RetrogeneDB ID: retro_eeur_321

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_253473:4253..4968(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: COQ6
• Ensembl ID: ENSEEUG00000000826
• Aliases: None
• Description: coenzyme Q6 monooxygenase [Source:HGNC Symbol;Acc:20233]

Sequence

>retro_eeur_321
GTCCAGATTGTTAGCTGGAACTATGACCAGTCTGCTGTTGTAACTACTCTGCGTTCATCAGAGGTCACAGAAAATAATGC
AGCTTGCCAGAGATTTCTTCCCTCTGGGCCCATTGCTCTGCTCCTGCTCTCAGACACCTCGAGTTCCTAGGTTTGGTCCA
TATCCTATGGACATGCAGCAAAGCTGATCAGCATGGATAAGGAAAAGTTTGTAAATGCCATTAACTCTGCCTTTGGGGGT
TATGTTAACCATGCAGACTTCATCGACTTCACTGGCACTATACTGCAATATGCTGTTGCCCTTCTGAAGCCTACTACTGT
TTCAGCTTGCCAGCTGCCCCCAAATGTGGTCAAGGTGGATGCCCAGAGCAGAGCACTGTTTCCTCTTGGGTTGGGACATG
CTGCTGAGTACGTGTGGCCTTGAGTGGCACTCAGTGAGGATGCATCCCACAGAGTCCATCCACTGGTGGGACAAGGTATC
AACATGGGCTTTGGGGATATTTCCAGTTTGGCTCATCATCTCAGTGCTGTAGCCTTCAATGGGAAAGACTTGGGTTCTAA
GAACCACCTCACAGGTTATGAGAAAGACAGACAGTGTCACACAACTGCTCTTCTGGTTGCTACAGATCTTCTAATAAAAA
TACTATTCCACCAATGCTAGTGTGCTTCTCAGGATGTAGGGATTGCAGACCACAAATGCATTATCTCCACTCAAA

Alignment

ORF - retro_eeur_321 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.93 %
• Parental protein coverage: 51.17 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IQNVSWNYDQSAVVATLHLSEATENNVAWQRFLPSGPIALLPLSDTFSSLVWSTSHEHAAELVSMDEEKF
          .Q.VSWNYDQSAVV.TL..SE.TENN.A.QRFLPSGPIALL.LSDT.SS.VWS.S..HAA.L.SMD.EKF
Retrocopy VQIVSWNYDQSAVVTTLRSSEVTENNAACQRFLPSGPIALLLLSDTSSS*VWSISYGHAAKLISMDKEKF

Parental  VDAINSAFWSDVNHSDFIDSAGTILHYAVALLKPTKISARQLPPSVARVDAQSRALFPLGLGHAAEYVRP
          V.AINSAF...VNH.DFID..GTIL.YAVALLKPT..SA.QLPP.V..VDAQSRALFPLGLGHAAEYV.P
Retrocopy VNAINSAFGGYVNHADFIDFTGTILQYAVALLKPTTVSACQLPPNVVKVDAQSRALFPLGLGHAAEYVWP

Parental  RVALIGDAAHRVHPLAGQGVNMGFGDISSLVHHLSAAAFNGKDLGSMSHLTGYETDRQRHNTALLVATDL
          .VAL..DA.HRVHPL.GQG.NMGFGDISSL.HHLSA.AFNGKDLGS..HLTGYE.DRQ.H.TALLVATDL
Retrocopy *VALSEDASHRVHPLVGQGINMGFGDISSLAHHLSAVAFNGKDLGSKNHLTGYEKDRQCHTTALLVATDL

Parental  LKRL-YSTSVTPLVLLRTWGLQATNAVSPLK
          L....YST.....VLLR..GLQ.TNA.SPLK
Retrocopy LIKI>YSTNAS--VLLRM*GLQTTNALSPLK

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	29.49 RPM
SRP017611_kidney	0.00 RPM	44.63 RPM
SRP017611_liver	0.00 RPM	19.45 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_321 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000000826	1 retrocopy	retro_eeur_321 ,
Tupaia belangeri	ENSTBEG00000008327	3 retrocopies	retro_tbel_2585, retro_tbel_3750, retro_tbel_4713,