RetrogeneDB ID: retro_eeur_379

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_275604:4477..4942(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HSD17B10
• Ensembl ID: ENSEEUG00000005080
• Aliases: None
• Description: hydroxysteroid (17-beta) dehydrogenase 10 [Source:HGNC Symbol;Acc:4800]

Sequence

>retro_eeur_379
AAAACATACAACTCAGAGGACTTTCAGCGAGTTCTCAATGTGCATCTTTCAGGTACCTTCAAGGTAATCTGCCTGGTAGC
TGGTGAGATGGGCCAAAATGACTCAGACCTAGGAAGCCAAGGTGGAGTCATCATCAACACTGCCAGTGTGGCTGCCTTTG
AGGGCCAGGTTGAACAAGCTGCATACTCTGCTTCCAAAGGGGACAAAGTGGGCATGACACTACCTATTGCTCGAGATCTG
GCTCCCATTGGCATCTGAGTGATGACCATTGCTCCTGGCCTATTTGGCAGCTCTCTGCTAACCACTCTACCAGAGAAAGT
ACAAAACTTCCTGGCCAGCCAAATACCCTTCCCTAGCCGACTGGGTGACCCTGCTGAATATGCTCATCCAGTACAGGACA
TCATGGAGAACCCATTCATCAATGGAGAGGTCATCTGGCTAGATGGGGCCATTTGCCTGCAACCT

Alignment

ORF - retro_eeur_379 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.65 %
• Parental protein coverage: 59.39 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAHTLEDFQRVLNVNLLGTFNVIRLAAGEMGQNEPDQGGQRGVIINTASVAAFEGQVGQAAYSASKGGIV
          .....EDFQRVLNV.L.GTF.VI.L.AGEMGQN..D.G.Q.GVIINTASVAAFEGQV.QAAYSASKG..V
Retrocopy KTYNSEDFQRVLNVHLSGTFKVICLVAGEMGQNDSDLGSQGGVIINTASVAAFEGQVEQAAYSASKGDKV

Parental  GMTLPIARDLAPMGIRVMTIAPGLFGTPLLTTLPEKVRNFLASQVPFPSRLGDPSEYAHLVQAIIENPFI
          GMTLPIARDLAP.GI.VMTIAPGLFG..LLTTLPEKV.NFLASQ.PFPSRLGDP.EYAH.VQ.I.ENPFI
Retrocopy GMTLPIARDLAPIGI*VMTIAPGLFGSSLLTTLPEKVQNFLASQIPFPSRLGDPAEYAHPVQDIMENPFI

Parental  NGEVIRLDGAIRLQP
          NGEVI.LDGAI.LQP
Retrocopy NGEVIWLDGAICLQP

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	0.16 RPM	26.91 RPM
SRP017611_kidney	0.00 RPM	138.22 RPM
SRP017611_liver	0.00 RPM	189.88 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_379 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005036	1 retrocopy	retro_amel_371,
Canis familiaris	ENSCAFG00000016277	1 retrocopy	retro_cfam_545,
Choloepus hoffmanni	ENSCHOG00000000939	1 retrocopy	retro_chof_582,
Cavia porcellus	ENSCPOG00000009594	1 retrocopy	retro_cpor_535,
Dipodomys ordii	ENSDORG00000004051	1 retrocopy	retro_dord_532,
Erinaceus europaeus	ENSEEUG00000005080	1 retrocopy	retro_eeur_379 ,
Felis catus	ENSFCAG00000013899	1 retrocopy	retro_fcat_1827,
Macropus eugenii	ENSMEUG00000008565	1 retrocopy	retro_meug_2184,
Myotis lucifugus	ENSMLUG00000000175	1 retrocopy	retro_mluc_4,
Otolemur garnettii	ENSOGAG00000002951	1 retrocopy	retro_ogar_1823,
Tarsius syrichta	ENSTSYG00000005340	3 retrocopies	retro_tsyr_1000, retro_tsyr_1542, retro_tsyr_2078,
Xenopus tropicalis	ENSXETG00000007721	1 retrocopy	retro_xtro_39,