RetrogeneDB ID: retro_eeur_232

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_215660:10257..10499(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MAGOH
• Ensembl ID: ENSEEUG00000015908
• Aliases: None
• Description: mago-nashi homolog, proliferation-associated (Drosophila) [Source:HGNC Symbol;Acc:6815]

Sequence

>retro_eeur_232
CAGAGTCACTTTTATCTGTGTTAACCACATGGGTCACAAGAGAAAGTTCATTCATGTGTTTCTGGAATTTGAATTCTGAT
TTGATGAGAAATTGAGATATGCCACCAACAGCAATTACAAAAATGACTGATAATCAGAAAAGAGGCTTATGTACATAAAG
TGTAATGGTGGACCTGAAGAGAATAATTAATGATGACAATATTACTAAAGAAGATGATGTCTTGTGGCCAAAAATTGAAA
GG

Alignment

ORF - retro_eeur_232 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.86 %
• Parental protein coverage: 94.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  ESDFYLR-YYVGHKGKFGHEFLEFEFRPDGKLRYANNSNYKND-VMIRKEAYVHK-SVMEELKRIIDDSE
          .S.FYL.....GHK.KF.H.FLEFEF..D.KLRYA.NSNYKND...IRKEAYVHK.SVM..LKRII.D..
Retrocopy QSHFYLC>NHMGHKRKFIHVFLEFEF*FDEKLRYATNSNYKND<LIIRKEAYVHK<SVMVDLKRIINDDN

Parental  ITKEDDALWPPPDR
          ITKEDD.LWP...R
Retrocopy ITKEDDVLWPKIER

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	1.13 RPM
SRP017611_kidney	0.00 RPM	6.00 RPM
SRP017611_liver	0.00 RPM	1.61 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_232 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 6 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009587	1 retrocopy	retro_amel_853,
Erinaceus europaeus	ENSEEUG00000015908	6 retrocopies	retro_eeur_232 , retro_eeur_275, retro_eeur_387, retro_eeur_45, retro_eeur_463, retro_eeur_568,
Felis catus	ENSFCAG00000025232	2 retrocopies	retro_fcat_1246, retro_fcat_980,
Rattus norvegicus	ENSRNOG00000012778	1 retrocopy	retro_rnor_1168,
Sorex araneus	ENSSARG00000012081	2 retrocopies	retro_sara_142, retro_sara_150,
Sus scrofa	ENSSSCG00000003849	3 retrocopies	retro_sscr_1007, retro_sscr_706, retro_sscr_977,