RetrogeneDB ID: retro_eeur_438

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_302981:4241..4600(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EXOSC1
• Ensembl ID: ENSEEUG00000005647
• Aliases: None
• Description: exosome component 1 [Source:HGNC Symbol;Acc:17286]

Sequence

>retro_eeur_438
GGCACACTTCCCATTGTATCTGTTGCGAGAGAAACAAGAGTCCCAGTTACTGCCAGATGTACGAGCTATTGTAACCTGTA
AGGTCTCTAGCATCAATTCATGGTTTGCCAAAGTACACATTCTCTATGTGGGGTCCACACCACTTAAGGACTCTTTTTGA
GAACCTAACCACAAGGAAGATGAGCTATTGAAAAAGACAAGGTTGAAATTTATAAGTTTCCACCCAGGTGACAATGTCTT
GGCCAAAGTGATTTCCCTAGGTGACACACAGTCCAACCACCTCTGTGACTACTGCCGAAAATGAGCTGGGGGTGGTGGTG
GCCCACAGTGAGTCATGTGTCCAGATGGTTCCCATCAGC

Alignment

ORF - retro_eeur_438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.8 %
• Parental protein coverage: 62.05 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  GALPIVSVTRET-ESQLLPDVGAIVTCKVSSINSRFAKVHILYVGSTPLKNSFRGTIRKEDVRATEKDKV
          G.LPIVSV.RET.ESQLLPDV.AIVTCKVSSINS.FAKVHILYVGSTPLK.SF.....KED.....K...
Retrocopy GTLPIVSVARET>ESQLLPDVRAIVTCKVSSINSWFAKVHILYVGSTPLKDSF*EPNHKED-ELLKKTRL

Parental  EIYKSFRPGDIVLAKVISLGDAQSNYL-LTTAENELGVVVAHSESGVQMDPIS
          ....SF.PGD.VLAKVISLGD.QSN.L..TTAENELGVVVAHSES.VQM.PIS
Retrocopy K-FISFHPGDNVLAKVISLGDTQSNHL>VTTAENELGVVVAHSESCVQMVPIS

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	4.03 RPM
SRP017611_kidney	0.00 RPM	9.94 RPM
SRP017611_liver	0.00 RPM	5.95 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_438 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006477	1 retrocopy	retro_chof_2075,
Dasypus novemcinctus	ENSDNOG00000007983	1 retrocopy	retro_dnov_104,
Erinaceus europaeus	ENSEEUG00000005647	3 retrocopies	retro_eeur_270, retro_eeur_438 , retro_eeur_464,
Macropus eugenii	ENSMEUG00000002246	2 retrocopies	retro_meug_1799, retro_meug_951,
Myotis lucifugus	ENSMLUG00000009228	1 retrocopy	retro_mluc_1563,
Mus musculus	ENSMUSG00000034321	1 retrocopy	retro_mmus_691,
Oryctolagus cuniculus	ENSOCUG00000011898	1 retrocopy	retro_ocun_173,
Otolemur garnettii	ENSOGAG00000016259	1 retrocopy	retro_ogar_2496,
Pteropus vampyrus	ENSPVAG00000003372	1 retrocopy	retro_pvam_686,
Rattus norvegicus	ENSRNOG00000048708	1 retrocopy	retro_rnor_899,
Ictidomys tridecemlineatus	ENSSTOG00000006615	1 retrocopy	retro_itri_1253,