RetrogeneDB ID: retro_eeur_130

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_8059:14247..14569(-)
• Located in intron of: ENSEEUG00000004247

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF3F
• Ensembl ID: ENSEEUG00000001226
• Aliases: None
• Description: eukaryotic translation initiation factor 3, subunit F [Source:HGNC Symbol;Acc:3275]

Sequence

>retro_eeur_130
GACCTGATTTTGAAGACCTGTTTCAGCCCCAACCAAGTGATTGGCCTCTCGAGTGACTTCCAGCAAGTAGGATGTGCATC
AGCTAGAATCCAGCATGCCCTCAGCTCAGTACTGCAGTATGCCTAGGGCATGCTGTCTGGAAAGGTGTCGGCGATAATAC
CATGCGCCGGCTCTTGATGAGTCTGGTAACCAAGTCCCCAGAATTATTCCTGATGATTTTAAGAGCATGCTCTACAGTCA
CATTAATAATCTGTTGATGGTGATGTACCTGGCCAATCTCACACAATCTGAGATTGCCTTCAATAAAAAATTTGTAAACC
TG

Alignment

ORF - retro_eeur_130 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.45 %
• Parental protein coverage: 58.38 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  DLIMKTCFSSNRVIGLSSDLQQVGGASARIQDALSTVLQYAEDVLSGKVSA-DNTVGRFLMSLV-NQVPK
          DLI.KTCFS.N.VIGLSSD.QQVG.ASARIQ.ALS.VLQYA...LSGKVSA.DNT..R.LMSLV.NQVP.
Retrocopy DLILKTCFSPNQVIGLSSDFQQVGCASARIQHALSSVLQYA*GMLSGKVSA<DNTMRRLLMSLV<NQVPR

Parental  IVPDDFETMLNSNINDLLMVTYLANLTQSQIALNEKLVNL
          I.PDDF..ML.S.IN.LLMV.YLANLTQS.IA.N.K.VNL
Retrocopy IIPDDFKSMLYSHINNLLMVMYLANLTQSEIAFNKKFVNL

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	57.05 RPM
SRP017611_kidney	0.00 RPM	102.21 RPM
SRP017611_liver	0.00 RPM	64.95 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_130 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 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004861	1 retrocopy	retro_btau_527,
Callithrix jacchus	ENSCJAG00000011903	1 retrocopy	retro_cjac_1416,
Erinaceus europaeus	ENSEEUG00000001226	1 retrocopy	retro_eeur_130 ,
Echinops telfairi	ENSETEG00000002717	2 retrocopies	retro_etel_1583, retro_etel_35,
Gorilla gorilla	ENSGGOG00000011702	5 retrocopies	retro_ggor_1566, retro_ggor_1567, retro_ggor_1568, retro_ggor_1589, retro_ggor_1590,
Myotis lucifugus	ENSMLUG00000000825	1 retrocopy	retro_mluc_2356,
Otolemur garnettii	ENSOGAG00000003220	3 retrocopies	retro_ogar_3041, retro_ogar_859, retro_ogar_863,