RetrogeneDB ID: retro_eeur_156

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_106386:392..717(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000003783
• Aliases: None
• Description: None

Sequence

>retro_eeur_156
GCTTCTGAAGACCTTCTCAAAGAACACTACATTGACCTGAAGGACAGCTCGTTCTTTACTGGCCTGGTGAAATACATGCA
CTCGGGGCCAGTGGTGGCTATGGTCTGGCAGGGGCTGAATGTAGTGAAGACAGGGAGAGTGGTGCTTGGGGAAACCAGCA
GATTCTAAGCTAGGCACCATTTGAAGGGACTTCTGTATTCAGGTTGGCAGGAACATCATCAGGGCTGTGACTCAGTAAAA
AAGCGCTGAGAAAGAAATCAGCCTGCGGTTTAAGCCTGAAGAATTGGTTAGCCACAAGTCCTGTGCTTTTGACTGGATTT
ATGAA

Alignment

ORF - retro_eeur_156 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.48 %
• Parental protein coverage: 57.59 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ASEELLKQHYIDLKDRPFFPGLVKYMNSGPVVAMVWEGLNVVKTGRVM-LGETNPADSKPGTIRGDFCIQ
          ASE.LLK.HYIDLKD..FF.GLVKYM.SGPVVAMVW.GLNVVKTGRV..LG...PADSK.GTI..DFCIQ
Retrocopy ASEDLLKEHYIDLKDSSFFTGLVKYMHSGPVVAMVWQGLNVVKTGRVV>LGK--PADSKLGTI*RDFCIQ

Parental  VGRNIIHGSDSVKSAEKEISLWFKPEELLNYKSCAFDWIYE
          VGRNII......KSAEKEISL.FKPEEL...KSCAFDWIYE
Retrocopy VGRNIIRAVTQ*KSAEKEISLRFKPEELVSHKSCAFDWIYE

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	0.48 RPM	6.12 RPM
SRP017611_kidney	0.00 RPM	17.63 RPM
SRP017611_liver	0.00 RPM	8.04 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_156 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 18 parental genes, and 56 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008022	3 retrocopies	retro_amel_1573, retro_amel_390, retro_amel_538,
Callithrix jacchus	ENSCJAG00000018395	5 retrocopies	retro_cjac_1765, retro_cjac_2517, retro_cjac_2642, retro_cjac_3940, retro_cjac_471,
Equus caballus	ENSECAG00000021658	1 retrocopy	retro_ecab_404,
Erinaceus europaeus	ENSEEUG00000003783	2 retrocopies	retro_eeur_156 , retro_eeur_5,
Felis catus	ENSFCAG00000006742	5 retrocopies	retro_fcat_1083, retro_fcat_1117, retro_fcat_1475, retro_fcat_216, retro_fcat_663,
Homo sapiens	ENSG00000011052	1 retrocopy	retro_hsap_1063,
Loxodonta africana	ENSLAFG00000007784	1 retrocopy	retro_lafr_636,
Myotis lucifugus	ENSMLUG00000016929	3 retrocopies	retro_mluc_1422, retro_mluc_1882, retro_mluc_637,
Macaca mulatta	ENSMMUG00000001940	1 retrocopy	retro_mmul_1827,
Monodelphis domestica	ENSMODG00000012580	1 retrocopy	retro_mdom_1811,
Mustela putorius furo	ENSMPUG00000015573	4 retrocopies	retro_mputfur_1236, retro_mputfur_1590, retro_mputfur_327, retro_mputfur_912,
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221,
Oryctolagus cuniculus	ENSOCUG00000024946	1 retrocopy	retro_ocun_418,
Otolemur garnettii	ENSOGAG00000025331	9 retrocopies	retro_ogar_1326, retro_ogar_1875, retro_ogar_1997, retro_ogar_2373, retro_ogar_2393, retro_ogar_2779, retro_ogar_3299, retro_ogar_483, retro_ogar_95,
Rattus norvegicus	ENSRNOG00000002671	8 retrocopies	retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966, retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Sarcophilus harrisii	ENSSHAG00000014470	3 retrocopies	retro_shar_130, retro_shar_554, retro_shar_781,
Tupaia belangeri	ENSTBEG00000013053	6 retrocopies	retro_tbel_1271, retro_tbel_1386, retro_tbel_2497, retro_tbel_294, retro_tbel_4620, retro_tbel_820,
Tursiops truncatus	ENSTTRG00000007433	1 retrocopy	retro_ttru_1821,