RetrogeneDB ID: retro_dnov_125

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: GeneScaffold_1911:28658..29133(+)
• Located in intron of: ENSDNOG00000008591

Retrocopy information

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

Parental gene information

• Parental gene symbol: SAV1
• Ensembl ID: ENSDNOG00000005318
• Aliases: None
• Description: salvador homolog 1 (Drosophila) [Source:HGNC Symbol;Acc:17795]

Sequence

>retro_dnov_125
AACCATGGCTCTGAAGATTTACCCCTTTTTCCTGGCAGGTCTGTGGACAGGACAATGAGAGGAAGAAAGTATTACACGGA
TCGTGACACAATAAATACAACTCACTGGAGCCATCCTCTTGAGTGGGAAGGCCCTCCTCCAGGATGCGAGCAAGTTGAGT
CATCAGAATTTGGAACCTATTATGCAGATCCCATAAGTAAGGCGGCTCCCTGCAGGCTTCCCTGTTTACCTAGCATACCT
CGGTACGGTCACCCTCCTCCAGTCACACACCAGCCACAGCAAACTGAAAGAAATCAGTCTCCTTCTGGTACCCGCAAATC
CATATCCCACTGCAGAAATTCCTAACTGGTTTCAGGTTTACATGTGAACCCCTGTGAAACGTGACCACATTCTGAAACGG
GAACTCTTCCAGCTGCCTGATCTGGATACATACCAGAGAATGCTAAAATTGTTCTTCATGAAAGAACTGGAGCAG

Alignment

ORF - retro_dnov_125 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.99 %
• Parental protein coverage: 76.96 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NHGSEDLPLPPGWSVDWTMRGRKYYIDHNT-NTTHWSHPLEREGLPPGWERVESSEFGTYYVDHINKKAQ
          NHGSEDLPL.PG.SVD.TMRGRKYY.D..T.NTTHWSHPLE.EG.PPG.E.VESSEFGTYY.D.I.K.A.
Retrocopy NHGSEDLPLFPGRSVDRTMRGRKYYTDRDTINTTHWSHPLEWEGPPPGCEQVESSEFGTYYADPISKAAP

Parental  YRHPCAPSVPRYDQPPPVTYQPQQTERNQS-LLVPANPYHTAEIPDWLQVYARAPVKYDHILKWELFQLA
          .R.PC.PS.PRY..PPPVT.QPQQTERNQS.LLVPANPY.TAEIP.W.QVY...PVK.DHILK.ELFQL.
Retrocopy CRLPCLPSIPRYGHPPPVTHQPQQTERNQS>LLVPANPYPTAEIPNWFQVYM*TPVKRDHILKRELFQLP

Parental  DLDTYQGMLKLLFMKELEQ
          DLDTYQ.MLKL.FMKELEQ
Retrocopy DLDTYQRMLKLFFMKELEQ

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	6.81 RPM
SRP012922_cerebellum	0.41 RPM	5.22 RPM
SRP012922_heart	0.00 RPM	4.18 RPM
SRP012922_kidney	0.82 RPM	2.46 RPM
SRP012922_liver	0.00 RPM	2.17 RPM
SRP012922_lung	0.46 RPM	18.79 RPM
SRP012922_quadricep_muscle	0.00 RPM	4.50 RPM
SRP012922_spleen	0.11 RPM	7.33 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_125 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 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006590	1 retrocopy	retro_cjac_443,
Dasypus novemcinctus	ENSDNOG00000005318	1 retrocopy	retro_dnov_125 ,