RetrogeneDB ID: retro_eeur_129

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_7951:55633..56001(-)
• Located in intron of: ENSEEUG00000006518

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOQ
• Ensembl ID: ENSEEUG00000015226
• Aliases: None
• Description: ras homolog family member Q [Source:HGNC Symbol;Acc:17736]

Sequence

>retro_eeur_129
GATCGTCTGAGGCCTTTATATTATCCAGTGACTGATGTCTTCTTTATGTGCATCTTGGTGGTAAAGTCCATCTCATTTCA
AAATGTAAAAGGAGTGGGTGCCAGAACTGCAGGAATATGCACCCAATGTACCCTGCTTATTAAAAGGAACTCAGATTGAT
CTCTGAGATGACCCCAAAACTCTGGCAACTGAATGACATGAAAGAAAAGCCTCTATGTTTGGAACAAGGACAGAAACTAG
CAAAAGAGATAGCAGCATGCTGCTCTGTGGCATATTCAGCTTTAACCCTGAAGGGACTGGAGACTGTTTTTGATGAGGCT
GTCATAGCCATTTTAACTCCCAAGAAACACACAGAATCAAGATATATT

Alignment

ORF - retro_eeur_129 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.02 %
• Parental protein coverage: 78.98 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DRLRPLSYPMTDVFLICFSVV-NPASFQNVKEEWVPELKEYAPNVPFLLIGTQIDLRDD-PKTLARLNDM
          DRLRPL.YP.TDVF..C..VV..P..F...KE.WVPEL.EYAPNVP.LL.GTQIDL.DD.PK.L..LNDM
Retrocopy DRLRPLYYPVTDVFFMCILVV>SPSHFKM*KE-WVPELQEYAPNVPCLLKGTQIDL*DD>PK-LWQLNDM

Parental  KEKPICLEQGQKLAKEIGACCYVECSALTQKGLKTVFDEAIIAILTPKKHTVKKRI
          KEKP.CLEQGQKLAKEI.ACC.V..SALT.KGL.TVFDEA.IAILTPKKHT....I
Retrocopy KEKPLCLEQGQKLAKEIAACCSVAYSALTLKGLETVFDEAVIAILTPKKHTESRYI

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	16.11 RPM
SRP017611_kidney	0.00 RPM	6.19 RPM
SRP017611_liver	0.00 RPM	4.50 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_129 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 18 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006082	1 retrocopy	retro_amel_383,
Choloepus hoffmanni	ENSCHOG00000000549	3 retrocopies	retro_chof_2030, retro_chof_457, retro_chof_914,
Callithrix jacchus	ENSCJAG00000000685	1 retrocopy	retro_cjac_2403,
Erinaceus europaeus	ENSEEUG00000009509	1 retrocopy	retro_eeur_20,
Erinaceus europaeus	ENSEEUG00000015226	1 retrocopy	retro_eeur_129 ,
Echinops telfairi	ENSETEG00000019234	3 retrocopies	retro_etel_1468, retro_etel_596, retro_etel_672,
Felis catus	ENSFCAG00000015608	1 retrocopy	retro_fcat_795,
Homo sapiens	ENSG00000119729	3 retrocopies	retro_hsap_1333, retro_hsap_2158, retro_hsap_2316,
Loxodonta africana	ENSLAFG00000004327	1 retrocopy	retro_lafr_316,
Microcebus murinus	ENSMICG00000009124	1 retrocopy	retro_mmur_29,
Myotis lucifugus	ENSMLUG00000001567	1 retrocopy	retro_mluc_595,
Otolemur garnettii	ENSOGAG00000033272	1 retrocopy	retro_ogar_742,
Pongo abelii	ENSPPYG00000012439	2 retrocopies	retro_pabe_1107, retro_pabe_2195,
Pteropus vampyrus	ENSPVAG00000013691	1 retrocopy	retro_pvam_611,
Rattus norvegicus	ENSRNOG00000015415	1 retrocopy	retro_rnor_473,
Sus scrofa	ENSSSCG00000008439	1 retrocopy	retro_sscr_102,
Tarsius syrichta	ENSTSYG00000002837	1 retrocopy	retro_tsyr_1609,
Tursiops truncatus	ENSTTRG00000011892	1 retrocopy	retro_ttru_805,