RetrogeneDB ID: retro_eeur_514

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_333298:4315..4597(+)
• Located in intron of: None

Retrocopy information

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

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_514
ACCTTCCAGACTCACAGCCAGACCTGCGTAGTGCACTACATGGGGATGCTTGAAGATAGAAAGAAATTTGATTCCTCCTG
GGACAGAAACAAGCCCTTCAAATTTATGCTAGGCAAGCAGGAGGTGATCCGAGGCTGGGAAGAAGGAGTTGCCCAGATGA
GTATGGGTCAGCGAGCCAAACTGATTATCTTTCCAGATTATGCCTATGGTTCCACTGGCCACCCTGGCATCACCCCACCA
AATGCCACTCTCATCTTTGACGTGGAACTTCTAAAACTGGAG

Alignment

ORF - retro_eeur_514 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.53 %
• Parental protein coverage: 98.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TFPKKGQTCVVHYTGMLQNGKKFDSSRDRNKPFKFRIGKQEVIKGFEEGAAQMSLGQRAKLTCTPDVAYG
          TF....QTCVVHY.GML...KKFDSS.DRNKPFKF..GKQEVI.G.EEG.AQMS.GQRAKL...PD.AYG
Retrocopy TFQTHSQTCVVHYMGMLEDRKKFDSSWDRNKPFKFMLGKQEVIRGWEEGVAQMSMGQRAKLIIFPDYAYG

Parental  ATGHPGVIPPNATLIFDVELLNLE
          .TGHPG..PPNATLIFDVELL.LE
Retrocopy STGHPGITPPNATLIFDVELLKLE

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	2.42 RPM	11.44 RPM
SRP017611_kidney	0.94 RPM	0.19 RPM
SRP017611_liver	0.32 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_514 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,