RetrogeneDB ID: retro_dnov_1723

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_277094:186..811(-)
• 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_1723
AACTTGCAGTCTTATAGAGGAACTGACCGTGAAATACAAGAGGCAATCCAGCATCCAGCAGATGAGAAGTTGTAACACAA
GGCATGGAGGGCAGTTGTTCCACAAGCAGGTAAATTAAAGAAATTTTGTGAATTTTCTCAGAGGTTAGAAGCAGCATTAA
GAGGCCTTCTGGAAGCTTTGACAAATACCCCATATTCTCCCACCCAGCACCTAGAGCAAGAGCAGGCTGTTGTTAAACAG
TTTGCAGAAATTCTTCACTTCGCACTTGGTTTGATGAACTCAAGATAACAAATCTTGCCATACAGAATGATTTCAGCAAT
TATAGAAGAACATTGAGTTGTATGAGGATTAATAATGTTCCAGCAGGAGAAAATGAAGTAAATAGTGAATTGGCAAATCA
AATATCTTTATTTTATGCTGAGGCAACCCCAATACTGAAAACTTTAAGTGATGCCACAACAAAATTTGTATAAGAGAATA
AAAATTTACCAACAGAAAATACCACAGATTGTTTAAGCACCATAACTAGTGTGTGCAGAATCATCCTCGGATGCTGGAAT
ACAGAAGCAGGTTTACAAATGAGACGGTGTCCTGTTTGTGGGTCATGGTGGGTGTCTTCATCCTC

Alignment

ORF - retro_dnov_1723 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.44 %
• Parental protein coverage: 66.04 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLQSYRGAGHEIREAIQHPADEKLQEKAWGAVIPLVGKLKKFYEFSQRLETALRGLLGALTSTPYSPTQH
          .LQSYRG...EI.EAIQHPADEKL..KAW.AV.P..GKLKKF.EFSQRLE.ALRGLL.ALT.TPYSPTQH
Retrocopy NLQSYRGTDREIQEAIQHPADEKL*HKAWRAVVPQAGKLKKFCEFSQRLEAALRGLLEALTNTPYSPTQH

Parental  LEREQALAKQFAEILHFTLR-FDELKMTNPAIQNDFSYYRRTLSRMRINNVPAEGENEVNNELANRMSLF
          LE.EQA..KQFAEILHF.L..FDELK.TN.AIQNDFS.YRRTLS.MRINNVPA.GENEVN.ELAN..SLF
Retrocopy LEQEQAVVKQFAEILHFALG<FDELKITNLAIQNDFSNYRRTLSCMRINNVPA-GENEVNSELANQISLF

Parental  YAEATPMLKTLSDATTKFVSENKNLPIENTTDCLSTMASVCRVML-ETPEYRSRFTNEETVSFCLRVMVG
          YAEATP.LKTLSDATTKFV.ENKNLP.ENTTDCLST..SVCR..L....EYRSRFTN.ETVS.CL.VMVG
Retrocopy YAEATPILKTLSDATTKFV*ENKNLPTENTTDCLSTITSVCRIIL<RMLEYRSRFTN-ETVS-CLWVMVG

Parental  VIIL
          V.IL
Retrocopy VFIL

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	44.34 RPM
SRP012922_cerebellum	0.14 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	0.00 RPM	23.06 RPM
SRP012922_quadricep_muscle	0.17 RPM	26.14 RPM
SRP012922_spleen	0.11 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_1723 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,