RetrogeneDB ID: retro_dnov_1288

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_176544:811..1415(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TRAPPC13
• Ensembl ID: ENSDNOG00000006386
• Aliases: None
• Description: trafficking protein particle complex 13 [Source:HGNC Symbol;Acc:25828]

Sequence

>retro_dnov_1288
TTAATGTTCACTGCAGCAGAATTAAACACTCTCAACCCAAACTGGAGAAGATGAATGCACCTTTGGTACTAGGACATTTT
TGCAATCAATGGAAGGACGCCAGTACTTATACCACCTGCAGCTCAAGCAGGAATTTTCGGAGAAAGCTGCTATCACTAGA
GGACTAACAAAAATGGGAAAATTGGATATAATGTGGAAAAAAAATCTAGGTGAAATGGCAATTCTACAAACAGTCCACCT
TGAAAGAGAAGCTCCAGGTTATGGAAACATGAGGCTGTCTTTGGAGACAATCCCAGATACTGTAATTCTAGAAGAACCTT
TTCAAATTACCTGTAAGATAACAAACTACAGTGATAGGAAAGTGAAATTGGCTTTGAAAATGTATGATAAAGATTCTATT
CGTTGGTGTGGAAGTTCAGGACGGTATCTTGGAAAGCTCTCTCCAAATTCATCTCTTTGTTTTACTCTAACACTGTTGTC
TTTAAAATTGGGCCTTCAAAGTGTCTCTGGGATACAGATAACAGAAAAATTATTAAAGAAAACATATGAATATGATGATA
TTGCGAAAGTTTTTGTAATACCTTCTATGGTTAAAATGAAAAGT

Alignment

ORF - retro_dnov_1288 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.89 %
• Parental protein coverage: 56.62 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IMYNVAELNSVN-QAGECVSTFGSRAYLQPMDTRQYLYCLKPKKEFSEKAGIIKGVTVIGKLDIVWKTNL
          .M...AELN..N.Q.GE...TFG.R..LQ.M..RQYLY.L..K.EFSEKA.I..G.T..GKLDI.W...L
Retrocopy LMFTAAELNTLN>QTGEDECTFGTRTFLQSMEGRQYLYHLQLKQEFSEKAAITRGLTKMGKLDIMWXXXL

Parental  GERGRLQTSQLQRMAPGYGDVRLSLEAIPDTVNLEEPFHITCKITNCSERTMDLVLEMCNTNSIHWCGIS
          GE...LQT..L.R.APGYG..RLSLE.IPDTV.LEEPF.ITCKITN.S.R...L.L.M....SI.WCG.S
Retrocopy GEMAILQTVHLEREAPGYGNMRLSLETIPDTVILEEPFQITCKITNYSDRKVKLALKMYDKDSIRWCGSS

Parental  GRQLGKLHPSSSLCLALTLLSSVQGLQSVSGLRLTDTFLKRTYEYDDIAQVCVVSSAIKVES
          GR.LGKL.P.SSLC..LTLLS...GLQSVSG...T...LK.TYEYDDIA.V.V..S..K..S
Retrocopy GRYLGKLSPNSSLCFTLTLLSLKLGLQSVSGIQITEKLLKKTYEYDDIAKVFVIPSMVKMKS

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	9.92 RPM
SRP012922_cerebellum	0.00 RPM	27.49 RPM
SRP012922_heart	0.00 RPM	5.80 RPM
SRP012922_kidney	0.00 RPM	7.67 RPM
SRP012922_liver	0.00 RPM	6.19 RPM
SRP012922_lung	0.00 RPM	12.37 RPM
SRP012922_quadricep_muscle	0.00 RPM	9.17 RPM
SRP012922_spleen	0.00 RPM	13.16 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_1288 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006026	1 retrocopy	retro_chof_1834,
Dasypus novemcinctus	ENSDNOG00000006386	1 retrocopy	retro_dnov_1288 ,
Equus caballus	ENSECAG00000011983	1 retrocopy	retro_ecab_1074,
Pteropus vampyrus	ENSPVAG00000008275	1 retrocopy	retro_pvam_980,
Sorex araneus	ENSSARG00000000639	1 retrocopy	retro_sara_394,
Ictidomys tridecemlineatus	ENSSTOG00000021318	1 retrocopy	retro_itri_1455,
Tarsius syrichta	ENSTSYG00000004582	1 retrocopy	retro_tsyr_18,
Tursiops truncatus	ENSTTRG00000006537	1 retrocopy	retro_ttru_1068,