RetrogeneDB ID: retro_eeur_394

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_282786:226..681(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: DESI2
• Ensembl ID: ENSEEUG00000009507
• Aliases: None
• Description: desumoylating isopeptidase 2 [Source:HGNC Symbol;Acc:24264]

Sequence

>retro_eeur_394
GGTGGCCATCCTTACCCCTTTCTGGAATATTTGAAATTTCCCCTGGAAATGCTTCTGAATTGGGAGAAACATTTAAATTT
AAAGAAGCTGTTGTTTTAGGGAGTCCTGACTTCCTAGAAGATGATATAGAAAAAATTGTAGAAGAACTGGGAAAAGAATA
CAAAGGCAATGCCTATCATTTGATGCATAAAAACTGCAATCATTTTTCTTCAGCTTTATCAGAGATTCTTTGTGGGAAAG
ACATTCCGAGCTGGATAAATCGCCTGGCCTACTTCAGTTCCTGCATACCCTTTCTCCAGAGTTGCCTCTGGAAGGAGTGG
CTCACTCTGGCAGCCCTGCAGTCCAGTGTCAACCAGGAGCTGCAGGATGAACTGGAGGAAGCCGAGGATGCAGCTGTGTC
AGCCTCTATGGGCAGTGCTGCTGCTGGCTCCCGGCCAGGTCGCCACACCAAACTG

Alignment

ORF - retro_eeur_394 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.46 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  GGHPYPF-SGISDISPGNASELGETFKF-EAVVLGSTDFLEDDIEKIVEELGKEYKGNAYHLMHKNCNHF
          GGHPYPF.SGI..ISPGNASELGETFKF.EAVVLGS.DFLEDDIEKIVEELGKEYKGNAYHLMHKNCNHF
Retrocopy GGHPYPF<SGIFEISPGNASELGETFKFKEAVVLGSPDFLEDDIEKIVEELGKEYKGNAYHLMHKNCNHF

Parental  SSALSEILCGKEIPRWINRLAYFSSCIPFLQSCLPKEWLTPAALQSSVNQELQDELEEAEDAAASASMGS
          SSALSEILCGK.IP.WINRLAYFSSCIPFLQSCL.KEWLT.AALQSSVNQELQDELEEAEDAA.SASMGS
Retrocopy SSALSEILCGKDIPSWINRLAYFSSCIPFLQSCLWKEWLTLAALQSSVNQELQDELEEAEDAAVSASMGS

Parental  AAAGSRPGRHTKL
          AAAGSRPGRHTKL
Retrocopy AAAGSRPGRHTKL

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	0.32 RPM	1.45 RPM
SRP017611_kidney	0.19 RPM	2.81 RPM
SRP017611_liver	0.16 RPM	0.80 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_394 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000016	1 retrocopy	retro_chof_2439,
Dasypus novemcinctus	ENSDNOG00000003484	3 retrocopies	retro_dnov_1042, retro_dnov_2533, retro_dnov_539,
Erinaceus europaeus	ENSEEUG00000009507	2 retrocopies	retro_eeur_394 , retro_eeur_470,
Homo sapiens	ENSG00000121644	1 retrocopy	retro_hsap_2071,
Gorilla gorilla	ENSGGOG00000009797	1 retrocopy	retro_ggor_1493,
Nomascus leucogenys	ENSNLEG00000004019	1 retrocopy	retro_nleu_2734,
Ochotona princeps	ENSOPRG00000015368	2 retrocopies	retro_opri_1007, retro_opri_963,
Pongo abelii	ENSPPYG00000000055	1 retrocopy	retro_pabe_1685,
Pan troglodytes	ENSPTRG00000002180	1 retrocopy	retro_ptro_1384,
Sus scrofa	ENSSSCG00000010876	1 retrocopy	retro_sscr_388,
Drosophila melanogaster	FBgn0033551	1 retrocopy	retro_dmel_30,