RetrogeneDB ID: retro_eeur_543

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_341990:5833..6025(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UXT
• Ensembl ID: ENSEEUG00000006151
• Aliases: None
• Description: ubiquitously-expressed, prefoldin-like chaperone [Source:HGNC Symbol;Acc:12641]

Sequence

>retro_eeur_543
AGAGCTGAGACCTTCACCAGTGAAATGCTCTAGTGTCACTTGCAAAATGTGCTGGAACATTGTGACTAAGTATATAAGTA
TTTGGCTAAATACCTTCAGCTGAGAAATGTTACTGAGAAAATCCAGGAAATGAAGCACTTAGAGCTGTATAGGCAGGTGG
ATCTGGGCTGTAAATTCTTCATTGATACAGTG

Alignment

ORF - retro_eeur_543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.31 %
• Parental protein coverage: 69.57 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RYETFISDVLQRDLQKVLEHRDKVYEQLAKYLQLRNVIERIQETKHSELYMQVDLGCNFFVDTV
          R.ETF.S..L...LQ.VLEH.D.VY..LAKYLQLRNV.E.IQE.KH.ELY.QVDLGC.FF.DTV
Retrocopy RAETFTSEML*CHLQNVLEHCD*VYKYLAKYLQLRNVTEKIQEMKHLELYRQVDLGCKFFIDTV

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	2.26 RPM
SRP017611_kidney	0.00 RPM	6.38 RPM
SRP017611_liver	0.00 RPM	4.98 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_543 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000009154	1 retrocopy	retro_cpor_1302,
Dipodomys ordii	ENSDORG00000001025	1 retrocopy	retro_dord_627,
Erinaceus europaeus	ENSEEUG00000006151	1 retrocopy	retro_eeur_543 ,
Macropus eugenii	ENSMEUG00000003352	1 retrocopy	retro_meug_59,
Microcebus murinus	ENSMICG00000016263	1 retrocopy	retro_mmur_1156,
Mustela putorius furo	ENSMPUG00000013405	1 retrocopy	retro_mputfur_999,
Mus musculus	ENSMUSG00000001134	3 retrocopies	retro_mmus_1424, retro_mmus_1766, retro_mmus_715,
Rattus norvegicus	ENSRNOG00000009893	5 retrocopies	retro_rnor_521, retro_rnor_522, retro_rnor_683, retro_rnor_692, retro_rnor_882,
Tarsius syrichta	ENSTSYG00000012719	2 retrocopies	retro_tsyr_237, retro_tsyr_778,