RetrogeneDB ID: retro_eeur_465

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_3141:766..1005(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SNRPF
• Ensembl ID: ENSEEUG00000013509
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide F [Source:HGNC Symbol;Acc:11162]

Sequence

>retro_eeur_465
CCCAAGACTTTCCTCAGCGGATGAACAGGAAAGCCAGTAACAGTGAAGCTTAAGTGGGGAATGGAGTTCAAGGGCTGCCT
GGAATCTGCAAGTGGCTATGTGAATACGCAGCTCGCGGACACAGAAGATACATAGGTGGTGCATTGTCTGGACATCTGGG
TAAAGTTTTAATAAGGTGTAATGATGCCCTTTATATCAGAGGGGTTGAAGAAGAGGAAGAAGATGGAGAAATGAGAGAC

Alignment

ORF - retro_eeur_465 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.54 %
• Parental protein coverage: 94.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  PKPFLNGLTGKPVMVKLKWGMEYKGYLVSVDGYMNMQLANTEE-YIDGALSGHLGEVLIRCNNVLYIRGV
          PK.FL.G.TGKPV.VKLKWGME.KG.L.S..GY.N.QLA.TE..YI.GALSGHLG.VLIRCN..LYIRGV
Retrocopy PKTFLSG*TGKPVTVKLKWGMEFKGCLESASGYVNTQLADTED<YIGGALSGHLGKVLIRCNDALYIRGV

Parental  EEEEEDGEMRE
          EEEEEDGEMR.
Retrocopy EEEEEDGEMRD

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	0.16 RPM	8.70 RPM
SRP017611_kidney	0.00 RPM	23.07 RPM
SRP017611_liver	0.00 RPM	19.29 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_465 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 9 parental genes, and 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002166	3 retrocopies	retro_amel_1239, retro_amel_42, retro_amel_883,
Canis familiaris	ENSCAFG00000006395	6 retrocopies	retro_cfam_110, retro_cfam_1975, retro_cfam_372, retro_cfam_619, retro_cfam_742, retro_cfam_763,
Callithrix jacchus	ENSCJAG00000002705	2 retrocopies	retro_cjac_1705, retro_cjac_3039,
Erinaceus europaeus	ENSEEUG00000013509	4 retrocopies	retro_eeur_241, retro_eeur_465 , retro_eeur_467, retro_eeur_636,
Felis catus	ENSFCAG00000029966	4 retrocopies	retro_fcat_280, retro_fcat_66, retro_fcat_77, retro_fcat_861,
Loxodonta africana	ENSLAFG00000017426	1 retrocopy	retro_lafr_241,
Pelodiscus sinensis	ENSPSIG00000016462	2 retrocopies	retro_psin_31, retro_psin_54,
Sarcophilus harrisii	ENSSHAG00000012294	1 retrocopy	retro_shar_468,
Tarsius syrichta	ENSTSYG00000006837	4 retrocopies	retro_tsyr_1239, retro_tsyr_1782, retro_tsyr_192, retro_tsyr_2115,