RetrogeneDB ID: retro_eeur_392

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_282386:182..1018(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCGF2
• Ensembl ID: ENSEEUG00000011789
• Aliases: None
• Description: polycomb group ring finger 2 [Source:HGNC Symbol;Acc:12929]

Sequence

>retro_eeur_392
ATGCATCGAACCACACGGATCAAAATCACGGAGCTGAACCCCAGCTCATGTGTGTCCTCTGTGGGGGTTACTTCATCGAC
TGCACGACCACAGCGGAGTGCCTGCATTCCTTCTGCAAAACCTGCATCGTGCTCTACCTGGAGACCAGCAAGTACTGCCC
CGTGTGTGATGCGCAGGTCCACAAAACCCGGCCGCTGCTGAGCATCAGATCCGACAAAACCCTCCAAGACATTGTTTACA
AATTGGTCCCTGGGCTTTTTAAAGATGAGATGAAACGGAGGCGGGATTTCTATGCAGCTTATCCCCTAACAGAAGTCCCC
AATGGCTCCAGTGAAGACCAAGGTGAGGTCCTGGAGCAGGAGAAGCGGGCTCCGAAGGACGAGATTGTCAGCCTCAGCAT
CGAGTTCTATGCAGGCATCAGAGGTAGAGAAGAGAAGACGTGCCCCCCGGAGAATGAAGATGGGGACAAGGAGAAGCAGA
CTGGGGGTGCGCTTCCCGCGATGCCCAGCAGCCATGACTTTCATAGCACCTCCCTAAATTTCTCCGCAACAAGATGGATG
TGCCCAGCAAATACAAGGTGCAGGTTGTATATGAGGACGAGCCTTTGAAGGAGTACTACACCCTCGTGGACATTGCCTAC
ATCTACCCCTGGCGGCGGAATGGCCCTCTCCCCCTCAAGTTCCGTGTCCAGCCAGCCTGCAAGCGGCTCACCTTGCCCAC
AGTACCCACCCCATCCGAGGGCACCAACACCAGCAGGGCGTCCGGGCAGCAACAAGGCTCCCAGCTCTGCCACGCTGCCT
GCCACCTCTTCTTCCCTGCCCAGCCCAGCCCAGCCA

Alignment

ORF - retro_eeur_392 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.96 %
• Parental protein coverage: 81.98 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MHRTTRIKITELNP-HLMCALCGGYFIDATTIVECLHSFCKTCIVRYLETNKYCPMCDVQVHKTRPLLSI
          MHRTTRIKITELNP..LMC.LCGGYFID.TT..ECLHSFCKTCIV.YLET.KYCP.CD.QVHKTRPLLSI
Retrocopy MHRTTRIKITELNP<QLMCVLCGGYFIDCTTTAECLHSFCKTCIVLYLETSKYCPVCDAQVHKTRPLLSI

Parental  XXXXXXXXXXXXXXXXXXXXEMKRRRDFYAAYPLTEVPNGSNEDRGEVLEQEKGALSDDEIVSLSIEFYE
          ....................EMKRRRDFYAAYPLTEVPNGS.ED.GEVLEQEK.A...DEIVSLSIEFY.
Retrocopy RSDKTLQDIVYKLVPGLFKDEMKRRRDFYAAYPLTEVPNGSSEDQGEVLEQEKRA-PKDEIVSLSIEFYA

Parental  GIRDREEKKGPLENGDGDKEK-TG-VRFLRCPAAMTVM-HLAKFLRNKMDVPSKYKVEVLYEDEPLKEYY
          GIR.REEK..P.EN.DGDKEK.TG.VRF.RCPAAMT...HL.KFLRNKMDVPSKYKV.V.YEDEPLKEYY
Retrocopy GIRGREEKTCPPENEDGDKEKQTG>VRFPRCPAAMTFI>HLPKFLRNKMDVPSKYKVQVVYEDEPLKEYY

Parental  TLMDIAYIYPWRRNGPLPLKYRVQPACKRLTLPTVPTPSEGTNTSGASECESVS-DKAPSPATLPATSSS
          TL.DIAYIYPWRRNGPLPLK.RVQPACKRLTLPTVPTPSEGTNTS.AS.....S...A..PAT....SSS
Retrocopy TLVDIAYIYPWRRNGPLPLKFRVQPACKRLTLPTVPTPSEGTNTSRASGQQQGS>SSATLPAT----SSS

Parental  LPSPATP
          LPSPA.P
Retrocopy LPSPAQP

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	0.48 RPM	12.09 RPM
SRP017611_kidney	0.94 RPM	16.50 RPM
SRP017611_liver	0.80 RPM	9.81 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_392 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000011789	1 retrocopy	retro_eeur_392 ,
Pan troglodytes	ENSPTRG00000009074	1 retrocopy	retro_ptro_11,