RetrogeneDB ID: retro_eeur_104

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_6429:603477..603834(-)
• Located in intron of: ENSEEUG00000003129

Retrocopy information

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

Parental gene information

• Parental gene symbol: COX20
• Ensembl ID: ENSEEUG00000012147
• Aliases: None
• Description: COX20 cytochrome C oxidase assembly factor [Source:HGNC Symbol;Acc:26970]

Sequence

>retro_eeur_104
ATGGCGGCAGCGCAGGAACCCGGCGAGCCAGAGAAAGAGAAGCCCTTTAAGCTCCTAGGATTTTTAGACATTGAAAACAT
TCCCTGTGCACGGCAATCAATATTATATGGTTCGTTGGGATCGGTTGTGACTGGCCTTGGACATTTTTTGTTAACCAGTA
GAATTAGACGATCATGTGATGTTGGAGTAGGAGGATTTATCTTGGTGACGTTAGGATGCTGGTTCCACTGTAGGTATAAT
TACGCAAAACAAAGAATCCAGGAAAGAATTGCCAGAAAAGGAATTAAAAACAAGATTCTGTATGAAAGCACCCACCTTGA
TCCCGAAAAAAATCAAAGCAACAGCAAGAGTGACAAC

Alignment

ORF - retro_eeur_104 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 100. %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAAQEPGEPEKEKPFKLLGFLDIENIPCARQSILYGSLGSVVTGLGHFLLTSRIRRSCDVGVGGFILVT
          MAAAQEPGEPEKEKPFKLLGFLDIENIPCARQSILYGSLGSVVTGLGHFLLTSRIRRSCDVGVGGFILVT
Retrocopy MAAAQEPGEPEKEKPFKLLGFLDIENIPCARQSILYGSLGSVVTGLGHFLLTSRIRRSCDVGVGGFILVT

Parental  LGCWFHCRYNYAKQRIQERIARKGIKNKILYESTHLDPEKNQSNSKSDN
          LGCWFHCRYNYAKQRIQERIARKGIKNKILYESTHLDPEKNQSNSKSDN
Retrocopy LGCWFHCRYNYAKQRIQERIARKGIKNKILYESTHLDPEKNQSNSKSDN

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	0.48 RPM	15.63 RPM
SRP017611_kidney	1.69 RPM	29.82 RPM
SRP017611_liver	0.64 RPM	14.15 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_104 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 14 parental genes, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000001381	4 retrocopies	retro_chof_1820, retro_chof_207, retro_chof_299, retro_chof_825,
Erinaceus europaeus	ENSEEUG00000012147	1 retrocopy	retro_eeur_104 ,
Homo sapiens	ENSG00000203667	1 retrocopy	retro_hsap_587,
Myotis lucifugus	ENSMLUG00000026132	7 retrocopies	retro_mluc_1273, retro_mluc_1505, retro_mluc_1863, retro_mluc_1954, retro_mluc_2343, retro_mluc_792, retro_mluc_958,
Monodelphis domestica	ENSMODG00000024669	1 retrocopy	retro_mdom_2014,
Mus musculus	ENSMUSG00000026500	1 retrocopy	retro_mmus_2957,
Nomascus leucogenys	ENSNLEG00000004027	1 retrocopy	retro_nleu_2518,
Ochotona princeps	ENSOPRG00000004534	6 retrocopies	retro_opri_1072, retro_opri_287, retro_opri_31, retro_opri_585, retro_opri_676, retro_opri_720,
Pongo abelii	ENSPPYG00000000053	1 retrocopy	retro_pabe_2090,
Pteropus vampyrus	ENSPVAG00000002577	1 retrocopy	retro_pvam_945,
Rattus norvegicus	ENSRNOG00000004553	2 retrocopies	retro_rnor_1033, retro_rnor_2184,
Sorex araneus	ENSSARG00000004625	2 retrocopies	retro_sara_167, retro_sara_470,
Tupaia belangeri	ENSTBEG00000015272	4 retrocopies	retro_tbel_1186, retro_tbel_3207, retro_tbel_3838, retro_tbel_3926,
Tarsius syrichta	ENSTSYG00000005644	1 retrocopy	retro_tsyr_100,