RetrogeneDB ID: retro_eeur_443

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_305725:3616..4456(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NUS1
• Ensembl ID: ENSEEUG00000008948
• Aliases: None
• Description: nuclear undecaprenyl pyrophosphate synthase 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:21042]

Sequence

>retro_eeur_443
ATGACGGGGCTGTATGAGCTGGTGTGGCGGGTGCTGCATGCTCTGCCCTGTCTGCACCGCACGCTCACCTCCTGGATCCG
CGTTCGGCTGGGCACCTGGAACTGGATCTGGAGGCGCTGCTGCAACGCCGCCTCTGCCGCGGTCCTAGCGCCCCTCGTCT
TCACGCTCCGCAAGTCCCTGGCTGCGGGCAGGAACCGCCGGCACCACCGGCAGCCGCGCGGCGGACTCGGCCGGGCCGCC
GCCCACCCCCGGCTGCGCTGGCGCGCGGATGGCCGTTCCCTGGAGAAGCTGCCTTTGCACATGGGCCTGGTGATCACCGA
GGAGGAGCCGGAGCCCAGCTTCTCGGACATCGCCAGCCTCGTGGTTTGGTGTATGGCCGTGGGCATCTCCTACATTAGCG
TCTAAGACCACCAAGGTATTTTTAAGAGAAATAATTCCAGGTTGATGGATGAAATTTTAAAGCAGCAGCAGGAACTTCTG
GGCTTAGATTGTTCCAAATACTCACCAGAGTTTGCAAACAGTAATGACAAAGATGATGAAGTTTTAAATTGCCGCTCGGA
AGTCAAGGTGCTGTCTCCGGAAGATGGAAAAGCAGATATTGTGAGAGCTGCTCAGGACTTTTGCCAGTTAGTAGCCCAAG
CAGCAGAAGAGGTCCACAGATTTGGATGTAGATTTGGTTAGACAGTTTACTTAGTACAAATGGTTTCCCTGATCCCTGAT
TTGGTCTTGAAGTTTGGTCCCCGTGAACAGCACATTAGGCTATTTTTCATGGCACATTCAATTTGACTGAAATTATGTCT
TTAGCCTTCCCACCTAAACATCAACTATCAGGACTTTTAT

Alignment

ORF - retro_eeur_443 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.99 %
• Parental protein coverage: 94.88 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 6

Retrocopy - Parental Gene Alignment:

Parental  MTGLYELVWRVLHALPCLHRTLTSWIRVRLGTWNWIWRRCCNAASAAVLAPLVFTLRKSLAAGRNRRHHR
          MTGLYELVWRVLHALPCLHRTLTSWIRVRLGTWNWIWRRCCNAASAAVLAPLVFTLRKSLAAGRNRRHHR
Retrocopy MTGLYELVWRVLHALPCLHRTLTSWIRVRLGTWNWIWRRCCNAASAAVLAPLVFTLRKSLAAGRNRRHHR

Parental  QPRGGLGRAAAHPRLRWRADGRSLEKLPLHMGLVITEEEPEPSFSDIASLVVWCMAVGISYISVYDHQGI
          ....................GRSLEKLPLHMGLVITEEEPEPSFSDIASLVVWCMAVGISYISV.DHQGI
Retrocopy XXXXXXXXXXXXXXXXXXXXGRSLEKLPLHMGLVITEEEPEPSFSDIASLVVWCMAVGISYISV*DHQGI

Parental  FKRNNSRLMDEILKQQHELLGLDCSXXXXXXXXXXXXXXXXLNCRSAVKVLSPEDGKADIVRAAQDFCQL
          FKRNNSRLMDEILKQQ.ELLGLDCS................LNCRS.VKVLSPEDGKADIVRAAQDFCQL
Retrocopy FKRNNSRLMDEILKQQQELLGLDCSKYSPEFANSNDKDDEVLNCRSEVKVLSPEDGKADIVRAAQDFCQL

Parental  VAQ-QQKRSTDLDVDL-LDSLLSTNGFPD-PDLVLKFG-PVDSTLGFLPWHIR-LTEIISL-PSHLNISY
          VAQ.QQKRSTDLDVDL.LDSLLSTNGFPD.PDLVLKFG.PV.STLG...WHI..LTEI.SL.PSHLNI.Y
Retrocopy VAQ>QQKRSTDLDVDL>LDSLLSTNGFPD>PDLVLKFG>PVNSTLGYFSWHIQ>LTEIMSL>PSHLNINY

Parental  EDFF
          .DF.
Retrocopy QDFY

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	2.58 RPM	10.15 RPM
SRP017611_kidney	5.63 RPM	20.07 RPM
SRP017611_liver	1.45 RPM	4.02 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_443 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000001780	1 retrocopy	retro_dnov_1639,
Erinaceus europaeus	ENSEEUG00000008948	1 retrocopy	retro_eeur_443 ,
Homo sapiens	ENSG00000153989	4 retrocopies	retro_hsap_1174, retro_hsap_1176, retro_hsap_1289, retro_hsap_4825,
Gorilla gorilla	ENSGGOG00000022321	4 retrocopies	retro_ggor_1012, retro_ggor_914, retro_ggor_915, retro_ggor_993,
Microcebus murinus	ENSMICG00000007831	1 retrocopy	retro_mmur_423,
Nomascus leucogenys	ENSNLEG00000013457	1 retrocopy	retro_nleu_2411,
Oryctolagus cuniculus	ENSOCUG00000011553	1 retrocopy	retro_ocun_1713,
Pongo abelii	ENSPPYG00000025886	1 retrocopy	retro_pabe_81,
Pan troglodytes	ENSPTRG00000018547	1 retrocopy	retro_ptro_808,
Tarsius syrichta	ENSTSYG00000003212	1 retrocopy	retro_tsyr_633,
Tursiops truncatus	ENSTTRG00000007352	2 retrocopies	retro_ttru_358, retro_ttru_684,