RetrogeneDB ID: retro_eeur_502

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_328838:1393..1573(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000009790
• Aliases: None
• Description: None

Sequence

>retro_eeur_502
TTCTACCCCTGCCCATGTGGGGATAATTTTTGCATCACTTAAGTAGGAGATGGAGAGTGGAGAAGACATGGCAACCTCTC
TTAGCTGCTCTCTTATTATAAAAGTGATTTTGACAAAGCTCAGTTGATATATGGAGAAACAGTCCCAGCCCCTACTAGCA
ACAAAGAATTAGTTACATGC

Alignment

ORF - retro_eeur_502 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.19 %
• Parental protein coverage: 73.17 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FYPCPCGDNFCIT-KEDLENGEDVATCPSCSLIIKVI-YDKDQFMCGETVPAPSSNKELVKC
          FYPCPCGDNFCIT.K...E.GED.AT..SCSLIIKVI..DK.Q...GETVPAP.SNKELV.C
Retrocopy FYPCPCGDNFCIT>K*EMESGEDMATSLSCSLIIKVI<FDKAQLIYGETVPAPTSNKELVTC

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	5.00 RPM
SRP017611_kidney	0.00 RPM	7.13 RPM
SRP017611_liver	0.00 RPM	4.82 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_502 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 20 parental genes, and 29 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003916	2 retrocopies	retro_btau_797, retro_btau_967,
Canis familiaris	ENSCAFG00000005881	1 retrocopy	retro_cfam_273,
Dasypus novemcinctus	ENSDNOG00000012030	1 retrocopy	retro_dnov_39,
Dipodomys ordii	ENSDORG00000011642	1 retrocopy	retro_dord_167,
Equus caballus	ENSECAG00000016591	1 retrocopy	retro_ecab_1095,
Erinaceus europaeus	ENSEEUG00000009790	1 retrocopy	retro_eeur_502 ,
Echinops telfairi	ENSETEG00000016272	1 retrocopy	retro_etel_1879,
Felis catus	ENSFCAG00000006355	1 retrocopy	retro_fcat_656,
Homo sapiens	ENSG00000154813	1 retrocopy	retro_hsap_2438,
Gorilla gorilla	ENSGGOG00000022108	1 retrocopy	retro_ggor_174,
Loxodonta africana	ENSLAFG00000025650	3 retrocopies	retro_lafr_31, retro_lafr_545, retro_lafr_87,
Macaca mulatta	ENSMMUG00000022692	2 retrocopies	retro_mmul_2085, retro_mmul_497,
Monodelphis domestica	ENSMODG00000025472	3 retrocopies	retro_mdom_131, retro_mdom_1434, retro_mdom_609,
Mus musculus	ENSMUSG00000021905	1 retrocopy	retro_mmus_196,
Nomascus leucogenys	ENSNLEG00000001096	2 retrocopies	retro_nleu_2876, retro_nleu_2913,
Oryctolagus cuniculus	ENSOCUG00000015862	1 retrocopy	retro_ocun_1662,
Pongo abelii	ENSPPYG00000014083	1 retrocopy	retro_pabe_1795,
Pan troglodytes	ENSPTRG00000014671	1 retrocopy	retro_ptro_1409,
Tupaia belangeri	ENSTBEG00000011675	1 retrocopy	retro_tbel_58,
Tursiops truncatus	ENSTTRG00000007739	3 retrocopies	retro_ttru_1474, retro_ttru_31, retro_ttru_907,