RetrogeneDB ID: retro_eeur_301

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_247006:3987..4287(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AP4S1
• Ensembl ID: ENSEEUG00000013009
• Aliases: None
• Description: adaptor-related protein complex 4, sigma 1 subunit [Source:HGNC Symbol;Acc:575]

Sequence

>retro_eeur_301
ATAATGGTGAATAGACTAGGACAGACTCGACTTCCTAAGTACTATGAACATGTGGAGATTAATAAACATATACTTCTGGA
AACAGAAGTTATAAAGAGCTGTCTTTCTTGATCCAACGAACAGTGCTTTTTCATTGAATATAAGGATTCTCAGCTAGTTT
ATCAGCACTATGCAGCTCTCTTCATTATGGTTGGAGTTAATGATGCTGAGAATGAGATGGCAACTTACGAATTCATTCAT
AACTTTGTTGAAGTTTTAGATGAGTACTTCAGCCAAGTGAGTGAATTAGATAAAATGTTT

Alignment

ORF - retro_eeur_301 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82. %
• Parental protein coverage: 81.15 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LMVNKQGQTRLSRYYEHVDINKRILLETEVIKSCLSRS-EQCSFIEYKDFKLVYRQYAALFIVVGVNDAE
          .MVN..GQTRL..YYEHV.INK.ILLETEVIKSCLS.S.EQC.FIEYKD..LVY..YAALFI.VGVNDAE
Retrocopy IMVNRLGQTRLPKYYEHVEINKHILLETEVIKSCLS*SNEQCFFIEYKDSQLVYQHYAALFIMVGVNDAE

Parental  NEMAVYEFIHNFVEVLDEYFSQVSELDVSF
          NEMA.YEFIHNFVEVLDEYFSQVSELD..F
Retrocopy NEMATYEFIHNFVEVLDEYFSQVSELDKMF

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	8.86 RPM
SRP017611_kidney	0.00 RPM	9.56 RPM
SRP017611_liver	0.00 RPM	3.05 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_301 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 13 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013301	4 retrocopies	retro_chof_2345, retro_chof_2677, retro_chof_393, retro_chof_820,
Dipodomys ordii	ENSDORG00000009468	1 retrocopy	retro_dord_595,
Erinaceus europaeus	ENSEEUG00000013009	1 retrocopy	retro_eeur_301 ,
Homo sapiens	ENSG00000100478	1 retrocopy	retro_hsap_3496,
Gorilla gorilla	ENSGGOG00000003198	1 retrocopy	retro_ggor_2363,
Macaca mulatta	ENSMMUG00000003123	1 retrocopy	retro_mmul_17,
Monodelphis domestica	ENSMODG00000017579	1 retrocopy	retro_mdom_1774,
Nomascus leucogenys	ENSNLEG00000015901	1 retrocopy	retro_nleu_788,
Ornithorhynchus anatinus	ENSOANG00000014031	1 retrocopy	retro_oana_60,
Pongo abelii	ENSPPYG00000005723	1 retrocopy	retro_pabe_2889,
Pan troglodytes	ENSPTRG00000006239	1 retrocopy	retro_ptro_2368,
Pteropus vampyrus	ENSPVAG00000017161	1 retrocopy	retro_pvam_1455,
Ictidomys tridecemlineatus	ENSSTOG00000010759	1 retrocopy	retro_itri_1050,