RetrogeneDB ID: retro_dnov_1758

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_28975:8070..8490(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB3C
• Ensembl ID: ENSDNOG00000025047
• Aliases: None
• Description: RAB3C, member RAS oncogene family [Source:HGNC Symbol;Acc:30269]

Sequence

>retro_dnov_1758
GACACGGCCGGACAAAAGCGGTCCCGGGCCTTCGCCGCAGCCTCCTCCCGGGGTGCCGCGGGCTTCATCCTCGTGCGCGA
CATCTCCAACGAGGAGTCCTTCAACGCCGGGCGGGACTGGTCCACCCAACTCAAGACGCACCCCTGGGACGACGCGCAGG
TGCGGCAGGTGGGAACAAGGTGTCCCCGGGGACCAGCGGGCGGCGTCGCCTGAGCGCGGCGGCAGCTGGCGGGCCGCGCG
GGGTTCGAGTTCTTCCAGGCCAGCGCCAAGCACAGCATCAACGTCAAGCGGACCTTCCAGTGCCTGGTGAAGGTCATCTG
CGAGATGTCCGAGTCGCTGGACGCAGCGGACCCCGCGGTCACCGCGGCCGAGCAGGGGCCGCAGCTCACCCACCGGCAGG
CGCCCCCTCTCCAGGACTGC

Alignment

ORF - retro_dnov_1758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.52 %
• Parental protein coverage: 62.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DTAGQERYRTITTAYYRGAMGFILMYDITNEESFNAVQDWSTQIKTYSWDNAQVILVGNKCDMEDERVIS
          DTAGQ.R.R....A..RGA.GFIL..DI.NEESFNA..DWSTQ.KT..WD.AQV..VG..C.........
Retrocopy DTAGQKRSRAFAAASSRGAAGFILVRDISNEESFNAGRDWSTQLKTHPWDDAQVRQVGTRCPRGPAGGVA

Parental  TERGQHLGEQLGFEFFETSAKDNVNVKQTFERLVDIICEKMSESLE-TDPAITAAKQNTRLKETPPPPQP
          ..R.Q.L....GFEFF..SAK...NVK.TF..LV..ICE.MSESL...DPA.TAA.Q...L.....PP..
Retrocopy *ARRQ-LAGRAGFEFFQASAKHSINVKRTFQCLVKVICE-MSESLDAADPAVTAAEQGPQLTHRQAPPLQ

Parental  NC
          .C
Retrocopy DC

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	2.14 RPM
SRP012922_cerebellum	0.00 RPM	10.59 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	0.00 RPM
SRP012922_liver	0.00 RPM	0.00 RPM
SRP012922_lung	0.00 RPM	0.31 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	1.14 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_1758 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 2 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000023965	3 retrocopies	retro_dnov_1191, retro_dnov_1981, retro_dnov_23,
Dasypus novemcinctus	ENSDNOG00000025047	1 retrocopy	retro_dnov_1758 ,