGCTGATCGAGAACGGGGAGAAGATCACCACCCTGCACCGCG
AGGTGGAGAAGGTGAAGCTGGACCAGAGGCGGCTGGACCAAGAGCTCGACTTCATCCTGTCCCAGCAGAAGGAGCTGGAA
GACCTGCTGAGCCCGCTGGAGGAGTCGGTCAAGGAGCAGAGCGGGACCATCTACCTGCAGCACGCCGACGAGGAGCGCGA
GAAGACCTACAAGCTGGCGGAGAACATCGACGCGCAGCTGAAGCGCATGGCCCAGGACCTCAAGGACGTCATCGAGCACC
TGAACACGTGCGGGGGCTCGCCGACACCAGCGACCGCTGCAGCAGATCTGCAAGATCCTCAACGCGCACATGGACTCGCT
GCAGTGGGTCGACCAG

Alignment

ORF - retro_dnov_1108 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.57 %
• Parental protein coverage: 61.71 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TPVMTYDKLEGLINKRSLELEDQEKHFLHQATQVNACDRTLIENGEQIYTLHGEVEKVKLDQKRLEQELD
          .P.MTY..LE.LINK.SLELEDQE.HFL.QATQVNA.DRTLIENGE.I.TLH.EVEKVKLDQ.RL.QELD
Retrocopy SPAMTYAQLESLINKWSLELEDQERHFLQQATQVNAWDRTLIENGEKITTLHREVEKVKLDQRRLDQELD

Parental  FILSQQKKLIDPSIPLEESVKGQSGSIYLQHANKERERTYKLSENINVQLKRMAQDLKDIIEHLNTFGSP
          FILSQQK.L.D...PLEESVK.QSG.IYLQHA..ERE.TYKL.ENI..QLKRMAQDLKD.IEHLNT.G..
Retrocopy FILSQQKELEDLLSPLEESVKEQSGTIYLQHADEEREKTYKLAENIDAQLKRMAQDLKDVIEHLNTCGGS

Parental  -ADTMDL-LQQICKILNAHMDSLQWIDQ
          .ADT.D..LQQICKILNAHMDSLQW.DQ
Retrocopy <ADTSDR<LQQICKILNAHMDSLQWVDQ

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	11.47 RPM	0.00 RPM
SRP012922_cerebellum	27.22 RPM	0.55 RPM
SRP012922_heart	2.32 RPM	0.23 RPM
SRP012922_kidney	3.83 RPM	0.55 RPM
SRP012922_liver	2.94 RPM	0.00 RPM
SRP012922_lung	6.72 RPM	1.07 RPM
SRP012922_quadricep_muscle	4.15 RPM	0.17 RPM
SRP012922_spleen	10.53 RPM	0.23 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_1108 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017963	1 retrocopy	retro_cfam_218,
Dasypus novemcinctus	ENSDNOG00000001467	1 retrocopy	retro_dnov_1108 ,
Felis catus	ENSFCAG00000001984	1 retrocopy	retro_fcat_120,
Macropus eugenii	ENSMEUG00000001005	1 retrocopy	retro_meug_1130,
Nomascus leucogenys	ENSNLEG00000013865	1 retrocopy	retro_nleu_2076,
Pteropus vampyrus	ENSPVAG00000001787	1 retrocopy	retro_pvam_694,
Vicugna pacos	ENSVPAG00000003649	1 retrocopy	retro_vpac_448,