RetrogeneDB ID: retro_eeur_4

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_1335:23198..23987(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000002025
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SCO1
• Ensembl ID: ENSEEUG00000011060
• Aliases: None
• Description: SCO1 cytochrome c oxidase assembly protein [Source:HGNC Symbol;Acc:10603]

Sequence

>retro_eeur_4
ATGTCACTGCTGGCTCGGGCGCCCACTGGCTGGCATAGGCTCTCTCAGCTCAGGCCCCCAGCCCTACCCAGGACCATAGG
AGGTGAAGCCCTCCATGTGTGTTGTCGGCTCTCAAGGCAGAGCCCCCCAGAGGTGGGCAGACAGGGCAGGCCCCAGGGCC
CTGGGCTGCGAACTAGACTGCTGATCACAGCCTTGTTTGGGGCTGGGCTGGGTGGGGCCTGGCTGGCTGCAAAGAATGAG
AAGGAGCGGCGACGCCATAAGCAACGGACAGAGGCCCTGCGCCAGATAGCTCTGGGCCAGGGGAACTTCAGCCTGGTGGA
CCACCAGGGCCAGCCTCGCTGCAAAACCGACTTCCGGGGCTGCTGGGTGCTGATGTATTTTGGCTTCACTCACTGCCCTG
ACATCTGCCCAGATGAGCTGGAGAAGCTGGTGCAGGTGGTCCGGCAGCTGGAAGCTGAGCCCGGCTTGCCCCCGGTGCAG
CCCGTATTCATCACTGTGGACCCTGAGCGGGATGACGTCACAGCCATGGCCCGCTACGTGCAGGATTTCCACCCAAAGCT
CCTGGGTCTCACTGGCTCTACTGAGCAGGTGTCTCACGTGACCCGTAGCTACCGTGTGTACTACAGTGCTGGCCCCAAGG
ACGAGGACCAGGATTATATTGTGGACCACTCCATTGCCATCTACCTGCTCAACCCTGATGGCCTCTTCACAGACTTCTAC
ACCCGGGCCAGGTCAGCTGAACAGATCGCAGACAGTGTGCGGCACCATATGGCCCTCTTCCAAAGTGTC

Alignment

ORF - retro_eeur_4 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 50.75 %
• Parental protein coverage: 67.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RRTSKPGPVSWKSLAFTFAVGGALLAGMKYFKNEKTKYLEKQRQRSIGRPLLG-GPFSLITHLGDPKTDQ
          R.....GP.....L..T...G..L.......KNEK.....KQR........LG.G.FSL..H.G.P....
Retrocopy RQGRPQGPGLRTRLLITALFGAGLGGAWLAAKNEKERRRHKQRTEALRQIALGQGNFSLVDHQGQPRCKT

Parental  DYLGQWVLIYFGFTHCPDICPEELEKMIQVVDEIDSCSTLPNLTPLFITIDPERDTKEAIANYVKDFSPK
          D..G.WVL.YFGFTHCPDICP.ELEK..QVV........LP...P.FIT.DPERD...A.A.YV.DF.PK
Retrocopy DFRGCWVLMYFGFTHCPDICPDELEKLVQVVRQLEAEPGLPPVQPVFITVDPERDDVTAMARYVQDFHPK

Parental  LIGLTGTKEAIDQVARAYRVYYSPGPKDEDEDYIVDHTIVMYLIGPDGGFLDFGQNKKKRE
          L.GLTG..E....V.R.YRVYYS.GPKDED.DYIVDH.I..YL..PDG.F.DF.......E
Retrocopy LLGLTGSTEQVSHVTRSYRVYYSAGPKDEDQDYIVDHSIAIYLLNPDGLFTDFYTRARSAE

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	14.50 RPM	23.85 RPM
SRP017611_kidney	19.32 RPM	36.95 RPM
SRP017611_liver	8.36 RPM	18.65 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_4 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000325	1 retrocopy	retro_amel_67,
Bos taurus	ENSBTAG00000021780	1 retrocopy	retro_btau_393,
Choloepus hoffmanni	ENSCHOG00000007572	7 retrocopies	retro_chof_2118, retro_chof_2547, retro_chof_2648, retro_chof_447, retro_chof_516, retro_chof_68, retro_chof_827,
Danio rerio	ENSDARG00000067593	1 retrocopy	retro_drer_14,
Equus caballus	ENSECAG00000025151	1 retrocopy	retro_ecab_50,
Erinaceus europaeus	ENSEEUG00000011060	1 retrocopy	retro_eeur_4 ,
Felis catus	ENSFCAG00000003959	1 retrocopy	retro_fcat_36,
Homo sapiens	ENSG00000133028	1 retrocopy	retro_hsap_1112,
Gallus gallus	ENSGALG00000013382	1 retrocopy	retro_ggal_14,
Loxodonta africana	ENSLAFG00000005056	1 retrocopy	retro_lafr_567,
Oreochromis niloticus	ENSONIG00000009584	1 retrocopy	retro_onil_50,
Oryzias latipes	ENSORLG00000001047	1 retrocopy	retro_olat_14,