RetrogeneDB ID: retro_eeur_148

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_102830:3173..3368(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FXYD4
• Ensembl ID: ENSEEUG00000010030
• Aliases: None
• Description: FXYD domain containing ion transport regulator 4 [Source:HGNC Symbol;Acc:4028]

Sequence

>retro_eeur_148
CTTCCTGCCCTGGAAGCCAGTGAGTCCATAGATGAGAGCAGTCCCTTCTACTATGACTGAGAGACCCTGCAGCTGGCAGG
AGTCATCTGCTTGGTCAGCATAGCCTTCGCCCTGAGCAACAAATGTAAATGCAAAACTAAAAAGGAGTAGAGCCTGATAC
CTGAGAGAGCTGTCCCATTCATTATGCCAGGGTCT

Alignment

ORF - retro_eeur_148 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.97 %
• Parental protein coverage: 95.95 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LPALEADEATADESSPFYYDWETLQLAGTICAGVLCLVGIAFALSNKCKCKTKKEQSPVPESAIPFIVPG
          LPALEA.E...DESSPFYYD.ETLQLAG.IC...L.....A.....KC..KTKKE.S..PE.A.PFI.PG
Retrocopy LPALEASESI-DESSPFYYD*ETLQLAGVIC---LVSIAFALSNKCKC--KTKKE*SLIPERAVPFIMPG

Parental  S
          S
Retrocopy S

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	0.64 RPM
SRP017611_kidney	0.00 RPM	5.06 RPM
SRP017611_liver	0.00 RPM	0.32 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_148 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 8 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000024923	1 retrocopy	retro_cfam_1820,
Dasypus novemcinctus	ENSDNOG00000017385	1 retrocopy	retro_dnov_643,
Erinaceus europaeus	ENSEEUG00000010030	4 retrocopies	retro_eeur_148 , retro_eeur_264, retro_eeur_524, retro_eeur_559,
Felis catus	ENSFCAG00000022417	2 retrocopies	retro_fcat_284, retro_fcat_990,
Monodelphis domestica	ENSMODG00000027578	1 retrocopy	retro_mdom_976,
Oryctolagus cuniculus	ENSOCUG00000006722	1 retrocopy	retro_ocun_1050,
Tupaia belangeri	ENSTBEG00000016033	1 retrocopy	retro_tbel_1911,
Tarsius syrichta	ENSTSYG00000014460	3 retrocopies	retro_tsyr_1494, retro_tsyr_70, retro_tsyr_875,