RetrogeneDB ID: retro_eeur_212

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_210329:2824..3505(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS7
• Ensembl ID: ENSEEUG00000015775
• Aliases: None
• Description: mitochondrial ribosomal protein S7 [Source:HGNC Symbol;Acc:14499]

Sequence

>retro_eeur_212
GTACTGAACTTGCGGAACGCCAGCCTGAAGCTTCCAGGGTTAATCCAGGTGAGGTGGAGCCACTACGGTCCTGATTTCAT
GGATCCCCAGACTGACAAGGACTATCACTGCAAGCCCTTGGCTGAACTGAATGAGGAAGAGAAGTATGAATGAAAGCTAA
AGAAAACTCAGCTTTTCAAGGCTGCCCCAGCGACAAAAATAAGTTCTGTGTTTAAAGACCCTGTGATCAGTAAATTCACA
AATATGATAATGAAAGGAGGAAACAAAATACTGGCCAGATCCCTCATGACACAGACTCTGGAAGCTGTGAAAAGGAAGCA
GTTTTAGAAGTACCATACTGCTTCTGCAGAAGCACAGGCATCCACTGAATGCAACCCCTACACCATCTTCCACCAAGCAC
TGAAAAACTGTGAACCTGTGATTGGGCTGGTATCCATTCTCAAGGGTGCCCATTTCTACCAGGTTCCTGTGCCACTAGCA
GAGCAACACCGTCGCTTCCTGGCTATGAAGTGGATGATTACTGATTGCAGAAAGAAGAAGAACCGGAGGATGCTACTGCC
AGAGAAGTTGTCACATGAGCTGATAGAAGCTTTTCACAACCAAGGTCCCGTGATCAAGAAGAAGCACAAGATGCACAAGA
TGACTGAGGCCAACCGAGAGCTGGCCCACTACTGTTGGTGG

Alignment

ORF - retro_eeur_212 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.3 %
• Parental protein coverage: 93.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  VLNLPNAGLKLPG-IQVRWRRYCSEIMDPPTD-DYYRQALGELSEEEKYERELKKTRLIKAAPAAKTSSV
          VLNL.NA.LKLPG.IQVRW..Y....MDP.TD.DY....L.EL.EEEKYE..LKKT.L.KAAPA.K.SSV
Retrocopy VLNLRNASLKLPGLIQVRWSHYGPDFMDPQTDKDYHCKPLAELNEEEKYE*KLKKTQLFKAAPATKISSV

Parental  FEDPVISKFTNMIMKGGNKILARSLVTQTLEAVKRKQFEKYHTASAETQAAIERNPYTIFHQALKNCEPV
          F.DPVISKFTNMIMKGGNKILARSL.TQTLEAVKRKQF.KYHTASAE.QA..E.NPYTIFHQALKNCEPV
Retrocopy FKDPVISKFTNMIMKGGNKILARSLMTQTLEAVKRKQF*KYHTASAEAQASTECNPYTIFHQALKNCEPV

Parental  IGLVPILRGAHFYQVPVPLAERRRRFLAMKWMITECR-KKNRRMLLPEKLSHELIEAFHNQGPVIKKKHE
          IGLV.IL.GAHFYQVPVPLAE..RRFLAMKWMIT.CR.KKNRRMLLPEKLSHELIEAFHNQGPVIK....
Retrocopy IGLVSILKGAHFYQVPVPLAEQHRRFLAMKWMITDCRKKKNRRMLLPEKLSHELIEAFHNQGPVIKXXXX

Parental  MHKMAEANRALAHYRWW
          .....EANR.LAHY.WW
Retrocopy XXXXTEANRELAHYCWW

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	0.97 RPM	18.85 RPM
SRP017611_kidney	1.13 RPM	39.95 RPM
SRP017611_liver	1.45 RPM	19.61 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_212 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 11 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000009287	1 retrocopy	retro_amel_1444,
Canis familiaris	ENSCAFG00000004752	5 retrocopies	retro_cfam_2020, retro_cfam_2197, retro_cfam_438, retro_cfam_443, retro_cfam_540,
Callithrix jacchus	ENSCJAG00000014458	2 retrocopies	retro_cjac_290, retro_cjac_3316,
Erinaceus europaeus	ENSEEUG00000015775	1 retrocopy	retro_eeur_212 ,
Felis catus	ENSFCAG00000028759	2 retrocopies	retro_fcat_2013, retro_fcat_424,
Loxodonta africana	ENSLAFG00000002873	1 retrocopy	retro_lafr_945,
Macropus eugenii	ENSMEUG00000012264	1 retrocopy	retro_meug_1826,
Mustela putorius furo	ENSMPUG00000013928	1 retrocopy	retro_mputfur_976,
Procavia capensis	ENSPCAG00000015942	1 retrocopy	retro_pcap_327,
Pteropus vampyrus	ENSPVAG00000008433	3 retrocopies	retro_pvam_610, retro_pvam_615, retro_pvam_678,
Ictidomys tridecemlineatus	ENSSTOG00000015200	2 retrocopies	retro_itri_1805, retro_itri_461,