RetrogeneDB ID: retro_eeur_538

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_341036:7916..8528(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3H
• Ensembl ID: ENSEEUG00000010464
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide H (22.9kD) [Source:HGNC Symbol;Acc:30349]

Sequence

>retro_eeur_538
ATGTTAGTCCTGGTAGAAATGGCGGACACCATGCGGATCCCACCATAGCAATTTGAGAGGAAGCTCAATGACTCCATCGC
CGAGGAACTGAACAAGGAGCTGGCCAACAAGGTTGTCTACAACGTGGGACTTTGCATCTGCTTGTTTGACATCACCAAGC
TGGAGGATGCCTATGTATTCCCGGGGGATCGTGCATCACTCACAAAAGTTCACTTCTGCTATGTAGTGTTCCACCCATTC
CTGGATGAGATTTTGATTGGAAAGATCAAAGGCTGCAGTCCAGAGGGAGTGCATATCTCTCTAGGGTTCTTCGATGACAT
TCTCATTCCACTGGAGTCCTTGCAGCAGCCAGCCAGGTTTGATGAGGCAGAACAGGTGTGGGTGTGGGAGTACGAGACAG
AAGGAGCACGTGACCTGCACATGGACACTGGGGAGGAGATCACATTCCAGCTGGTGGACGAGAGCTTTGTGGACATGTCC
CCAACAGGGCTCAGCTCGGCAGAGGCCACCACCTCTTCTAATGAGGAACAGCCGAAGAAGGAGGCTCTGTATATACTTGT
GGGATTCATCAGTGAAATGGGCCCAGGCCTTCTCTCCTGGTGGACTAGCAGC

Alignment

ORF - retro_eeur_538 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 84.39 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MFVLVEMVDTVRIPPWQFERKLNDSIAEELNKKLANKVVYNVGLCICLFDITKLEDAYVFPGDGASHTKV
          M.VLVEM.DT.RIPP.QFERKLNDSIAEELNK.LANKVVYNVGLCICLFDITKLEDAYVFPGD.AS.TKV
Retrocopy MLVLVEMADTMRIPP*QFERKLNDSIAEELNKELANKVVYNVGLCICLFDITKLEDAYVFPGDRASLTKV

Parental  HFRYVVFHPFLDEILIGKIKGCSPEGVHVSLGFFDDILIPPESLQQPAKFDEAKQVWVWEYETKEGAHDF
          HF.YVVFHPFLDEILIGKIKGCSPEGVH.SLGFFDDILIP.ESLQQPA.FDEA.QVWVWEYET.EGA.D.
Retrocopy HFCYVVFHPFLDEILIGKIKGCSPEGVHISLGFFDDILIPLESLQQPARFDEAEQVWVWEYET-EGARDL

Parental  YMDTGEEIGFGVVNESFVDTSPTGPSSPEPTTSFSEEQPKKEARYTLVGSISEPGLGLLSWWTSN
          .MDTGEEI.F..V.ESFVD.SPTG.SS.E.TTS..EEQPKKEA.Y.LVG.ISE.G.GLLSWWTS.
Retrocopy HMDTGEEITFQLVDESFVDMSPTGLSSAEATTSSNEEQPKKEALYILVGFISEMGPGLLSWWTSS

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	1.45 RPM	34.65 RPM
SRP017611_kidney	1.13 RPM	37.32 RPM
SRP017611_liver	0.48 RPM	10.29 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_538 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000010464	1 retrocopy	retro_eeur_538 ,
Otolemur garnettii	ENSOGAG00000002850	1 retrocopy	retro_ogar_243,
Pongo abelii	ENSPPYG00000011872	1 retrocopy	retro_pabe_167,