RetrogeneDB ID: retro_eeur_481

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_322303:6307..6904(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000010991
• Aliases: None
• Description: None

Sequence

>retro_eeur_481
TGCATGATTCAGTATGGGGCTGCAGGTGTTCATTTTATCTTCACAGGAGAAGGTAGGCAGAGTGGTGAGGTTTTTGTTGA
ACTTGAATCAGATGATGAAATAAAGTTCGCGCTGAAGAAAAGACAGGGAAAGCCTGGGACACTGATAAACTGAGGTGTGC
AAGTCTCACAGAACCAAGATGGAGTGGGTGTTGAAGCACAGTGGTCCTGACAGTGCTGATACTGTCAATGATGGCTTCAT
AAGACTTTGAGGATTCCCATTTGGATGCACCAAAGAAGAAATTATTGTTCAGTTCTTCTCAGGGGTGAAAATTGTGCCAA
ATGGGATCACATTGCCTGTTGACCCTGAAGGCAAGATCACTGGGAAAGCATTCAGGCAGTTTGCTTCCCAGGAGTTAGCT
GAGAAGGCTCTAGGCATGCAAGGAGAGAATAAGGCACAGATATATTGAAGTGTTCAAGGAAGTAAGGAAGAAGTGAGGTC
ATATTCATATCCCCCTCTGAAGTTCATATCTGCACAGTGGCCAGGCCCCTATGACTGACCTGACACAGGCAGGAGATACA
TTGCATTGTTAAATGGGCAGGCTTGGATAAGATGAGG

Alignment

ORF - retro_eeur_481 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.41 %
• Parental protein coverage: 79.28 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CKIQNGAQGIRFIYTREGRPSGEAFVELESEDEVKLALKK-DRETMGHRYVEVFKSNNVEMDWVLKHTGP
          C.IQ.GA.G..FI.T.EGR.SGE.FVELES.DE.K.ALKK.DRE..GH...EV.KS....M.WVLKH.GP
Retrocopy CMIQYGAAGVHFIFTGEGRQSGEVFVELESDDEIKFALKK>DRESLGH**TEVCKSHRTKMEWVLKHSGP

Parental  NSPDTANDGFVRLRGLPFGCSKEE-IVQFFSGLEIVPNGITLPVDFQGRSTGEAFVQFASQEIAEKALKK
          .S.DT.NDGF.RL.G.PFGC.KEE.IVQFFSG..IVPNGITLPVD..G..TG.AF.QFASQE.AEKAL..
Retrocopy DSADTVNDGFIRL*GFPFGCTKEEIIVQFFSGVKIVPNGITLPVDPEGKITGKAFRQFASQELAEKALGM

Parental  HKERIGHRYIEIFKSSRAEVRTHYDPPRKLMAMQRPGPYDRPGAGRGYNSIGRG-AGFERMR
          ..E.....Y......S..EVR....PP.K....Q.PGPYD.P..GR.Y.....G.AG...MR
Retrocopy QGENKAQIY*SV-QGSKEEVRSYSYPPLKFISAQWPGPYD*PDTGRRYIALLNG<AGLDKMR

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	88.79 RPM
SRP017611_kidney	0.00 RPM	109.71 RPM
SRP017611_liver	0.00 RPM	45.50 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_481 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 15 parental genes, and 23 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003841	4 retrocopies	retro_chof_1051, retro_chof_1235, retro_chof_1491, retro_chof_2650,
Equus caballus	ENSECAG00000014429	1 retrocopy	retro_ecab_94,
Erinaceus europaeus	ENSEEUG00000010991	1 retrocopy	retro_eeur_481 ,
Erinaceus europaeus	ENSEEUG00000013364	2 retrocopies	retro_eeur_478, retro_eeur_649,
Echinops telfairi	ENSETEG00000011303	1 retrocopy	retro_etel_50,
Loxodonta africana	ENSLAFG00000015766	2 retrocopies	retro_lafr_366, retro_lafr_74,
Myotis lucifugus	ENSMLUG00000016625	1 retrocopy	retro_mluc_124,
Macaca mulatta	ENSMMUG00000010843	1 retrocopy	retro_mmul_2,
Monodelphis domestica	ENSMODG00000009436	3 retrocopies	retro_mdom_1301, retro_mdom_1302, retro_mdom_333,
Ochotona princeps	ENSOPRG00000003513	1 retrocopy	retro_opri_11,
Procavia capensis	ENSPCAG00000006715	1 retrocopy	retro_pcap_4,
Pteropus vampyrus	ENSPVAG00000007670	1 retrocopy	retro_pvam_23,
Sorex araneus	ENSSARG00000003024	1 retrocopy	retro_sara_29,
Sarcophilus harrisii	ENSSHAG00000018204	1 retrocopy	retro_shar_674,
Vicugna pacos	ENSVPAG00000007485	2 retrocopies	retro_vpac_594, retro_vpac_614,