RetrogeneDB ID: retro_eeur_404

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_285997:1623..1913(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SUMO1
• Ensembl ID: ENSEEUG00000013161
• Aliases: None
• Description: small ubiquitin-like modifier 1 [Source:HGNC Symbol;Acc:12502]

Sequence

>retro_eeur_404
GATCAGGAGGCAAACCTTTCAGCAGAGGACTTGAGAGATTAGAAGGAAGGAGAATATATTAAACTCAAAGTAATTGGACA
GCAGAGCAGTGAGATTTACTTTAAATTGAAAATGACATTGCATCTCAAGTAAATCAAAGAATCATACTGTCAAAGTTAGG
GAGTCCCAGTGGATTCACTCCAGCTTCTCTTTAAGGTCAGAGAATTTCTAATATTCACACTCCAAAAGAAAAGGGAATGG
AGAAAAAAGATGTGATTGAAGTTTATCAGGAACATACAGGGTGGAACTCA

Alignment

ORF - retro_eeur_404 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.43 %
• Parental protein coverage: 96.04 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DQEAKPSTEDLGDKKEGEYIKLKVIGQDSSEIHFKVKMTTHLKKLKESYCQRQGVPMNSLRFLFE-GQRI
          DQEA..S.EDL.D.KEGEYIKLKVIGQ.SSEI.FK.KMT.HLK..KESYCQ..GVP..SL..LF..GQRI
Retrocopy DQEANLSAEDLRD*KEGEYIKLKVIGQQSSEIYFKLKMTLHLK*IKESYCQS*GVPVDSLQLLFK<GQRI

Parental  ADNHTPKELGMEEEDVIEVYQEQTGGHS
          ...HTPKE.GME..DVIEVYQE.TG..S
Retrocopy SNIHTPKEKGMEKKDVIEVYQEHTGWNS

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	28.36 RPM
SRP017611_kidney	0.00 RPM	32.07 RPM
SRP017611_liver	0.00 RPM	14.31 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_404 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 13 parental genes, and 52 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000009859	6 retrocopies	retro_btau_112, retro_btau_1512, retro_btau_1705, retro_btau_357, retro_btau_363, retro_btau_499,
Canis familiaris	ENSCAFG00000012431	8 retrocopies	retro_cfam_1226, retro_cfam_1253, retro_cfam_139, retro_cfam_1815, retro_cfam_1912, retro_cfam_2048, retro_cfam_386, retro_cfam_985,
Equus caballus	ENSECAG00000024693	4 retrocopies	retro_ecab_199, retro_ecab_365, retro_ecab_570, retro_ecab_935,
Erinaceus europaeus	ENSEEUG00000013161	6 retrocopies	retro_eeur_40, retro_eeur_404 , retro_eeur_428, retro_eeur_644, retro_eeur_645, retro_eeur_651,
Felis catus	ENSFCAG00000031005	6 retrocopies	retro_fcat_1520, retro_fcat_218, retro_fcat_26, retro_fcat_472, retro_fcat_6, retro_fcat_862,
Myotis lucifugus	ENSMLUG00000007504	2 retrocopies	retro_mluc_1346, retro_mluc_188,
Mustela putorius furo	ENSMPUG00000000335	2 retrocopies	retro_mputfur_257, retro_mputfur_33,
Otolemur garnettii	ENSOGAG00000030345	1 retrocopy	retro_ogar_215,
Pongo abelii	ENSPPYG00000013083	3 retrocopies	retro_pabe_11, retro_pabe_1830, retro_pabe_775,
Pan troglodytes	ENSPTRG00000012817	1 retrocopy	retro_ptro_119,
Sorex araneus	ENSSARG00000008205	8 retrocopies	retro_sara_130, retro_sara_429, retro_sara_433, retro_sara_456, retro_sara_487, retro_sara_679, retro_sara_758, retro_sara_763,
Sarcophilus harrisii	ENSSHAG00000011968	1 retrocopy	retro_shar_375,
Tursiops truncatus	ENSTTRG00000000642	4 retrocopies	retro_ttru_1646, retro_ttru_1652, retro_ttru_309, retro_ttru_399,