RetrogeneDB ID: retro_eeur_259

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_226498:830..1252(-)
• 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_259
ATGCCTGGAGTTACTGTAAAAGACATGAACCAACAGGAGTTCTTTCGAGCTCTGGCAGCCTTCCTCAAAAAGTCCGGGAA
GCTGAAGGTCCCAGAATGGGTGAACACGGTCAAGCTGGCTAAGCATAAAGAGCTTGCTCCCTTCAGCGAGAACTGGTTCT
ACACACAAGCTGCTTCCACAGCACAGCACCTGTACCTTCGGGGTGGTGCTGGGGTTGGCTCCATGACCAAGATTTATGGA
GGACGTCAGAGAAAAGGTGTCATGCCCAGCCACTTCAAGAGTATGGCCCGCCAAGTCCTCCAAGCCCTAGAAGGGCTGAA
AATGGTGGAAAAGGACCAAGATGGGGCCGCAAACTGACACCTCAGGGACAGAAAGATCTGGACAGAATCGCCAGACAGGT
GGCAGCTGCCAACAAGAAGCAT

Alignment

ORF - retro_eeur_259 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.19 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MPGVTVKDVNQQEFVRALAAFLKKSEKLKVLELFDFVKLVKHKEFALYEENWFYTQTASTARHLYLRGGA
          MPGVTVKD.NQQEF.RALAAFLKKS.KLKV.E....VKL.KHKE.A...ENWFYTQ.ASTA.HLYLRGGA
Retrocopy MPGVTVKDMNQQEFFRALAAFLKKSGKLKVPEWVNTVKLAKHKELAPFSENWFYTQAASTAQHLYLRGGA

Parental  GVGSMTKIYGGRQRNGVMPSHFSRGSKSVARRVLQALEGLKMVEKDQDG-GRKLTPQGQRDLDRIAGQVA
          GVGSMTKIYGGRQR.GVMPSHF....KS.AR.VLQALEGLKMVEKDQDG.GRKLTPQGQ.DLDRIA.QVA
Retrocopy GVGSMTKIYGGRQRKGVMPSHF----KSMARQVLQALEGLKMVEKDQDG<GRKLTPQGQKDLDRIARQVA

Parental  AASKKH
          AA.KKH
Retrocopy AANKKH

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	1.61 RPM	4.03 RPM
SRP017611_kidney	6.00 RPM	8.25 RPM
SRP017611_liver	2.57 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_259 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,