RetrogeneDB ID: retro_eeur_135

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_8480:74007..74292(-)
• Located in intron of: ENSEEUG00000003846

Retrocopy information

• Ensembl ID: ENSEEUG00000003944
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: FKBP1B
• Ensembl ID: ENSEEUG00000013920
• Aliases: None
• Description: FK506 binding protein 1B, 12.6 kDa [Source:HGNC Symbol;Acc:3712]

Sequence

>retro_eeur_135
CGCATCTTCCCGAAACGCGGCCAGACCTGCGTGGTGCACTACACGGGGATGCTTGAAGATGGAAAGGAATTTGATTCCTC
CTGGGACAGAAACAAGCCCTTCAAGTTTATGCTAGGCAAGCAGGAAGTGATCCGGGGCTGGGAAGGAGGAGTTGCCCAGA
TGAGTGTGGGTCAGCGAGCCAAACTGATTATCTCTCCAGATTATGCATATGGTTCTACTGGCCACCCTGGCATCATCCCA
CGAAATGCCACTCTCGTCTTTGATGTGAAACGTCTAAAATTGGAA

Alignment

ORF - retro_eeur_135 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.74 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RTFPKKGQTCVVHYTGMLQNGKKFDSSRDRNKPFKFRIGKQEVIKGFEEGAAQMSLGQRAKLTCTPDVAY
          R.FPK.GQTCVVHYTGML..GK.FDSS.DRNKPFKF..GKQEVI.G.E.G.AQMS.GQRAKL...PD.AY
Retrocopy RIFPKRGQTCVVHYTGMLEDGKEFDSSWDRNKPFKFMLGKQEVIRGWEGGVAQMSVGQRAKLIISPDYAY

Parental  GATGHPGVIPPNATLIFDVELLNLE
          G.TGHPG.IP.NATL.FDV..L.LE
Retrocopy GSTGHPGIIPRNATLVFDVKRLKLE

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	9.35 RPM	11.44 RPM
SRP017611_kidney	2.81 RPM	0.19 RPM
SRP017611_liver	2.41 RPM	0.48 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_135 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 10 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002797	1 retrocopy	retro_amel_1717,
Ciona savignyi	ENSCSAVG00000006859	1 retrocopy	retro_csav_11,
Erinaceus europaeus	ENSEEUG00000013920	2 retrocopies	retro_eeur_135 , retro_eeur_514,
Echinops telfairi	ENSETEG00000018990	2 retrocopies	retro_etel_186, retro_etel_2071,
Homo sapiens	ENSG00000119782	1 retrocopy	retro_hsap_1329,
Macropus eugenii	ENSMEUG00000010689	1 retrocopy	retro_meug_14,
Microcebus murinus	ENSMICG00000001530	1 retrocopy	retro_mmur_257,
Pan troglodytes	ENSPTRG00000011708	1 retrocopy	retro_ptro_906,
Sorex araneus	ENSSARG00000013808	1 retrocopy	retro_sara_24,
Tupaia belangeri	ENSTBEG00000012282	1 retrocopy	retro_tbel_56,