RetrogeneDB ID: retro_eeur_350

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_266976:9333..9660(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM60A
• Ensembl ID: ENSEEUG00000012617
• Aliases: None
• Description: family with sequence similarity 60, member A [Source:HGNC Symbol;Acc:30702]

Sequence

>retro_eeur_350
GTGCATGAGACTCGGTCAGGAGACATTTGTAATGCCTGTGTCTTGCTTGTGAAAAGATGGAAGAAATTACCAGCAGGATC
CAAAAAAAACTGGAATCATGTGGTAGATGCAAGGGCTGGACCCAGTCTAAAGACTACGTTGAAACCAAAGAAAGTGAAAA
CTCTATCTGGAAACAGGATAAAAAGCAACCAGATCAGTAAACTACAGAAGGAATTTAAACGACACAATTCTGATGCTCAC
AGTACCACCTCAAGTGCCTCTCCTGCTCAGTCTCCTTGTTACAGTAACCAGTCAGATGAAGGCTCAGATACAGAAATGGC
TCCTGGC

Alignment

ORF - retro_eeur_350 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.41 %
• Parental protein coverage: 70.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LHETRSGDICNACVLLVKRWKKLPAGSKKNWNHVVDARAGPSLKTTLKPKKVKTLSGNRIKSNQISKLQK
          .HETRSGDICNACVLLVKRWKKLPAGS...WNHVVDARAGPSLKTTLKPKKVKTLSGNRIKSNQISKLQK
Retrocopy VHETRSGDICNACVLLVKRWKKLPAGSXXXWNHVVDARAGPSLKTTLKPKKVKTLSGNRIKSNQISKLQK

Parental  EFKRHNSDAHSTTSSASPAQSPCYSNQSDEGSDTEMASG
          EFKRHNSDAHSTTSSASPAQSPCYSNQSDEGSDTEMA.G
Retrocopy EFKRHNSDAHSTTSSASPAQSPCYSNQSDEGSDTEMAPG

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	2.26 RPM
SRP017611_kidney	0.38 RPM	1.88 RPM
SRP017611_liver	0.00 RPM	0.96 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_350 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 13 parental genes, and 30 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000010685	4 retrocopies	retro_cfam_1120, retro_cfam_1552, retro_cfam_1692, retro_cfam_1837,
Callithrix jacchus	ENSCJAG00000001215	3 retrocopies	retro_cjac_1072, retro_cjac_3154, retro_cjac_3289,
Dasypus novemcinctus	ENSDNOG00000016873	2 retrocopies	retro_dnov_1674, retro_dnov_2668,
Equus caballus	ENSECAG00000009655	2 retrocopies	retro_ecab_287, retro_ecab_385,
Erinaceus europaeus	ENSEEUG00000012617	2 retrocopies	retro_eeur_350 , retro_eeur_372,
Echinops telfairi	ENSETEG00000002888	2 retrocopies	retro_etel_1087, retro_etel_427,
Felis catus	ENSFCAG00000008955	4 retrocopies	retro_fcat_1311, retro_fcat_1339, retro_fcat_58, retro_fcat_965,
Microcebus murinus	ENSMICG00000003460	2 retrocopies	retro_mmur_1176, retro_mmur_409,
Otolemur garnettii	ENSOGAG00000008927	4 retrocopies	retro_ogar_1253, retro_ogar_1762, retro_ogar_2117, retro_ogar_251,
Rattus norvegicus	ENSRNOG00000046048	1 retrocopy	retro_rnor_2858,
Rattus norvegicus	ENSRNOG00000049943	2 retrocopies	retro_rnor_1121, retro_rnor_2917,
Sarcophilus harrisii	ENSSHAG00000006261	1 retrocopy	retro_shar_670,
Ictidomys tridecemlineatus	ENSSTOG00000007097	1 retrocopy	retro_itri_16,