RetrogeneDB ID: retro_eeur_539

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_341050:74820..75107(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C6orf57
• Ensembl ID: ENSEEUG00000011260
• Aliases: None
• Description: chromosome 6 open reading frame 57 [Source:HGNC Symbol;Acc:20957]

Sequence

>retro_eeur_539
GGCCTGGTCCCAACCATGTCTTGAAAAGCAACAAGATCTCCTTTTCTGTGTCATTCCTTGAGGAAAATGAGTTATCAAGG
AGGGAAATCTGAACCCATCAAACAATCCCTTACGAAGTCAGAGTTACCATGAGGTCAGATTGATGTTCCAGAAGATTTCA
ATGTAGAGAAAGAACCACTGGCAAAATTTCAGGTGATAGTAATCCCATCACCAAAGAAAAAAGAGGATTCGGTGGCCCAG
ATCCTACTAGATAAGGAGAATGGAAATGAAAAGGACACTATATTGAT

Alignment

ORF - retro_eeur_539 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.86 %
• Parental protein coverage: 89.72 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GRVPAVARRVTRSPLLCHSLRKMNYKGGKSEHFKQSLEKPKLPEGHFDVLEDSNLEKEPLTKF-PDDVNP
          G.VP......TRSP.LCHSLRKM.Y.GGKSE..KQSL.K..LP.G..DV.ED.N.EKEPL.KF...D.NP
Retrocopy GLVPTMS*KATRSPFLCHSLRKMSYQGGKSEPIKQSLTKSELP*GQIDVPEDFNVEKEPLAKF<SGDSNP

Parental  VTKEKGGPRGPEPTRYGDWERKGRCID
          .TKEK.G..GP.PTR.G.W..KG..ID
Retrocopy ITKEKRGFGGPDPTR*GEWK*KGHYID

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	3.87 RPM
SRP017611_kidney	0.00 RPM	4.13 RPM
SRP017611_liver	0.00 RPM	3.05 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_539 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000002602	2 retrocopies	retro_cfam_268, retro_cfam_657,
Choloepus hoffmanni	ENSCHOG00000011410	6 retrocopies	retro_chof_176, retro_chof_1854, retro_chof_252, retro_chof_465, retro_chof_694, retro_chof_966,
Erinaceus europaeus	ENSEEUG00000011260	1 retrocopy	retro_eeur_539 ,
Echinops telfairi	ENSETEG00000011154	1 retrocopy	retro_etel_1362,
Felis catus	ENSFCAG00000026799	1 retrocopy	retro_fcat_986,
Rattus norvegicus	ENSRNOG00000028087	1 retrocopy	retro_rnor_1514,
Tupaia belangeri	ENSTBEG00000004344	2 retrocopies	retro_tbel_3788, retro_tbel_4408,
Tarsius syrichta	ENSTSYG00000001769	1 retrocopy	retro_tsyr_67,