RetrogeneDB ID: retro_eeur_560

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_344546:55515..55806(-)
• Located in intron of: None

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_560
CCCCAGAGTCTATGGTGCCGTCCGTGGACACAGGCAATGGAGGATTCTAGCAGGCCTTGGCTGGATGCTAAATCCAAGGT
CACCAACCAGCTTGTAGATTTTCAGTGGAAACTAGGTATGGCTGTAAGCTCGGACAGTTGCAGATCACTTAAGTATCCTT
ATGTTGCCCTGATGTTAAAAGTGGCAGATCACTCCGGCCAAGTAAAGAATAAGTCTTCTGAAATGACAATTCCACAATTT
CAGAATTTCTACAGACAATTTAAGGAAATTGCTGCAACTATTGAAACTGTG

Alignment

ORF - retro_eeur_560 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.88 %
• Parental protein coverage: 80.17 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PQSLWCGPWTQAMEDSSGPRLDAKSKVTNQLVDFQWKLGMAVSSDSCRSLKYPYVALMLKVADHSGQVKN
          PQSLWC.PWTQAMEDSS.P.LDAKSKVTNQLVDFQWKLGMAVSSDSCRSLKYPYVALMLKVADHSGQVKN
Retrocopy PQSLWCRPWTQAMEDSSRPWLDAKSKVTNQLVDFQWKLGMAVSSDSCRSLKYPYVALMLKVADHSGQVKN

Parental  KSFEMTIPQFQNFYRQFKEIAATIETV
          KS.EMTIPQFQNFYRQFKEIAATIETV
Retrocopy KSSEMTIPQFQNFYRQFKEIAATIETV

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	1.29 RPM	9.99 RPM
SRP017611_kidney	4.88 RPM	17.07 RPM
SRP017611_liver	1.61 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_560 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,