RetrogeneDB ID: retro_dnov_128

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1939:630411..630915(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: JOSD1
• Ensembl ID: ENSDNOG00000016015
• Aliases: None
• Description: Josephin domain containing 1 [Source:HGNC Symbol;Acc:28953]

Sequence

>retro_dnov_128
GTGAATTGTGTGTCATGGAAAGGAGACAAGGCCAAGTCTGAATCATTGGAGCTGCCCCAGGCCGCACCCCCTCAGATCTA
TCAAGAGAAACAGGGCAGGGAGCTTTCCCCCGCCCTCCATGCCCTCAATAACGTCTTCCAGGACAGCCACGCCTTCACCC
AGGAAGCTCTGCAAGAGATTTTTCAGAAGTTGTCTTCAAAGACCATGGTGACACCCCACGAGAAGAGCGTGTTGGGAAAT
GAGAACTGCTATAGGAACATCATCATGGCAGCACTTCAGACCGAAGGCTGTGAAGCTGTTTGGTGGACAAGGCAGGGACG
TCAGTGTATTGCTCTCTCTAATGTCTTGGCTTTATTGTGAATCTGCTCTCCAGCCTGTGCTGGAGTCCACTGAAGTTGCT
TCTCAAAGGTAGCACTGGATCTGCATTGAGAGAGCAGAGGTGCCTACCACAACCCAGACTCCAAACTCAAGATGCCTGAG
TGGATTGGAGGCCGGAGCGACCTC

Alignment

ORF - retro_dnov_128 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.16 %
• Parental protein coverage: 82.74 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  IRCMPWKGEKTKFESLELP-AVPPWIYHEEQCRQLY-ALHALNNIFP----FTQEML-DIFQRLSPNTMV
          ..C..WKG.K.K.ESLELP.A.PP.IY.E.Q.R.L..ALHALNN.F.....FTQE.L..IFQ.LS..TMV
Retrocopy VNCVSWKGDKAKSESLELPQAAPPQIYQEKQGRELSPALHALNNVFQDSHAFTQEALQEIFQKLSSKTMV

Parental  TPHKKSMLGNGNYDVNVIMAALQTKGYEAVWWDKRRDVSVIALTNV-MGFIMNLPSSLCWGPLKLPLK-R
          TPH.KS.LGN.N...N.IMAALQT.G.EAVWW..R.....IAL.NV..GFI.NL.SSLCW.PLKL.LK.R
Retrocopy TPHEKSVLGNENCYRNIIMAALQTEGCEAVWW-TRQGRQCIALSNV<LGFIVNLLSSLCWSPLKLLLK<R

Parental  QHWICVR-EVGGAYYNLDSKLKMPEWIGGESEL
          .HWIC...E..GAY.N.DSKLKMPEWIGG.S.L
Retrocopy *HWICIE<ESRGAYHNPDSKLKMPEWIGGRSDL

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	4.86 RPM
SRP012922_cerebellum	0.00 RPM	3.57 RPM
SRP012922_heart	0.00 RPM	1.86 RPM
SRP012922_kidney	0.00 RPM	1.10 RPM
SRP012922_liver	0.00 RPM	5.73 RPM
SRP012922_lung	0.00 RPM	5.35 RPM
SRP012922_quadricep_muscle	0.00 RPM	3.12 RPM
SRP012922_spleen	0.00 RPM	5.84 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_128 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.

---

Parental genes homology:

Parental genes homology involve 4 parental genes, and 5 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000016015	1 retrocopy	retro_dnov_128 ,
Macropus eugenii	ENSMEUG00000002899	2 retrocopies	retro_meug_1507, retro_meug_531,
Sarcophilus harrisii	ENSSHAG00000015931	1 retrocopy	retro_shar_643,
Ictidomys tridecemlineatus	ENSSTOG00000024999	1 retrocopy	retro_itri_193,