RetrogeneDB ID: retro_eeur_628

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_369955:56912..57284(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LYPD6B
• Ensembl ID: ENSEEUG00000008315
• Aliases: None
• Description: LY6/PLAUR domain containing 6B [Source:HGNC Symbol;Acc:27018]

Sequence

>retro_eeur_628
GCATTTATCAAGAACATCAACTCCCATAATGTGAGGCCTCCACTTGACCCTATAACTATTTCTGAACAGTGTTTTACCTA
TGAAAATACAGGGGCTATTTATAACTGCAATCAATGGGCAAGAAATAATAGGTGTCCATAAAATACACAGTGCTGTTTGA
CAGTTTGTTATTCACCAGCTGTAGAAGAGTACATCTATCATCAAAGATGTACCTTCAGACACAAATGCCATTTTGTTGGT
TGCCACAGCCAAGATTCTGAACATACAGAATGTATGTTTTACTGCTAAAGAGCAACCTACAATGTAGAATTACCTACCAA
TCACACAAATATGGTCTTTCCTGTAATGCATGTTCAGGGAATACCTGGTAGC

Alignment

ORF - retro_eeur_628 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.54 %
• Parental protein coverage: 62.75 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  AFAKNINFYNVRPPLDPTPFPNSFKCFTCENAGDNYDCNRWAEDKWCPQNTQYCLTVHH-FTSLGR-STS
          AF.KNIN..NVRPPLDP.....S..CFT.EN.G..Y.CN.WA....CP.NTQ.CLTV...FTS..R.STS
Retrocopy AFIKNINSHNVRPPLDPITI--SEQCFTYENTGAIYNCNQWARNNRCP*NTQCCLTVCY<FTSCRR<STS

Parental  ITK-KCASGSECHFVGCHHSRDSEHTECRSCCEGMICNVDLPTNHTNAVFAVMHAQRTSGS
          I.K..C.....CHFVGCH.S.DSEHTEC...C.....NV.LPTNHTN.VF.VMH.Q...GS
Retrocopy IIK<RCTFRHKCHFVGCH-SQDSEHTECMFYC*RATYNVELPTNHTNMVFPVMHVQGIPGS

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	6.61 RPM
SRP017611_kidney	0.00 RPM	17.82 RPM
SRP017611_liver	0.00 RPM	0.96 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_628 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	ENSEEUG00000008315	1 retrocopy	retro_eeur_628 ,