RetrogeneDB ID: retro_eeur_656

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_376748:52894..53045(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: C3orf14
• Ensembl ID: ENSEEUG00000000474
• Aliases: None
• Description: chromosome 3 open reading frame 14 [Source:HGNC Symbol;Acc:25024]

Sequence

>retro_eeur_656
GATATAGAAGCAGCAGAAAGGTCTCTAAAACCAGGATTCACCCTCTTCTACCACCTGAGTAGTTCTCTGAGACTCTTACT
GGGCATCAGTAGAAGAATGTATTCCCAAATGGGAACAGTTTCTTTTAGGAAAATCACCATATCCCATTGTT

Alignment

ORF - retro_eeur_656 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.04 %
• Parental protein coverage: 75.36 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DIEAAERSLKTG-IHPLLPPEEVPPETL-YWASVEECIPKWEQFLLGKSPYPIV
          DIEAAERSLK.G.IHPLLPPE....ETL.YWASVEECIPKWEQFLLGKSPYPIV
Retrocopy DIEAAERSLKPG<IHPLLPPE*FS-ETL<YWASVEECIPKWEQFLLGKSPYPIV

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	9.35 RPM	0.64 RPM
SRP017611_kidney	10.88 RPM	1.69 RPM
SRP017611_liver	6.27 RPM	1.45 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_656 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 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015374	1 retrocopy	retro_amel_1312,
Canis familiaris	ENSCAFG00000007123	1 retrocopy	retro_cfam_1485,
Choloepus hoffmanni	ENSCHOG00000004965	7 retrocopies	retro_chof_138, retro_chof_2082, retro_chof_423, retro_chof_536, retro_chof_659, retro_chof_73, retro_chof_96,
Erinaceus europaeus	ENSEEUG00000000474	1 retrocopy	retro_eeur_656 ,
Felis catus	ENSFCAG00000027983	1 retrocopy	retro_fcat_577,
Macropus eugenii	ENSMEUG00000013085	2 retrocopies	retro_meug_1990, retro_meug_2091,
Microcebus murinus	ENSMICG00000016406	1 retrocopy	retro_mmur_461,
Mustela putorius furo	ENSMPUG00000016914	1 retrocopy	retro_mputfur_751,
Mus musculus	ENSMUSG00000033111	1 retrocopy	retro_mmus_1255,
Otolemur garnettii	ENSOGAG00000008107	2 retrocopies	retro_ogar_484, retro_ogar_485,
Tupaia belangeri	ENSTBEG00000017312	1 retrocopy	retro_tbel_1713,