RetrogeneDB ID: retro_dnov_855

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_114713:6283..6874(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000024913
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NFYB
• Ensembl ID: ENSDNOG00000009984
• Aliases: None
• Description: nuclear transcription factor Y, beta [Source:HGNC Symbol;Acc:7805]

Sequence

>retro_dnov_855
ATGACAATGGATGGTGACAGTTCTACAACAGATGCTTCTCAACTAGGAATTTCTGCAGACTATATTGGAGCAAGTCATTA
TGTTATAAAGCCTCATGATGATACTGAGGACAGCATGAATGATCATGAAGACACAAATGGCTCAAAAGAAAGTTTCAGAG
AACAAGATATATATCTTCCAATTGCAAATGTGGCAAGAATAATGAAAAATGCTATACCTCAAACAGGAAAGACTGCAAAA
GATGCCAAAGAATGTGTTCAGGAATGTGTGAGTGAATTCATCAGCTTTATAACTTCTGAAGCCAACGACAGATGCCATCA
AGAAAAACAGAAGACAGTCAATGGAGAAGATATTCTCTTTGCCATGTATACCTTAGGCTTTGACAGTTATGTAGAACCTC
TGAAATTATACCTTCAGAAATTCAGAGAGGCTATGAAAGGAGAGAAAGGAATTGGTGGAACAATCACAGCTACAGATGGA
CTCAGTGAAGAACTTACAGAGGAGGCATTTACTAATCAGTTACCAGCTGGCTTAATAACTGCAGATGGTCAGCAACAAAA
TGTTACGGTTTATACAATGTCATATCAACAG

Alignment

ORF - retro_dnov_855 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 94.42 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MTMDGDSSTTDASQLGISADYIGGSHYVIQPHDDTEDSMNDHEDTNGSKESFREQDIYLPIANVARIMKN
          MTMDGDSSTTDASQLGISADYIG.SHYVI.PHDDTEDSMNDHEDTNGSKESFREQDIYLPIANVARIMKN
Retrocopy MTMDGDSSTTDASQLGISADYIGASHYVIKPHDDTEDSMNDHEDTNGSKESFREQDIYLPIANVARIMKN

Parental  AIPQTGKIAKDAKECVQECVSEFISFITSEASERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQK
          AIPQTGK.AKDAKECVQECVSEFISFITSEA..RCHQEK.KT.NGEDILFAM.TLGFDSYVEPLKLYLQK
Retrocopy AIPQTGKTAKDAKECVQECVSEFISFITSEANDRCHQEKQKTVNGEDILFAMYTLGFDSYVEPLKLYLQK

Parental  FREAMKGEKGIGGTVTATDGLSEELTEEAFTNQLPAGLITADGQQQNVMVYTTSYQQ
          FREAMKGEKGIGGT.TATDGLSEELTEEAFTNQLPAGLITADGQQQNV.VYT.SYQQ
Retrocopy FREAMKGEKGIGGTITATDGLSEELTEEAFTNQLPAGLITADGQQQNVTVYTMSYQQ

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	0.78 RPM	9.33 RPM
SRP012922_cerebellum	0.55 RPM	6.05 RPM
SRP012922_heart	0.23 RPM	3.94 RPM
SRP012922_kidney	0.27 RPM	5.20 RPM
SRP012922_liver	1.08 RPM	34.99 RPM
SRP012922_lung	1.07 RPM	12.37 RPM
SRP012922_quadricep_muscle	0.00 RPM	5.88 RPM
SRP012922_spleen	0.92 RPM	14.65 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_855 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000014610	1 retrocopy	retro_cjac_1133,
Cavia porcellus	ENSCPOG00000003213	1 retrocopy	retro_cpor_901,
Dasypus novemcinctus	ENSDNOG00000009984	3 retrocopies	retro_dnov_1536, retro_dnov_758, retro_dnov_855 ,
Felis catus	ENSFCAG00000026471	1 retrocopy	retro_fcat_207,
Myotis lucifugus	ENSMLUG00000005468	1 retrocopy	retro_mluc_1764,
Ochotona princeps	ENSOPRG00000008117	2 retrocopies	retro_opri_36, retro_opri_657,
Pongo abelii	ENSPPYG00000004892	3 retrocopies	retro_pabe_2201, retro_pabe_2803, retro_pabe_3319,