RetrogeneDB ID: retro_eeur_647

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_374550:54268..54722(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS10
• Ensembl ID: ENSEEUG00000003376
• Aliases: None
• Description: ribosomal protein S10 [Source:HGNC Symbol;Acc:10383]

Sequence

>retro_eeur_647
ATGTTGATGCCCAAGAAGAACCGGATTGCCATTTACGAACTCCTTTTTAAGGAGGGAGTGATGGTGGCTAAGAAGGACGT
CCACATGCCCAAACACCCCGAGCTCGCAGACAAGAACGTCCCCAACCTTCACGTCATGAAGGCCATGCAGTCTCTCAAGT
CACAAGGCTACGTGAAGGAACAGTTTGCCTGGAGGCATTTTTACTGGTATCTTACCAACGAGGGTATCCAGTACCTCCGA
GATTACCTCCACCTGCCCCGAGATTGTGCCCGCCACCCTGCGTCGCAGCCGGCCTGAGACTGGCAGGCCGAGGCCCAAAG
GTCTGGAAGGTGAGCGACCTGCAAGATTCACACAAGGGGAGGCTGACAGAGATACTTACAGAAGAAGTGCTGTGCCCCCT
GGTGCCGACAAGAAAGCTGAGGCTGGTGCTGGGTCAGCAACCGAATTCCAGTTT

Alignment

ORF - retro_eeur_647 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.45 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSRGYVKEQFAWRHFYWY
          MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKS.GYVKEQFAWRHFYWY
Retrocopy MLMPKKNRIAIYELLFKEGVMVAKKDVHMPKHPELADKNVPNLHVMKAMQSLKSQGYVKEQFAWRHFYWY

Parental  LTNEGIQYLRDYLHLP-PEIVP-ATLRRSRPETGRPRPKGLEGERPARFTRGEADRDTYRRSAVPPGADK
          LTNEGIQYLRDYLHLP.P...P.ATLRRSRPETGRPRPKGLEGERPARFT.GEADRDTYRRSAVPPGADK
Retrocopy LTNEGIQYLRDYLHLP<PRLCP<ATLRRSRPETGRPRPKGLEGERPARFTQGEADRDTYRRSAVPPGADK

Parental  KAEAGAGSATEFQF
          KAEAGAGSATEFQF
Retrocopy KAEAGAGSATEFQF

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	20.47 RPM	34.97 RPM
SRP017611_kidney	54.01 RPM	97.52 RPM
SRP017611_liver	41.00 RPM	69.29 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_647 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 6 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000003376	2 retrocopies	retro_eeur_367, retro_eeur_647 ,
Latimeria chalumnae	ENSLACG00000017219	1 retrocopy	retro_lcha_26,
Loxodonta africana	ENSLAFG00000008539	1 retrocopy	retro_lafr_756,
Monodelphis domestica	ENSMODG00000013929	2 retrocopies	retro_mdom_1889, retro_mdom_437,
Pongo abelii	ENSPPYG00000016516	2 retrocopies	retro_pabe_2319, retro_pabe_97,
Sarcophilus harrisii	ENSSHAG00000000731	3 retrocopies	retro_shar_243, retro_shar_334, retro_shar_724,