RetrogeneDB ID: retro_eeur_250

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_223265:4483..4854(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000003647
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS25
• Ensembl ID: ENSEEUG00000014630
• Aliases: None
• Description: ribosomal protein S25 [Source:HGNC Symbol;Acc:10413]

Sequence

>retro_eeur_250
ATGCCACCCAAAGACTACAAGAAGAAAAAAAGATTCCAGAAAGTTGGCCAAGAAAAACAAAGAGCCAGTGAACAAGTCTG
GGGAAAAGGCCAAAATGAAGAAGTCGGCCAAAGGCAAATTTCAGGACAAGCTTAATAACCTTATCTTGTTTGACAAAGGC
ACATATGACAAGCTTTGTAAACAAATCCTCAAATATAAAAATCATAACCCCAACTTTTGTATTTGAGAAATATGAAGATT
TGTGGGTTGCTGGCTAGGGATGCCCCTCAGATGGCAGTAAAGGGCTTATTAACCTGGTATCAAAACACAGGGCTGAAGTC
ATATACACCAGAAACACCAAGAGTGGAGTTGCTCCAGCTTCTGGTGAAAAT

Alignment

ORF - retro_eeur_250 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.19 %
• Parental protein coverage: 99.2 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MPPKDDKKKK-DAGKSAKKDKDPVNKSGGKAKKKKWSKGKVRDKLNNLVLFDKATYDKLCKEV-PNYKLI
          MPPKD.KKKK.D..K.AKK.K.PVNKSG.KAK.KK..KGK..DKLNNL.LFDK.TYDKLCK....N.K.I
Retrocopy MPPKDYKKKK>DSRKLAKKNKEPVNKSGEKAKMKKSAKGKFQDKLNNLILFDKGTYDKLCKQI>SNIKII

Parental  TPAVVSER-LKIRGSLARAALQELLSKG-LIKLVSKHRAQVIYTRNTKGGDAPAAGED
          TP..V.E...KI.G.LAR.A.Q....KG.LI.LVSKHRA.VIYTRNTK.G.APA.GE.
Retrocopy TPTFVFEK>MKICGLLARDAPQ-MAVKG<LINLVSKHRAEVIYTRNTKSGVAPASGEN

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
SRP017611_brain	0.00 RPM	92.50 RPM
SRP017611_kidney	0.00 RPM	231.61 RPM
SRP017611_liver	0.00 RPM	165.28 RPM

ChIP-Seq

Erinaceus europaeus was not studied using ChIP-Seq data.

EST

Erinaceus europaeus was not studied using EST data.

TSS

Erinaceus europaeus was not studied using FANTOM5 data.

Lab

retro_eeur_250 was not experimentally validated.

Homology

Retrocopy orthology:

Erinaceus europaeus 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 7 parental genes, and 36 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000027772	2 retrocopies	retro_btau_203, retro_btau_9,
Callithrix jacchus	ENSCJAG00000013691	1 retrocopy	retro_cjac_208,
Dasypus novemcinctus	ENSDNOG00000007880	7 retrocopies	retro_dnov_1092, retro_dnov_1566, retro_dnov_2219, retro_dnov_2593, retro_dnov_346, retro_dnov_877, retro_dnov_973,
Equus caballus	ENSECAG00000020978	2 retrocopies	retro_ecab_89, retro_ecab_976,
Erinaceus europaeus	ENSEEUG00000014630	6 retrocopies	retro_eeur_250 , retro_eeur_281, retro_eeur_353, retro_eeur_424, retro_eeur_519, retro_eeur_675,
Mus musculus	ENSMUSG00000009927	15 retrocopies	retro_mmus_128, retro_mmus_1368, retro_mmus_1455, retro_mmus_1760, retro_mmus_1769, retro_mmus_1788, retro_mmus_2375, retro_mmus_2393, retro_mmus_2641, retro_mmus_2700, retro_mmus_2797, retro_mmus_3218, retro_mmus_336, retro_mmus_3523, retro_mmus_880,
Otolemur garnettii	ENSOGAG00000007265	3 retrocopies	retro_ogar_220, retro_ogar_257, retro_ogar_32,