RetrogeneDB ID: retro_eeur_430

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_296834:2982..3308(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RNF138
• Ensembl ID: ENSEEUG00000009856
• Aliases: None
• Description: ring finger protein 138, E3 ubiquitin protein ligase [Source:HGNC Symbol;Acc:17765]

Sequence

>retro_eeur_430
AGGAGTGAAACCTCTACATCAGATAACACAGAAACTTACCAAGAGAGTACAAGTTCCACCTTTAAGTGTCCCTTATGTCA
AGAGTCAAATTTTACCAGACAGCACTTATGGATCACTGTAACAATAACCACCTATTTCAGATAGTTGCTGTGACATGTCC
TATTTGTGTGTCTCTTCCTTGGGGAGATCCGAGCCAGATCATTAGAAATTTCGTTAGTCATCTAAATCAAAGACATCAGT
TTGATTATGGAGAATTTGTGAGTCTTCAACTAGATGAGGAAACCCAGTATCAAACTGCTGTTGAAGAATCTTTTCAAGTA
AACATC

Alignment

ORF - retro_eeur_430 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.5 %
• Parental protein coverage: 53.88 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RSETSTSDNTETYPESTSSGHPTFKCPLCQESNFTRQRL-LDHCNTNHLFQIVPVTCPICVSLPWGDPSQ
          RSETSTSDNTETY.ESTSS...TFKCPLCQESNFTRQ.L..DHCN.NHLFQIV.VTCPICVSLPWGDPSQ
Retrocopy RSETSTSDNTETYQESTSS---TFKCPLCQESNFTRQHL<MDHCNNNHLFQIVAVTCPICVSLPWGDPSQ

Parental  ITRNFVSHLNQRHQFDYGEFVNLQLDEETQYQTAVEE-FQVNL
          I.RNFVSHLNQRHQFDYGEFV.LQLDEETQYQTAVEE.FQVN.
Retrocopy IIRNFVSHLNQRHQFDYGEFVSLQLDEETQYQTAVEESFQVNI

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	12.09 RPM
SRP017611_kidney	1.13 RPM	7.31 RPM
SRP017611_liver	0.48 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_430 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 4 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000009856	1 retrocopy	retro_eeur_430 ,
Monodelphis domestica	ENSMODG00000010850	4 retrocopies	retro_mdom_1468, retro_mdom_387, retro_mdom_708, retro_mdom_725,
Mus musculus	ENSMUSG00000024317	2 retrocopies	retro_mmus_3726, retro_mmus_494,
Ochotona princeps	ENSOPRG00000011494	1 retrocopy	retro_opri_554,