RetrogeneDB ID: retro_dnov_1536

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_22904:32969..33296(-)
• Located in intron of: None

Retrocopy information

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

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_1536
GAGTTCTTCAGCTTTATAACTTCTGAAGCCATGAATGATGCCATCAAGCAAAACAGAAGACAATTACTGGAGGTGATATT
CTGTTTGTCATGTCTATCTTAAGCTTTGAAAGCTATGTAGAACCACTGAAATTATACCTTCAGAAATTCAGAGAGGCTAT
GAAAGGAGAAAAAGGAATTGGTGGAATTGGTGGAACAGTCACAGCTACAGATGGATTAAGTGAAGAGTTTACGGAGGAGG
AAATTTACTAACCAGTTACCAGCTGTCTTAATAACTTCAGATGATCAACAACAAAAAGTTAAGTTTTATACAATGTCATA
GCAACAG

Alignment

ORF - retro_dnov_1536 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.37 %
• Parental protein coverage: 53.81 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EFISFITSEAS-ERCHQEKRKTINGEDILFAMSTLGFDSYVEPLKLYLQKFREAM---KGEKGIGGTVTA
          EF.SFITSEA..E.CHQ.K.KTI.G.DILF.MS.L.F.SYVEPLKLYLQKFREAM...K........VTA
Retrocopy EFFSFITSEAM<E*CHQAKQKTITGGDILFVMSILSFESYVEPLKLYLQKFREAMKGEKXXXXXXXXVTA

Parental  TDGLSEELTEEA-FTNQLPAGLITADGQQQNVMVYTTSYQQ
          TDGLSEE.TEE..FTNQLPA.LIT.D.QQQ.V..YT.S.QQ
Retrocopy TDGLSEEFTEEE>FTNQLPAVLITSDDQQQKVKFYTMS*QQ

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	9.33 RPM
SRP012922_cerebellum	0.00 RPM	6.05 RPM
SRP012922_heart	0.00 RPM	3.94 RPM
SRP012922_kidney	0.00 RPM	5.20 RPM
SRP012922_liver	0.00 RPM	34.99 RPM
SRP012922_lung	0.00 RPM	12.37 RPM
SRP012922_quadricep_muscle	0.00 RPM	5.88 RPM
SRP012922_spleen	0.00 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_1536 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,