RetrogeneDB ID: retro_eeur_409

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_288499:5584..6106(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: IMPACT
• Ensembl ID: ENSEEUG00000003962
• Aliases: None
• Description: impact RWD domain protein [Source:HGNC Symbol;Acc:20387]

Sequence

>retro_eeur_409
GTAATGCTGCCTAATGAATACCCAGGTATAGCCCCACCCATTTATCACCTCAATGCCCCTTGGCTGAAAGGACAAGAACA
TGCAGATTTATCTAATAGCCTTGAGGAAATATATGTACAGAACATTGGTGAAAGTATCCTTTACCTGTGGGTAGAGAAAA
TAAGCGAAGATCTAATACAGAAATCTCAGATGACAGAACCAGGTCCAAACATAAAGAAGAAAACTGAAGAAGAGGATGTC
TAATGTGAAGAGGATCTCATTTTAGCTTGTCAACCAGAAAATCTAGTGAAAACATTAGATATTTCTGTCAGTAAAAATCC
AACAGAAATAGAAGAAATACCTCCAGTTGATCATGGCATACATATTGCAGACCGAAGAAGTACTTTCCAGGCACACCTGG
CTCCAGTAGTTTATTCCCAGCAGGTAAAAATGGTTCTTGCCAAATTGCATGAGAATAAGAAAATGGCTAGTGCTACCCAC
AACCTCTGTGCATACAGAATATATTGTGAGGATAAACAGACT

Alignment

ORF - retro_eeur_409 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76. %
• Parental protein coverage: 58.92 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VMLPNEYPGTAPPIYQLNAPWLKGQERADLSNSLEEIYIQNIGESILYXXXXXXXXXXXXXXXXXXXXPD
          VMLPNEYPG.APPIY.LNAPWLKGQE.ADLSNSLEEIY.QNIGESILY....................P.
Retrocopy VMLPNEYPGIAPPIYHLNAPWLKGQEHADLSNSLEEIYVQNIGESILYLWVEKISEDLIQKSQMTEPGPN

Parental  IKKKTEEEDVDCEEDLILACKPENPVKALDFAVSKNPTVEIEEIPPIDHGVPITDRRSTFQAHLAPVVCP
          IKKKTEEEDV.CEEDLILAC.PEN.VK.LD..VSKNPT.EIEEIPP.DHG..I.DRRSTFQAHLAPVV..
Retrocopy IKKKTEEEDV*CEEDLILACQPENLVKTLDISVSKNPT-EIEEIPPVDHGIHIADRRSTFQAHLAPVVYS

Parental  QQVKMVLAKLYENKKIASATHNIYAYRIYCEDKQT
          QQVKMVLAKL.ENKK.ASATHN..AYRIYCEDKQT
Retrocopy QQVKMVLAKLHENKKMASATHNLCAYRIYCEDKQT

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	0.16 RPM	10.80 RPM
SRP017611_kidney	0.19 RPM	12.38 RPM
SRP017611_liver	0.00 RPM	6.91 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_409 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 8 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013068	1 retrocopy	retro_chof_2523,
Erinaceus europaeus	ENSEEUG00000003962	1 retrocopy	retro_eeur_409 ,
Homo sapiens	ENSG00000154059	1 retrocopy	retro_hsap_3341,
Macaca mulatta	ENSMMUG00000004664	1 retrocopy	retro_mmul_1041,
Nomascus leucogenys	ENSNLEG00000006582	1 retrocopy	retro_nleu_1166,
Pongo abelii	ENSPPYG00000009071	1 retrocopy	retro_pabe_2753,
Pan troglodytes	ENSPTRG00000009927	1 retrocopy	retro_ptro_2141,
Sorex araneus	ENSSARG00000002836	1 retrocopy	retro_sara_719,