RetrogeneDB ID: retro_eeur_408

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_288351:573..789(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF1AX
• Ensembl ID: ENSEEUG00000007518
• Aliases: None
• Description: eukaryotic translation initiation factor 1A, X-linked [Source:HGNC Symbol;Acc:3250]

Sequence

>retro_eeur_408
AGAGGTAAGAATGAAAATTAATCCAAGAAGAGAGAGCTAGTATTCAAAGAAGATGGACAAGAGTAGGCACAAGTCATCAA
AATGTTGGGCAGTGATCGATTAGAAGCAGTGTGTTTTGATGGTGTAAAGAGGTTATGTCACATCAGAAGAAAATTGAGGA
AAAAGGTTTGGATAAAGACCTCAGACATTACATTGGTTGGTCTATGAGACTACCAG

Alignment

ORF - retro_eeur_408 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.11 %
• Parental protein coverage: 50.35 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RGKNENESEKRELVFKEDGQEYAQVIKMLGNGRLEAMCFDGVKRLCHIRGKLRKKVWINTSDIILVGLRD
          RGKNEN.S.KRELVFKEDGQE.AQVIKMLG..RLEA.CFDGVKRLCHIR.KLRKKVWI.TSDI.LVGL.D
Retrocopy RGKNEN*SKKRELVFKEDGQE*AQVIKMLGSDRLEAVCFDGVKRLCHIRRKLRKKVWIKTSDITLVGL*D

Parental  YQ
          YQ
Retrocopy YQ

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	1.13 RPM	27.39 RPM
SRP017611_kidney	2.25 RPM	44.63 RPM
SRP017611_liver	0.96 RPM	23.96 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_408 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 16 parental genes, and 25 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000017633	3 retrocopies	retro_btau_1293, retro_btau_293, retro_btau_381,
Callithrix jacchus	ENSCJAG00000005371	1 retrocopy	retro_cjac_66,
Erinaceus europaeus	ENSEEUG00000007518	3 retrocopies	retro_eeur_408 , retro_eeur_567, retro_eeur_686,
Homo sapiens	ENSG00000173674	2 retrocopies	retro_hsap_1431, retro_hsap_350,
Myotis lucifugus	ENSMLUG00000012977	2 retrocopies	retro_mluc_250, retro_mluc_3,
Monodelphis domestica	ENSMODG00000027820	1 retrocopy	retro_mdom_274,
Mus musculus	ENSMUSG00000067194	1 retrocopy	retro_mmus_264,
Otolemur garnettii	ENSOGAG00000008182	1 retrocopy	retro_ogar_128,
Pongo abelii	ENSPPYG00000020176	1 retrocopy	retro_pabe_1185,
Pan troglodytes	ENSPTRG00000022504	1 retrocopy	retro_ptro_978,
Rattus norvegicus	ENSRNOG00000005736	1 retrocopy	retro_rnor_24,
Sorex araneus	ENSSARG00000013528	1 retrocopy	retro_sara_324,
Sarcophilus harrisii	ENSSHAG00000010995	1 retrocopy	retro_shar_707,
Sus scrofa	ENSSSCG00000029864	1 retrocopy	retro_sscr_948,
Tursiops truncatus	ENSTTRG00000002012	1 retrocopy	retro_ttru_1009,
Vicugna pacos	ENSVPAG00000009927	4 retrocopies	retro_vpac_47, retro_vpac_531, retro_vpac_550, retro_vpac_590,