RetrogeneDB ID: retro_eeur_120

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_7461:75674..75980(-)
• Located in intron of: ENSEEUG00000005031

Retrocopy information

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

Parental gene information

• Parental gene symbol: COMMD6
• Ensembl ID: ENSEEUG00000006061
• Aliases: None
• Description: COMM domain containing 6 [Source:HGNC Symbol;Acc:24015]

Sequence

>retro_eeur_120
TGGCAGAGGATCAGGCCCCAGAGTCTATGGTGCCGTCTGTGGACACAGGCAATGGAGGATTCTAGCTGGCCTCAGCTGGA
TGCTAAATCCAAGGTCACCAACCAGCCTGTAGGTTTTCAGTGGAAACTAGGTATGGCTGTAAGCTCTGACAGTTGCAGAT
CACTTAAGTATCCTCATGTTGCCATGATGTTAAAAGTGGCAGATCACTCTGGCCAAGTAAAGAATAAGTCTTTTGAAATG
ACAATTCCACAATTTCAGAATTTCTACAGACAATTTAAGGAAATGGCTGCAACTACTGAAACTGTG

Alignment

ORF - retro_eeur_120 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.27 %
• Parental protein coverage: 84.3 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  WSEEGPQSLWCGPWTQAMEDSSGPRLDAKSKVTNQLVDFQWKLGMAVSSDSCRSLKYPYVALMLKVADHS
          W....PQSLWC..WTQAMEDSS.P.LDAKSKVTNQ.V.FQWKLGMAVSSDSCRSLKYP.VA.MLKVADHS
Retrocopy WQRIRPQSLWCRLWTQAMEDSSWPQLDAKSKVTNQPVGFQWKLGMAVSSDSCRSLKYPHVAMMLKVADHS

Parental  GQVKNKSFEMTIPQFQNFYRQFKEIAATIETV
          GQVKNKSFEMTIPQFQNFYRQFKE.AAT.ETV
Retrocopy GQVKNKSFEMTIPQFQNFYRQFKEMAATTETV

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	9.99 RPM
SRP017611_kidney	0.00 RPM	17.07 RPM
SRP017611_liver	0.48 RPM	5.31 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_120 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000011048	1 retrocopy	retro_dord_237,
Erinaceus europaeus	ENSEEUG00000006061	2 retrocopies	retro_eeur_120 , retro_eeur_560,
Myotis lucifugus	ENSMLUG00000010697	1 retrocopy	retro_mluc_1927,
Monodelphis domestica	ENSMODG00000000970	3 retrocopies	retro_mdom_111, retro_mdom_147, retro_mdom_76,
Nomascus leucogenys	ENSNLEG00000026952	1 retrocopy	retro_nleu_2240,
Rattus norvegicus	ENSRNOG00000038012	1 retrocopy	retro_rnor_2012,
Tursiops truncatus	ENSTTRG00000003379	2 retrocopies	retro_ttru_1697, retro_ttru_908,