RetrogeneDB ID: retro_eeur_653

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_375942:3780..4101(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSDC2
• Ensembl ID: ENSEEUG00000003639
• Aliases: None
• Description: cold shock domain containing C2, RNA binding [Source:HGNC Symbol;Acc:30359]

Sequence

>retro_eeur_653
AGTCCGCTGCCCACCTGCCGCACCAGGACCTTCTCTGCGACAGTGAGGGTGTCCCTGGGCACCGTGTACAAGGGCGTCTG
CAAGTGCTTCTGCTGTTCCAAGGGCCACGACTTCATCACGCTGGCCGATGGAGGCCCTGACATCTTCCTGCATATCTCTG
ACGTGGAAGGCGAGTACGTGTCTGTGGAAGGTGATGAGGTGACCTACAAGATGTGCTCGATCCCACCCAAGAACGAGAGG
CTGCAGGCCGTGGAAGTTGTCATCACCCACCTGGCGCCAGGCACCAAGCACGAGACCTGGTCGGGCCACGTGGTCAGCTC
C

Alignment

ORF - retro_eeur_653 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.03 %
• Parental protein coverage: 69.93 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SPLPTKRTRTYSATARASAGPVFKGVCKQFSRSQGHGFITPENGSEDIFVHVSDIEGEYVPVEGDEVTYK
          SPLPT.RTRT.SAT.R.S.G.V.KGVCK.F..S.GH.FIT...G..DIF.H.SD.EGEYV.VEGDEVTYK
Retrocopy SPLPTCRTRTFSATVRVSLGTVYKGVCKCFCCSKGHDFITLADGGPDIFLHISDVEGEYVSVEGDEVTYK

Parental  MCPIPPKNQKFQAVEVVLTQLAPHTPHETWSGQVVGS
          MC.IPPKN...QAVEVV.T.LAP.T.HETWSG.VV.S
Retrocopy MCSIPPKNERLQAVEVVITHLAPGTKHETWSGHVVSS

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	1.29 RPM	10.64 RPM
SRP017611_kidney	5.63 RPM	2.06 RPM
SRP017611_liver	2.41 RPM	0.00 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_653 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000003639	1 retrocopy	retro_eeur_653 ,