RetrogeneDB ID: retro_dnov_2095

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_47209:9275..9767(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GPN3
• Ensembl ID: ENSDNOG00000016646
• Aliases: None
• Description: GPN-loop GTPase 3 [Source:HGNC Symbol;Acc:30186]

Sequence

>retro_dnov_2095
CAGATTGAGTTGTCCACTCACCTGCCTTTGATGAAACAGCTGGTACAGCAGCTGGAACGGTGGGAGTTCGGAGTCTTCGG
TGTTTTCTTTGTTGATTCTCAGTTTCTGGTGGAGTCATTCAAGTTTCTCTCTGGCATCTTGGCAGCCCTGAGTGCAAGGA
TCTCTCTAGAAATTCCACAAATTAACATCATGACGAAAATGGATCTTCTGAGTGAGAAAGCTAAAAAAGAGATTGAAAAG
TTTCTAGATACATGATGTATATAGTTTGTTAGAGATTCTACAAGTGGCTTAAGAAGTGCAAAATTCAGAAAATTACCAAA
TGCTATTCGTGGACTGATCGATGACTACAGCACGGTTCGATTTTTACCTTACTATCAGTCAGACGAAGAAAGCATGAACA
TTGTATTATAGCATATTGATTTTGCCATTCAGTATGGAGAAGATTTGGAATGTAAAGAACCAAAGGAACATGAAGATGAG
TCATCTTCTATG

Alignment

ORF - retro_dnov_2095 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.35 %
• Parental protein coverage: 59.85 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QIELYTHLPVMKQLVQQLEQWEFRVCGVFLVDSQFMVESFKFLSGILAALSAMISLEIPQVNIMTKMDLL
          QIEL.THLP.MKQLVQQLE.WEF.V.GVF.VDSQF.VESFKFLSGILAALSA.ISLEIPQ.NIMTKMDLL
Retrocopy QIELSTHLPLMKQLVQQLERWEFGVFGVFFVDSQFLVESFKFLSGILAALSARISLEIPQINIMTKMDLL

Parental  SKKAKKEIEKFLDP-DVYSLLE-DPTSGLRSAKFKKLSNAICGLIDDYSMVRFLPYDQSDEESMNIVLQH
          S.KAKKEIEKFLD..DVYSLLE.D.TSGLRSAKF.KL.NAI.GLIDDYS.VRFLPY.QSDEESMNIVL.H
Retrocopy SEKAKKEIEKFLDT>DVYSLLE<DSTSGLRSAKFRKLPNAIRGLIDDYSTVRFLPYYQSDEESMNIVL*H

Parental  IDFAIQYGEDLEFKEPKEHEDESSSM
          IDFAIQYGEDLE.KEPKEHEDESSSM
Retrocopy IDFAIQYGEDLECKEPKEHEDESSSM

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	14.00 RPM
SRP012922_cerebellum	0.14 RPM	8.11 RPM
SRP012922_heart	0.23 RPM	5.10 RPM
SRP012922_kidney	0.27 RPM	6.30 RPM
SRP012922_liver	0.15 RPM	5.57 RPM
SRP012922_lung	0.31 RPM	9.01 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.81 RPM
SRP012922_spleen	0.00 RPM	8.47 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_2095 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009339	1 retrocopy	retro_cjac_2969,
Dasypus novemcinctus	ENSDNOG00000016646	1 retrocopy	retro_dnov_2095 ,
Homo sapiens	ENSG00000111231	1 retrocopy	retro_hsap_652,
Gorilla gorilla	ENSGGOG00000001697	1 retrocopy	retro_ggor_570,
Myotis lucifugus	ENSMLUG00000015510	1 retrocopy	retro_mluc_408,
Macaca mulatta	ENSMMUG00000006494	1 retrocopy	retro_mmul_2435,
Nomascus leucogenys	ENSNLEG00000002831	1 retrocopy	retro_nleu_2030,