RetrogeneDB ID: retro_eeur_304

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_247315:5039..5488(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000009651
• Aliases: None
• Description: None

Sequence

>retro_eeur_304
TGTCAGGCTGAACATAAAGTTAAAAATCAAGCTGCAAAAGGTGATGAAGTGACTCGAAAATTATTCTATGCATTTGTCCT
TTGTGGGGAAACTTTACCTTAACCTAGAGATTAAGAGAACAAATGGGCAGGTTACAAGAGCAGATATTCTTTGGGTCTGT
CTTCAGGAATTGCTGAATGCCCTCTTTTCTGATCCTGTGGATGACAACTTAATTTCTGCAGAAAAATTACTGAAGTTAAC
TGGATCCATTTTTGGAAGATGCCTGGAAGGAAAAAGGATGGAACTATATGGAAGAAATTAATCTGAGAATTGAAAATGTT
GTCCTAGGTGCAAATTATAGCAGAAATATAAAAAAGATGCTCTTGAAAATTGTAGGGCTGTGGTCAAGTAATTGGGGTAC
AGTCCATGCAACATCAACTTACAGAGAAGCAACACCTGAAAATGATCCT

Alignment

ORF - retro_eeur_304 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.97 %
• Parental protein coverage: 55.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  CRTEYEAKDQAAKGDEMTRKRFHAFVLFLGE-LYLNLEIKGTNGQVTRADILQAGLRELLNALFSNPVDD
          C..E...K.QAAKGDE.TRK.F.AFVL..GE.LYLNLEIK.TNGQVTRADIL...L.ELLNALFS.PVDD
Retrocopy CQAEHKVKNQAAKGDEVTRKLFYAFVL-CGE>LYLNLEIKRTNGQVTRADILWVCLQELLNALFSDPVDD

Parental  NVICAVKLLKLTGSV-LEDAWKEKGKNDMEEINQRIENVVLDANCSRDVKQMLLKLVELRSSNWGRVHAT
          N.I.A.KLLKLTGS..LEDAWKEKG.N.MEEIN.RIENVVL.AN.SR..K.MLLK.V.L.SSNWG.VHAT
Retrocopy NLISAEKLLKLTGSI>LEDAWKEKGWNYMEEINLRIENVVLGANYSRNIKKMLLKIVGLWSSNWGTVHAT

Parental  STYREATPENDP
          STYREATPENDP
Retrocopy STYREATPENDP

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	116.02 RPM
SRP017611_kidney	0.00 RPM	120.40 RPM
SRP017611_liver	0.00 RPM	72.03 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_304 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 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000020376	1 retrocopy	retro_btau_359,
Choloepus hoffmanni	ENSCHOG00000004961	1 retrocopy	retro_chof_762,
Callithrix jacchus	ENSCJAG00000001340	2 retrocopies	retro_cjac_3224, retro_cjac_3337,
Cavia porcellus	ENSCPOG00000002525	2 retrocopies	retro_cpor_133, retro_cpor_197,
Erinaceus europaeus	ENSEEUG00000009651	1 retrocopy	retro_eeur_304 ,
Homo sapiens	ENSG00000172239	1 retrocopy	retro_hsap_1726,
Otolemur garnettii	ENSOGAG00000001887	2 retrocopies	retro_ogar_1096, retro_ogar_1241,
Ochotona princeps	ENSOPRG00000000386	2 retrocopies	retro_opri_185, retro_opri_469,
Ictidomys tridecemlineatus	ENSSTOG00000011203	1 retrocopy	retro_itri_234,