RetrogeneDB ID: retro_eeur_705

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_92781:302..987(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3D
• Ensembl ID: ENSEEUG00000007632
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide D, 44kDa [Source:HGNC Symbol;Acc:1080]

Sequence

>retro_eeur_705
AGGGAAAAGCGGGGAGAGAGAGAGATCGCCAGAGAGATGGCCCATGGATGGGGGTAGAGGTCGCCCCAGAGCTGATCCCA
GTCCCCATTCCATCTTTGAGCAAGGCCCTGCAGAAATGATGAGGAAAACAGGGAACTGGGATAAGACAGTGGATATGTTG
GACGTGGGACCCTCTCATATCATCAGCATCAAAAAAGAAACGAGGGAGACGGATGAAGAGACCAAACAGATCCTGCGCAT
GCTAGAGAAGGATGACTTCATCGATGATCCGGACTGAGGAAAGACACTCGGAACATCTGTGCAGCTGCCACTGCCTCACT
CAGGGTGGCTTTTCAAGGAAGAAAACGAGGAGGCAGATGAGAAGCCTTCGCTGAGCAGCCCCAAGGAAGAGGATATGGAT
GTGGACATCCCTCCTGTGGAAAGAGGAGCCACGTGATGAGGATGATGAGACTAAGGTGAAGGCTCCTCCCAGAGTAGCCA
AGAAGACCCCTGGCCTCCTAAGGATGTGTCTGTGGCTGAGTTGCTCAGAGAGCTGAGCGTCACCCAGGAAGAGGAGTTGT
TGTTCCTCCAGCTGCCTGACACGCTTCCTGACCAGCCACCTACTCAGGACATCAAGCCTGTCAAGACAGAGGTGCAGAAT
GAGGATGGACAGATGGTGGTGATAAAGCAAGAAAAAGACGGAGAG

Alignment

ORF - retro_eeur_705 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.49 %
• Parental protein coverage: 57.79 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  KEKRERDRDRQRDGHG-RGRGRPELIQS-HSIFEQGPAEMMRKTGNWDKTVDMLDVGPSHIINIKKEKRE
          .EKR..........HG..GRGRP....S.HSIFEQGPAEMMRKTGNWDKTVDMLDVGPSHII.IKKE.RE
Retrocopy REKRXXXXXXXXXAHG>GGRGRPRADPSPHSIFEQGPAEMMRKTGNWDKTVDMLDVGPSHIISIKKETRE

Parental  TDEETKQILRMLEKDDFIDDPGLRNDTRNMPVQLPLAHSGWLFKEESEEADEKPSLSNPKEEDMDVDIPP
          TDEETKQILRMLEKDDFIDDP.....T....VQLPL.HSGWLFKEE.EEADEKPSLS.PKEE..D.D...
Retrocopy TDEETKQILRMLEKDDFIDDPD*-GKTLGTSVQLPLPHSGWLFKEENEEADEKPSLSSPKEE--DMDVDI

Parental  VKV-KEEPRDDDEETKVKAPPRVAKKTPGL-PKDVSVSELLRELSLTQEEELLFLQLPDTLPGQPPTQDI
          ..V.KEEPRD.D.ETKVKAPPRVAKKTPGL.PKDVSV.ELLRELS.TQEEELLFLQLPDTLP.QPPTQDI
Retrocopy PPV>KEEPRDEDDETKVKAPPRVAKKTPGL<PKDVSVAELLRELSVTQEEELLFLQLPDTLPDQPPTQDI

Parental  KPVKTEVQNEDGQMVVIKQEKDRE
          KPVKTEVQNEDGQMVVIKQEKD.E
Retrocopy KPVKTEVQNEDGQMVVIKQEKDGE

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	23.53 RPM
SRP017611_kidney	0.00 RPM	13.13 RPM
SRP017611_liver	0.00 RPM	8.20 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_705 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 12 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013488	1 retrocopy	retro_dnov_1681,
Equus caballus	ENSECAG00000025090	1 retrocopy	retro_ecab_43,
Erinaceus europaeus	ENSEEUG00000007632	2 retrocopies	retro_eeur_277, retro_eeur_705 ,
Homo sapiens	ENSG00000168495	1 retrocopy	retro_hsap_596,
Macropus eugenii	ENSMEUG00000000465	1 retrocopy	retro_meug_1550,
Myotis lucifugus	ENSMLUG00000002109	1 retrocopy	retro_mluc_2339,
Macaca mulatta	ENSMMUG00000023226	1 retrocopy	retro_mmul_2449,
Monodelphis domestica	ENSMODG00000009491	1 retrocopy	retro_mdom_988,
Nomascus leucogenys	ENSNLEG00000015502	1 retrocopy	retro_nleu_2218,
Pongo abelii	ENSPPYG00000018419	1 retrocopy	retro_pabe_594,
Pan troglodytes	ENSPTRG00000020056	1 retrocopy	retro_ptro_439,
Tursiops truncatus	ENSTTRG00000012745	1 retrocopy	retro_ttru_1189,