RetrogeneDB ID: retro_eeur_532

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_340535:7918..9009(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000008272
• Aliases: None
• Description: None

Sequence

>retro_eeur_532
GGTCACCTGGAGCCACTACCTCCCCCACTCATTGCTCAGCCATACATCCCATCCCCTGTGCAGCAGCAGGAAGAGGAGAT
GGCTGAGGCTGGACATTGGTGGCATCCCTATGATTGGTGGGTTTCTGATCCTGGACTCCCCCACTTATGTCCTGTACAGG
GACAGGGCAGAATAGGCTGAAATAGACCCAGTGTTGCAGAATGATGGCCTCAACCCAGTGGTCCAGATCATTTATAGTGG
AAACTTTAGAGATGCTTATGATTATTTCTGGGCAGTTCTACAGTGTGATGAAAGAAGTGAACAAGCTTTTAAACTAACCA
GAGATGGTAGTCAGTTAAATGTGGCCAATTATACAGTGTGGCATTTTTGGAGAGTTCTTCTAAAGTCACTTCAAAAGGAT
CTATATGAGGAAATGAACTATATCATTGCAATAATTGAGGAACAGCCAAAAAACTATCAAGTTTGGTATCATAGGTGAGT
ATTAGTTGAGTGGCTGGAAGATCCATCTCAGGAGCCTGAGTTTATCGCTGATATTCTTAATCAGGATGCAAAGAACTACC
ATGCCTGGGAGCATTGGCAGTGGGTTATTCAGGAATTTAAGTTTAGGATAACGAGCTGCAGTATGTAGACCAACTTCTCA
GAGAGGTTGTGAGAAATAACTCTTTTTGGAAGCAAAGATACTTTGTGATTTCTAGCACCACTAGCTACAATGATACTGCT
ATACTGGAAAGAGAAGTCCAGTGTGCTCTGGAAAGAATCGGACTAGTACCACATAATGAAAGTGCATGGAACTATCTGAA
AGAGATTTTATAAGACCTTGTTCTTTCCAAATATCCTAATTTGTTAAGTCAGTTACTTGACTTACCACCAAGTCACAGTT
CCCCCTAATTGCTTTTCTTGTGGATATCTATGAAGACATGCTAGAAAACCAAAGTGCAGACAAGGAGGACATTCTGAATA
AAGCACTAGAGTTATGTGAAATCCTAGCTAAAGAAAAGGACACTATAAGAAAGGAATATTGGAGATACATTGGGACATCT
CTTCAGAGCAAACACAGCATAGAAAATGACCCACCAATAAATGGACAGCAA

Alignment

ORF - retro_eeur_532 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.27 %
• Parental protein coverage: 96.53 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GQSEPPPP----QPHPPPAVQQQEEEMAEARE-VVAS-PMDDGFLSLDSPTYVLYRDRAEWADIDPVPQN
          G..EP.PP....QP..P..VQQQEEEMAEA....VAS.PM..GFL.LDSPTYVLYRDRAE.A.IDPV.QN
Retrocopy GHLEPLPPPLIAQPYIPSPVQQQEEEMAEAGH<LVAS<PMIGGFLILDSPTYVLYRDRAE*AEIDPVLQN

Parental  DGPNPVVQIIYSEKFRDVYDYFRAVLQRDERSERAFKLTRDAIELNAANYTVWHFRRVLLKSLQKDLYEE
          DG.NPVVQIIYS..FRD.YDYF.AVLQ.DERSE.AFKLTRD...LN.ANYTVWHF.RVLLKSLQKDLYEE
Retrocopy DGLNPVVQIIYSGNFRDAYDYFWAVLQCDERSEQAFKLTRDGSQLNVANYTVWHFWRVLLKSLQKDLYEE

Parental  LNYITAIIEEQPKNYQVWHHRRVLVEWLKDPSQELEFIADILNQDAKNYHAWQHRQWVIQEFK-LWNNEL
          .NYI.AIIEEQPKNYQVW.HR.VLVEWL.DPSQE.EFIADILNQDAKNYHAW.H.QWVIQEFK....NEL
Retrocopy MNYIIAIIEEQPKNYQVWYHR*VLVEWLEDPSQEPEFIADILNQDAKNYHAWEHWQWVIQEFK<V*DNEL

Parental  HYVDLLLREDVRNNSVWNQRYFVISNTTGYNDPAILEREVQYTLERIKLVPHNESAWNYLKGILQDLGLS
          .YVD.LLRE.VRNNS.W.QRYFVIS.TT.YND.AILEREVQ..LERI.LVPHNESAWNYLK.IL.DL.LS
Retrocopy QYVDQLLREVVRNNSFWKQRYFVISSTTSYNDTAILEREVQCALERIGLVPHNESAWNYLKEIL*DLVLS

Parental  KYPNLLNQLLDLQPSHSSPYLIAFL-VDIYEDMLENQCEDKEDILNKALELCEILAKEKDTIRKEYWRYI
          KYPNLL.QLLDL.PSHSSP.L..FL.VDIYEDMLENQ..DKEDILNKALELCEILAKEKDTIRKEYWRYI
Retrocopy KYPNLLSQLLDLPPSHSSP*LL-FL<VDIYEDMLENQSADKEDILNKALELCEILAKEKDTIRKEYWRYI

Parental  GRSLQSKHSTENDPATNVQQ
          G.SLQSKHS.ENDP..N.QQ
Retrocopy GTSLQSKHSIENDPPINGQQ

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	31.91 RPM
SRP017611_kidney	0.00 RPM	63.01 RPM
SRP017611_liver	0.00 RPM	36.66 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_532 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000008272	1 retrocopy	retro_eeur_532 ,
Homo sapiens	ENSG00000168522	1 retrocopy	retro_hsap_805,
Loxodonta africana	ENSLAFG00000000631	1 retrocopy	retro_lafr_506,
Monodelphis domestica	ENSMODG00000010003	1 retrocopy	retro_mdom_1656,
Nomascus leucogenys	ENSNLEG00000012979	1 retrocopy	retro_nleu_2408,
Sorex araneus	ENSSARG00000009660	1 retrocopy	retro_sara_109,
Ictidomys tridecemlineatus	ENSSTOG00000011626	1 retrocopy	retro_itri_1221,