RetrogeneDB ID: retro_eeur_681

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_586:563..1186(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000004422
• Aliases: None
• Description: None

Sequence

>retro_eeur_681
ACCTTCTTTGAGAAACCCCATGTGCAGATGGCATGTCAGAAGACCCTTCAGGACCTGAACTTAGACTATCTGGACATCTG
TCTTCTTCACTTTCCTCAGGGATTACAGTATATAACAGGTTAAAATGAGAAGTTGCCCAGAGATCCTAAAGGCAGTATTC
TTGATGGTAAGGCTACATTTCTGGATGCAAAGGAGACCAAAGAAGAGCGAGTGGGTGAGGTTCCCTTGAAAGCCACTGGA
ATCTCCAACTGCAACTACCTCCAGATTGATAGGCTGTTAAACAAACCTGACTGAAATATAAACCAGTGACTAACCAGGTT
GAATGTCACCTATACCTCACAAAGGAGAAATTGGCCCAGTACTGTCACTCCAAGGGCATCTCTTTCACTGCTTACAGCCC
TCTGGAGTCTCCAGACAGACCTTGAACCAAGCCAGATGGCCCTTGCCTATTGGAGGATTCCAAGATTAAGGCAATTGCTG
CTAAGCACAACAAGTCCACAGCTCAGATTCTGATCTGATTCCAAATTCACAGGAATGTGGTTATGATCCCCAAGTCAGTG
ACCCCAGCACCCATCAGAGAGAATTTTGATATCTTTGACTTTAAACTGAGTGATGAGAAGATG

Alignment

ORF - retro_eeur_681 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.59 %
• Parental protein coverage: 65.29 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TFFEKARVKKACQKTLSDLKLDYLDIYLIHFPQGLQ---GEKDMFPKDANGKVLGGNTTFLEAWEGMEEL
          TFFEK..V..ACQKTL.DL.LDYLDI.L.HFPQGLQ...G.....P.D..G..L.G..TFL.A.E..EE.
Retrocopy TFFEKPHVQMACQKTLQDLNLDYLDICLLHFPQGLQYITG*NEKLPRDPKGSILDGKATFLDAKETKEER

Parental  VDEGLVKGIGISNFNHLQIERLLNKPG-LKHKPLTNQVESHPYLTQDKLIHYCRSNGIVITAYSPLGSPD
          V.E...K..GISN.N.LQI.RLLNKP..LK.KP.TNQVE.H.YLT..KL..YC.S.GI..TAYSPL.SPD
Retrocopy VGEVPLKATGISNCNYLQIDRLLNKPD<LKYKPVTNQVECHLYLTKEKLAQYCHSKGISFTAYSPLESPD

Parental  RPWAKLDDPSLMEDTKIKAIATKHKKSTAQILLRFQIQRNVAVIPKSVTPARIIENFNVFEFKLNDEYM
          RP..K.D.P.L.ED.KIKAIA.KH.KSTAQIL..FQI.RNV..IPKSVTPA.I.ENF..F.FKL.DE.M
Retrocopy RP*TKPDGPCLLEDSKIKAIAAKHNKSTAQILI*FQIHRNVVMIPKSVTPAPIRENFDIFDFKLSDEKM

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	0.00 RPM
SRP017611_kidney	0.00 RPM	0.00 RPM
SRP017611_liver	0.16 RPM	62.86 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_681 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 14 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000166	1 retrocopy	retro_chof_400,
Callithrix jacchus	ENSCJAG00000012250	1 retrocopy	retro_cjac_3038,
Erinaceus europaeus	ENSEEUG00000004422	1 retrocopy	retro_eeur_681 ,
Echinops telfairi	ENSETEG00000006005	3 retrocopies	retro_etel_1055, retro_etel_1643, retro_etel_748,
Homo sapiens	ENSG00000198074	1 retrocopy	retro_hsap_581,
Macaca mulatta	ENSMMUG00000013098	2 retrocopies	retro_mmul_1357, retro_mmul_2455,
Mus musculus	ENSMUSG00000029762	1 retrocopy	retro_mmus_627,
Mus musculus	ENSMUSG00000052131	1 retrocopy	retro_mmus_2860,
Mus musculus	ENSMUSG00000061758	1 retrocopy	retro_mmus_1490,
Nomascus leucogenys	ENSNLEG00000013088	1 retrocopy	retro_nleu_801,
Pongo abelii	ENSPPYG00000018018	1 retrocopy	retro_pabe_606,
Pan troglodytes	ENSPTRG00000019718	1 retrocopy	retro_ptro_428,
Rattus norvegicus	ENSRNOG00000009734	3 retrocopies	retro_rnor_2380, retro_rnor_2588, retro_rnor_657,
Sorex araneus	ENSSARG00000001396	1 retrocopy	retro_sara_608,