RetrogeneDB ID: retro_eeur_480

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_322007:1014..1410(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPD52L1
• Ensembl ID: ENSEEUG00000013289
• Aliases: None
• Description: tumor protein D52-like 1 [Source:HGNC Symbol;Acc:12006]

Sequence

>retro_eeur_480
ATGGAGACACAGGCACAAGGTTTGTTGGAGAGTGAACCATTGCAAGGAGTAAATGACGACTCTGTAGCCAGCACGGACTT
CTCTAGCATGCTCTCTGAGGAGGAAAAAGAAGAGTTAAAGGCAGAATTAGTTCAGCTGGAAGACGAAATTACAACTTTAC
GACAAGTTTTATCAGCAAAAGAAAGGTATCTGGTTGAGATCAAACAAAAACTCGGCATGAATTTGATGAATGAATTAAAA
CAGAACTTCAGCAAAAGCTGGCATGATATGCAGACTACTACTGCCTATAAGAAGACACATGAAACTCTGAGTCATGCCGG
GCAGAAAGCAACTGCAGCTTTCAGCAAAGTTGGAACAGCCATCAGCAAGAAGTTTGGAGATATGAGCTACTCCATT

Alignment

ORF - retro_eeur_480 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 96.21 %
• Parental protein coverage: 64.08 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  METQAQGLLESEPLQGVDDDSVASADFSSMLSEEEKEELKAELVQLEDEITTLRQVLSAKERHLVEIKQK
          METQAQGLLESEPLQGV.DDSVAS.DFSSMLSEEEKEELKAELVQLEDEITTLRQVLSAKER.LVEIKQK
Retrocopy METQAQGLLESEPLQGVNDDSVASTDFSSMLSEEEKEELKAELVQLEDEITTLRQVLSAKERYLVEIKQK

Parental  LGMNLMNELKQNFSKSWHDMQTTTAYKKTHETLSHAGQKATAAFSNVGTAISKKFGDMSDSI
          LGMNLMNELKQNFSKSWHDMQTTTAYKKTHETLSHAGQKATAAFS.VGTAISKKFGDMS.SI
Retrocopy LGMNLMNELKQNFSKSWHDMQTTTAYKKTHETLSHAGQKATAAFSKVGTAISKKFGDMSYSI

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	2.26 RPM	11.60 RPM
SRP017611_kidney	10.69 RPM	47.45 RPM
SRP017611_liver	0.64 RPM	4.82 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_480 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000013289	1 retrocopy	retro_eeur_480 ,