RetrogeneDB ID: retro_eeur_110

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_7058:519020..519558(-)
• Located in intron of: ENSEEUG00000006842

Retrocopy information

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

Parental gene information

• Parental gene symbol: IPMK
• Ensembl ID: ENSEEUG00000009958
• Aliases: None
• Description: inositol polyphosphate multikinase [Source:HGNC Symbol;Acc:20739]

Sequence

>retro_eeur_110
TTATACCTTAAACTGGAAGATGTGACCCACAGATTCCATAAACCCTGTATAATGGATGTAAAAATAGGGCGGAAAAGCTA
TGATCCTTTTGCCTCATCTGAGAAGATCAAGCAACAGGTCAGCAAGTACCCATTAATGGAAGAGACTGGGTTCTTGGTGC
CTGGCATGAGGGTCTACCGTGTTCATTCTGATGACTACAAGACGAAAAACCAGCACCACGGAAGAAGCTTAACAAGAGAA
ACGCTGAAGGACGGAGTCGCCAAGTTTTTCCATGATGGGTTCTGCTTACGGAAGGATGCCATTGCTGCCAGTATTCAGAA
AATCAAGAGCATCCTGCAGTGGTTTGAAAGCCAGCAGCAGCTAAATTTTTATGCAAGTTCATTACTGTTTGTTTATGAAG
GTTCATCTCAACCAACTACTACAAAATCAAACGACAGAACTTTAGCAGAGAAGTTTCTGGGCAAAGGACAACTAACTGTC
AGACACAGATGTACTAGAATATAATAACAACTTTCATATGTTAAGCTCTCCAGCCAAT

Alignment

ORF - retro_eeur_110 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.33 %
• Parental protein coverage: 50.57 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LYLKLEDVTHRFHKPCIMDVKIGRKSYDPFASSEKIKQQVSKYPLMEEIGFLLLGMRVYRVHSDDYETKN
          LYLKLEDVTHRFHKPCIMDVKIGRKSYDPFASSEKIKQQVSKYPLMEE.GFL..GMRVYRVHSDDY.TKN
Retrocopy LYLKLEDVTHRFHKPCIMDVKIGRKSYDPFASSEKIKQQVSKYPLMEETGFLVPGMRVYRVHSDDYKTKN

Parental  QHYGRSLTRETLKDGVAKFFHDGFCLRKDAIAASIQKVKSILQWFESQQQLNFYASSLLFVYEGSSQPTT
          QH.GRSLTRETLKDGVAKFFHDGFCLRKDAIAASIQK.KSILQWFESQQQLNFYASSLLFVYEGSSQPTT
Retrocopy QHHGRSLTRETLKDGVAKFFHDGFCLRKDAIAASIQKIKSILQWFESQQQLNFYASSLLFVYEGSSQPTT

Parental  TKSNDRTLAEK-FLGKGQ-LSDTDVLEYNNNFHMLSSPAN
          TKSNDRTLAEK.F..K...LSDTDVLEYNNNFHMLSSPAN
Retrocopy TKSNDRTLAEK>FWAKDN*LSDTDVLEYNNNFHMLSSPAN

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	16.28 RPM
SRP017611_kidney	0.38 RPM	15.75 RPM
SRP017611_liver	0.48 RPM	6.11 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_110 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 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Anas platyrhynchos	ENSAPLG00000011011	1 retrocopy	retro_apla_14,
Cavia porcellus	ENSCPOG00000000222	1 retrocopy	retro_cpor_369,
Erinaceus europaeus	ENSEEUG00000009958	1 retrocopy	retro_eeur_110 ,
Homo sapiens	ENSG00000151151	2 retrocopies	retro_hsap_1244, retro_hsap_2032,
Gorilla gorilla	ENSGGOG00000008790	1 retrocopy	retro_ggor_1464,
Myotis lucifugus	ENSMLUG00000015030	1 retrocopy	retro_mluc_518,
Nomascus leucogenys	ENSNLEG00000012319	2 retrocopies	retro_nleu_2419, retro_nleu_2622,
Pongo abelii	ENSPPYG00000002433	3 retrocopies	retro_pabe_1035, retro_pabe_1086, retro_pabe_1689,
Pan troglodytes	ENSPTRG00000002516	2 retrocopies	retro_ptro_1351, retro_ptro_855,