RetrogeneDB ID: retro_dnov_1746

Retrocopy location

• Organism: Armadillo (Dasypus novemcinctus)
• Coordinates: scaffold_2854:66924..67116(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSDNOG00000025274
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SERP1
• Ensembl ID: ENSDNOG00000013995
• Aliases: None
• Description: stress-associated endoplasmic reticulum protein 1 [Source:HGNC Symbol;Acc:10759]

Sequence

>retro_dnov_1746
GTGGTCGCAGAGCAGCAGATCCCCAGGGCCAAGGAGAAGCAGAGCAAGAGCACCCCCAGCGCGGCGACGAGGCCACGACC
TTGGGCAAAGCCCCCGAGAGAAGCAGCTGTGGGACACTGGTCACTGGCTTGCTTCGTTTTTGTTGTTTGTGGCGCTGCAA
CTCCACAGATTATTCAAAGTGTCAGGATGGGC

Alignment

ORF - retro_dnov_1746 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.35 %
• Parental protein coverage: 98.48 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  MVAKQRIRMANEKHSKNIT-QRGNVAKTSRNA-PEEK-ASVGPWLLALFIFVVCGSAIFQIIQSIRMG
          .VA.Q.I..A.EK.SK....QRG..A.T...A.P.EK.A.VG.W.LA.F.FVVCG.A..QIIQS.RMG
Retrocopy VVAEQQIPRAKEKQSKSTP<QRGDEATTLGKA<PREK<AAVGHWSLACFVFVVCGAATPQIIQSVRMG

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	43.76 RPM
SRP012922_cerebellum	0.00 RPM	11.96 RPM
SRP012922_heart	0.00 RPM	2.78 RPM
SRP012922_kidney	0.00 RPM	18.62 RPM
SRP012922_liver	0.00 RPM	33.28 RPM
SRP012922_lung	0.00 RPM	49.18 RPM
SRP012922_quadricep_muscle	0.00 RPM	1.21 RPM
SRP012922_spleen	0.00 RPM	55.06 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_1746 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 3 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013995	15 retrocopies	retro_dnov_1100, retro_dnov_1145, retro_dnov_1170, retro_dnov_1416, retro_dnov_1500, retro_dnov_1524, retro_dnov_1533, retro_dnov_1649, retro_dnov_1715, retro_dnov_1724, retro_dnov_1746 , retro_dnov_1784, retro_dnov_1847, retro_dnov_2299, retro_dnov_856,
Microcebus murinus	ENSMICG00000000414	1 retrocopy	retro_mmur_1429,
Oryctolagus cuniculus	ENSOCUG00000016085	2 retrocopies	retro_ocun_1542, retro_ocun_1835,