RetrogeneDB ID: retro_eeur_385

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_279493:3725..4160(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS19
• Ensembl ID: ENSEEUG00000013614
• Aliases: None
• Description: ribosomal protein S19 [Source:HGNC Symbol;Acc:10402]

Sequence

>retro_eeur_385
ATGCCTGGAGTTACCGTAAAAGACGTGAACCAGCAGGAGTTCGTCCAAGCTCTTGCAGCCTTCCTCAAAAAGTCCGGAAA
GCTGAAGGTCCCAGAATGGGTGAACACGGTCAAGCTGGCTAAGCATAAGGAGCTCGCTCCCTATGACGAGAACTGGTTCT
ACACACAAGCTGCTTCCACAGCACGGCACCTGTACCTTCGGGGTGGTGCTGGGGTTGGCTCCATGACCAAGATTTATGGA
GGACAGCAGAGAAACTGTGTCATGCCCAGCCACTTCAGCAGAGGCTCCAAAAGTGTGGCCCGCCGAGTCCTCCAAGCCCC
AGAAGGGCTGAAAATGGTGGAAAAGGACCAAGATGGGGGCCACAAACTGACACATCAGGGACAGAGAGATCTGGACAGAA
TCGCCGGACAGGTGGCAGCTGCCAACGAGCAGCAT

Alignment

ORF - retro_eeur_385 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.21 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MPGVTVKDVNQQEFVRALAAFLKKSEKLKVLELFDFVKLVKHKEFALYEENWFYTQTASTARHLYLRGGA
          MPGVTVKDVNQQEFV.ALAAFLKKS.KLKV.E....VKL.KHKE.A.Y.ENWFYTQ.ASTARHLYLRGGA
Retrocopy MPGVTVKDVNQQEFVQALAAFLKKSGKLKVPEWVNTVKLAKHKELAPYDENWFYTQAASTARHLYLRGGA

Parental  GVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDGGRKLTPQGQRDLDRIAGQVAA
          GVGSMTKIYGG.QRN.VMPSHFSRGSKSVARRVLQA.EGLKMVEKDQDGG.KLT.QGQRDLDRIAGQVAA
Retrocopy GVGSMTKIYGGQQRNCVMPSHFSRGSKSVARRVLQAPEGLKMVEKDQDGGHKLTHQGQRDLDRIAGQVAA

Parental  ASKKH
          A...H
Retrocopy ANEQH

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	83.96 RPM	4.03 RPM
SRP017611_kidney	172.91 RPM	8.25 RPM
SRP017611_liver	138.75 RPM	5.79 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_385 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 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000011963	2 retrocopies	retro_btau_722, retro_btau_77,
Canis familiaris	ENSCAFG00000028485	10 retrocopies	retro_cfam_1017, retro_cfam_1074, retro_cfam_1155, retro_cfam_1251, retro_cfam_1377, retro_cfam_149, retro_cfam_1998, retro_cfam_2212, retro_cfam_249, retro_cfam_499,
Callithrix jacchus	ENSCJAG00000020243	5 retrocopies	retro_cjac_1968, retro_cjac_2004, retro_cjac_2094, retro_cjac_2324, retro_cjac_3,
Erinaceus europaeus	ENSEEUG00000013614	4 retrocopies	retro_eeur_252, retro_eeur_259, retro_eeur_318, retro_eeur_385 ,
Rattus norvegicus	ENSRNOG00000048199	3 retrocopies	retro_rnor_221, retro_rnor_299, retro_rnor_51,
Sus scrofa	ENSSSCG00000003042	3 retrocopies	retro_sscr_1064, retro_sscr_308, retro_sscr_58,