RetrogeneDB ID: retro_dnov_1665

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_259629:310..1077(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000025056
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: DUSP5
• Ensembl ID: ENSDNOG00000001858
• Aliases: None
• Description: dual specificity phosphatase 5 [Source:HGNC Symbol;Acc:3071]

Sequence

>retro_dnov_1665
TATGAGACCTTCTACTCGTATATCCTGAGTGTTGTGTGGATGTAAAACCCATTTCACAAGAGAAGATTGAAACTGAGAGA
GCCCTCATCGGCCAATGTGGGAAACCAATGCTAAACATCAGCTACAAGCCGGCTTATGATCAGGGTGGCCCAGTTGAAAT
TCTTCCCTTCCTGTACCTTGGAAGTGCCTACCACGCATCCAAGTGCGAATTCCTCGCCAATCTGCACATCACGGCCCTGC
TGAATGTCTCACGGCGGGCGTCTGAGGCCTGCACGACCCACCTACACTACAAATGGATCCCCGTAGAAGACAGCCACACG
GCCGACATCAGCTCCCACTTTCAAGAAGCAATAGACTTCATTGACTGTGTCAGGGAAAAGGGAGGCAAGATCCTGGTCCA
CTGCGAGGCCGGGATCTCTCGCTCACCCACCATCTGCATGGCTTACCTCATGAAGACCAACCAATTCCGCCTGAAGGAGG
CCTTCGAGTACATCAAGCAGAGGAGGAGTGTGATCTCACCGAATTTTGGCTTCATGGGCCAGCTCCTGCAGTATGAATCT
GAGATCCTGCCCTCCACACCCAAACCCCAGGCTTCCTCCTGCCAAGGGGAGGCAGCAGGCTCTTCATTTCTAGACCATTT
GCAGACACTGAGCCCTGATGTGCAGGGTTCCTTCTGCACATTCCCTACCTCAGCACTGGCGCCTGTACCCACCCACTCAG
CCATCCCAGAGCTCAGCAGGAGCCCTGTGGCCACGGCCATGTCCCGC

Alignment

ORF - retro_dnov_1665 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.22 %
• Parental protein coverage: 99.61 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  YETFYSE-YPECCVDVKPISQEKIETERALIGQCGKPMLNISYKPAYDQGGPVEILPFLYLGSAYHASKC
          YETFYS..YPECCVDVKPISQEKIETERALIGQCGKPMLNISYKPAYDQGGPVEILPFLYLGSAYHASKC
Retrocopy YETFYSY<YPECCVDVKPISQEKIETERALIGQCGKPMLNISYKPAYDQGGPVEILPFLYLGSAYHASKC

Parental  EFLANLHITALLNVSRRASEACTTHLHYKWIPVEDSHTADISSHFQEAIDFIDCVREKGGKILVHCEAGI
          EFLANLHITALLNVSRRASEACTTHLHYKWIPVEDSHTADISSHFQEAIDFIDCVREKGGKILVHCEAGI
Retrocopy EFLANLHITALLNVSRRASEACTTHLHYKWIPVEDSHTADISSHFQEAIDFIDCVREKGGKILVHCEAGI

Parental  SRSPTICMAYLMKTNQFRLKEAFEYIKQRRSVISPNFGFMGQLLQYESEILPSTPKPQASSCQGEAAGSS
          SRSPTICMAYLMKTNQFRLKEAFEYIKQRRSVISPNFGFMGQLLQYESEILPSTPKPQASSCQGEAAGSS
Retrocopy SRSPTICMAYLMKTNQFRLKEAFEYIKQRRSVISPNFGFMGQLLQYESEILPSTPKPQASSCQGEAAGSS

Parental  FLDHLQTLSPDVQGSFCTFPTSALAPVPTHSAIPELSRSPVATAMSR
          FLDHLQTLSPDVQGSFCTFPTSALAPVPTHSAIPELSRSPVATAMSR
Retrocopy FLDHLQTLSPDVQGSFCTFPTSALAPVPTHSAIPELSRSPVATAMSR

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	1.94 RPM
SRP012922_cerebellum	0.00 RPM	3.85 RPM
SRP012922_heart	0.00 RPM	0.00 RPM
SRP012922_kidney	0.00 RPM	0.55 RPM
SRP012922_liver	0.15 RPM	2.79 RPM
SRP012922_lung	0.00 RPM	0.92 RPM
SRP012922_quadricep_muscle	0.00 RPM	0.00 RPM
SRP012922_spleen	0.00 RPM	2.06 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_1665 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015745	1 retrocopy	retro_amel_1630,
Dasypus novemcinctus	ENSDNOG00000001858	1 retrocopy	retro_dnov_1665 ,
Equus caballus	ENSECAG00000013514	2 retrocopies	retro_ecab_188, retro_ecab_612,
Myotis lucifugus	ENSMLUG00000013773	1 retrocopy	retro_mluc_1121,
Pteropus vampyrus	ENSPVAG00000016242	2 retrocopies	retro_pvam_1416, retro_pvam_480,