RetrogeneDB ID: retro_eeur_658

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_377253:64919..65167(+)
• Located in intron of: ENSEEUG00000009921

Retrocopy information

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

Parental gene information

• Parental gene symbol: C11orf1
• Ensembl ID: ENSEEUG00000009977
• Aliases: None
• Description: chromosome 11 open reading frame 1 [Source:HGNC Symbol;Acc:1163]

Sequence

>retro_eeur_658
ATGACTGCCTCCATTTGTCCCTGCTGCTCAGGATATCTCCAGAGATAGTCTCTTGCCTGCTATCTTGTAAACCCTCACTA
TGGCAGCCTCATTAATGCAAATGGTCATGCTGAAGTATGAACAGACTGGAATGATATGTCCAAGTTTTTTCAGTATGGAT
GGAGATGCACCACTACTGAGAATGCCTATTCAGACGCACACTCGTGGGCAACTGGAACCAGGAGAGATATGACCTAAAGA
ATATTGTG

Alignment

ORF - retro_eeur_658 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.06 %
• Parental protein coverage: 55.63 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTASICPCYSGLLCHRQSLACYLVNPHYGSLINADGHAEVWTDWNNMSKFFQYGWRCNTNENAYSD-RTL
          MTASICPC.SG.L..R.SLACYLVNPHYGSLINA.GHAEV.TDWN.MSKFFQYGWRC.T.ENAYSD.RTL
Retrocopy MTASICPCCSGYL-QR*SLACYLVNPHYGSLINANGHAEV*TDWNDMSKFFQYGWRCTTTENAYSD<RTL

Parental  VGNWNQERYDLKNIV
          VGNWNQERYDLKNIV
Retrocopy VGNWNQERYDLKNIV

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	0.00 RPM	6.77 RPM
SRP017611_kidney	0.00 RPM	8.06 RPM
SRP017611_liver	0.32 RPM	4.98 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_658 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000003039	3 retrocopies	retro_chof_1409, retro_chof_1629, retro_chof_888,
Cavia porcellus	ENSCPOG00000021163	1 retrocopy	retro_cpor_455,
Erinaceus europaeus	ENSEEUG00000009977	1 retrocopy	retro_eeur_658 ,
Mus musculus	ENSMUSG00000037971	1 retrocopy	retro_mmus_3061,