RetrogeneDB ID: retro_dnov_896

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_118904:3864..4673(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM49B
• Ensembl ID: ENSDNOG00000009323
• Aliases: None
• Description: family with sequence similarity 49, member B [Source:HGNC Symbol;Acc:25216]

Sequence

>retro_dnov_896
AACTTACAGTCATATAGAGGAGCTGGCCATGAAATACTAGAGGCAAACCAGCATCCAGCAGATGACAAGTTGCAAAAGAA
GGCATCAGGTGCGGTTATTCCACTAGTAGGCATACTAAAGAAATTTTATGAATTTTCTCAGAGGTTAAAAGCTGCATTAA
GAGGTCTTCCGGGAGCCTTGACAAGTACCCCATATTCTCCCACCCAGCATCAAGAGCAAGTGTAGGCTCTTGCTAAACAG
TTTGCAGAAATTCTTCACTTCACACTCCAGTTTGATGAACTTAAGATGACAAATCCTGCCATACAGAATGATTTCAGCTA
TTATAGAAGAACATTGAGTCATATGAGAATTAATAATGTTCCAGCAGACGGAGAAAAATGAAGTAAATAACGAATTGGCA
AATCGAATGTCATTATTTTATGCTGAGGCAACCCCAAAGCTGATAACTTTAAAAGATGCCACAACAAAATTTGTATGAGA
GAATAAAAATTTACCAATAGAAAATACCACAGATTGTTTAAGCACCATGGCTAGTGTGTGCAGAGTCATGTTCAAGATGC
CAGAATACAGAAACAGATTTTACAAATGAGGAGACAGTATCCTTCTGCTTATGGGTCACAGCGGCTATCATCATCCTCTA
TGACCAGGTACATTCAGTGGGAGCATTTGCCAAAACTTCAAAAATTGATATAAAAGTTTGTATCAAAGTTCTTAAGGAAC
AACCTCCTAATAGAGTAGAAGGTCTTCTAAATGTTTTCAGGTACACAACAAAACAATTGAATGATGAGACTACATCCAAG
CAAATTAAA

Alignment

ORF - retro_dnov_896 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.5 %
• Parental protein coverage: 83.8 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLQSYRGAGHEIREAIQHPADEKLQEKAWGAVIPLVGKLKKFYEFSQRLETALRGLLGALTSTPYSPTQH
          .LQSYRGAGHEI.EA.QHPAD.KLQ.KA.GAVIPLVG.LKKFYEFSQRL..ALRGL.GALTSTPYSPTQH
Retrocopy NLQSYRGAGHEILEANQHPADDKLQKKASGAVIPLVGILKKFYEFSQRLKAALRGLPGALTSTPYSPTQH

Parental  LEREQALAKQFAEILHFTLRFDELKMTNPAIQNDFSYYRRTLSRMRINNVPAEGE-NEVNNELANRMSLF
          .E...ALAKQFAEILHFTL.FDELKMTNPAIQNDFSYYRRTLS.MRINNVPA.GE.NEVNNELANRMSLF
Retrocopy QEQV*ALAKQFAEILHFTLQFDELKMTNPAIQNDFSYYRRTLSHMRINNVPADGE>NEVNNELANRMSLF

Parental  YAEATPMLKTLSDATTKFVSENKNLPIENTTDCLSTMASVCRVMLETPEYRSR-FTNEETVSFCLRVMVG
          YAEATP.L.TL.DATTKFV.ENKNLPIENTTDCLSTMASVCRVM...PEYR.R.FTNEETVSFCL.V...
Retrocopy YAEATPKLITLKDATTKFV*ENKNLPIENTTDCLSTMASVCRVMFKMPEYRNR>FTNEETVSFCLWVTAA

Parental  VIILYDHVHPVGAFAKTSKIDMKGCIKVLKDQPPNSVEGLLNALRYPTKHLNDETTSKQIK
          .IILYD.VH.VGAFAKTSKID.K.CIKVLK.QPPN.VEGLLN..RY.TK.LNDETTSKQIK
Retrocopy IIILYDQVHSVGAFAKTSKIDIKVCIKVLKEQPPNRVEGLLNVFRYTTKQLNDETTSKQIK

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	0.19 RPM	44.34 RPM
SRP012922_cerebellum	0.00 RPM	48.25 RPM
SRP012922_heart	0.00 RPM	7.19 RPM
SRP012922_kidney	0.00 RPM	17.25 RPM
SRP012922_liver	0.00 RPM	13.47 RPM
SRP012922_lung	0.31 RPM	23.06 RPM
SRP012922_quadricep_muscle	0.17 RPM	26.14 RPM
SRP012922_spleen	0.23 RPM	58.03 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_896 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000009323	3 retrocopies	retro_dnov_1596, retro_dnov_1723, retro_dnov_896 ,
Dipodomys ordii	ENSDORG00000005160	1 retrocopy	retro_dord_381,
Echinops telfairi	ENSETEG00000015647	1 retrocopy	retro_etel_1299,
Felis catus	ENSFCAG00000015625	1 retrocopy	retro_fcat_1690,
Oryctolagus cuniculus	ENSOCUG00000013690	1 retrocopy	retro_ocun_953,
Procavia capensis	ENSPCAG00000002866	3 retrocopies	retro_pcap_293, retro_pcap_332, retro_pcap_40,
Sus scrofa	ENSSSCG00000005959	1 retrocopy	retro_sscr_978,