RetrogeneDB ID: retro_eeur_586

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_349454:10067..10277(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SHFM1
• Ensembl ID: ENSEEUG00000002237
• Aliases: None
• Description: split hand/foot malformation (ectrodactyly) type 1 [Source:HGNC Symbol;Acc:10845]

Sequence

>retro_eeur_586
ATGTCAGAGGAAAAGCAGCTGGTGGACTTGGGTCTCCTGGAAGAAGATCCGAGTTTGAAGAGTTCCCCGCGGAAGACTGA
GCTGGTTTAGATGAAGATGAAGATGCACATGTCTGGAAGGATAATTGGGATGATGACAGTGTAGAGGTTGATTTTTTCCA
GTCAGTTACGAGCTGAACTTGAAAAACATGGTTATAAGGCGGAGACCTCA

Alignment

ORF - retro_eeur_586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.72 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MSEKKQPVDLGLLEED-DEFEEFPAEDWAGLDEDEDAHVWEDNWDDDNVEDD-FSNQLRAELEKHGYKME
          MSE.KQ.VDLGLLEED..EFEEFPAED.AGLDEDEDAHVW.DNWDDD.VE.D.FS.QLRAELEKHGYK.E
Retrocopy MSEEKQLVDLGLLEED<SEFEEFPAED*AGLDEDEDAHVWKDNWDDDSVEVD>FSSQLRAELEKHGYKAE

Parental  TS
          TS
Retrocopy TS

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	44.96 RPM
SRP017611_kidney	0.00 RPM	94.89 RPM
SRP017611_liver	0.00 RPM	57.40 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_586 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 9 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010434	1 retrocopy	retro_amel_1234,
Equus caballus	ENSECAG00000018179	1 retrocopy	retro_ecab_360,
Erinaceus europaeus	ENSEEUG00000002237	2 retrocopies	retro_eeur_290, retro_eeur_586 ,
Felis catus	ENSFCAG00000023254	2 retrocopies	retro_fcat_1138, retro_fcat_121,
Myotis lucifugus	ENSMLUG00000014208	1 retrocopy	retro_mluc_948,
Oryctolagus cuniculus	ENSOCUG00000026246	3 retrocopies	retro_ocun_1324, retro_ocun_452, retro_ocun_77,
Sus scrofa	ENSSSCG00000015337	1 retrocopy	retro_sscr_67,
Ictidomys tridecemlineatus	ENSSTOG00000011501	1 retrocopy	retro_itri_253,
Tupaia belangeri	ENSTBEG00000016474	3 retrocopies	retro_tbel_2837, retro_tbel_2998, retro_tbel_3844,