RetrogeneDB ID: retro_eeur_450

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_308367:2532..3345(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NOB1
• Ensembl ID: ENSEEUG00000014384
• Aliases: None
• Description: NIN1/RPN12 binding protein 1 homolog (S. cerevisiae) [Source:HGNC Symbol;Acc:29540]

Sequence

>retro_eeur_450
GGAAGAACATCTACACCATCCTCGATGTGGGGGGCGAGATCCGGGACAAGGCCACGCACAGGCGCCTCGCGGTCCTGCCC
TATGAGCTGCGCTTTCTGGCAGCCTGGCGCGGAGGCCGTGCGGCGCGTGGCTGAGTTTTCAAAGAAAACTGGAGACTAAC
CCCAGCCTCTCTGCTACCGATATTCAAGTTCTGGCCCTCACCTACCAAATGGAAGCAGAATTTGTTGGTATTTCTCACCT
AAAATAAGAACCAGAGAAGGTTAAAGTGAAGCTCGTTGATTCAGCATCCAGAAACTCCTCTACATATTTCTGGCTTCCAC
TTGCCCTCAAAGCCACAACACTCACAAGAACCCATAGAAAATGGGTACCCCACCAGTGAACCTGAGGATCTGGAATACAA
TTCCTTCACGTTCTGGAGAAACCCTCTGCCTAATATTGATCATGAGTTGCAAGAGCTGCTGGTTGACAAAGGTGAAGATG
TTCCAAGTGAAGAGGGGAAGAGAATGAAGAAAAAGACAGTGAAGATAGTGACAGTGATGGGGGTGGATGGAGAACCCCCA
GCAACATCAAGCAGGTCCAGCAGGAGCTGGGGCAGTGCACCATCCCAAAGGACATGCAGGTGCGCTGTGTGACCACGCAC
TTTGCCACGCAGAATGTTCGGCTCCAGATGGGGCTGCACGTGCTGGCTGTGAAAGGCAGGCTGATCCTGAGGCACCGAGT
TACAAGTTGCGCTGCCACAGCTGTTTCAAGACAACATCCGACAGGAGCCGCGTGTTCTGTTCACATTGCGGAAACAAGAC
TGAAGAAAGAGTC

Alignment

ORF - retro_eeur_450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.64 %
• Parental protein coverage: 63.79 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  GRISTPSAMWWARSGTRPRAGASRSCPTSCA-SGSPAPRPCGAVXXFQRKLET-TPASLLQIFKFWPLPT
          GR.STPS.MW.ARSGTRPR.GASRSCP.SCA.SGS.A.RPCGA...FQRKLET.TPASLL.IFKFWP.PT
Retrocopy GRTSTPSSMWGARSGTRPRTGASRSCPMSCA>SGSLARRPCGAWLSFQRKLET>TPASLLPIFKFWPSPT

Parental  NWKQNLGVSHL-KQEPEKVKVSSSIQHPETPLHISGFHLPSKPQHWQEPVENGHPTSEPEDLEYNSFMFW
          .WKQNL.V...........K.SS.IQHPETPLHISGFHLPSKPQH.QEP.ENG.PTSEPEDLEYNSF.FW
Retrocopy KWKQNLLVFLT*NKNQRRLK*SSLIQHPETPLHISGFHLPSKPQHSQEPIENGYPTSEPEDLEYNSFTFW

Parental  RNPLPNIDHELQELLVDKGEDVPSEQ-EENEE-RDSEDSDNYGGG--TPS-IQQGQQELEQCTIPKDIRV
          RNPLPNIDHELQELLVDKGEDVPSE...E..E..DSEDSD..GGG..TPS.I.Q.QQEL.QCTIPKD..V
Retrocopy RNPLPNIDHELQELLVDKGEDVPSEE<GEENEEKDSEDSDSDGGGWRTPSNIKQVQQELGQCTIPKDMQV

Parental  GCVTTDFGMQNVLLQMGLHVLAVNGMLI-REARSYILRCHGCFKTTSDMNRVFCSHCGNKTLKKV
          .CVTT.F..QNV.LQMGLHVLAV.G.LI..EA.SY.LRCH.CFKTTSD..RVFCSHCGNKT...V
Retrocopy RCVTTHFATQNVRLQMGLHVLAVKGRLI<PEAPSYKLRCHSCFKTTSDRSRVFCSHCGNKTEERV

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	1.61 RPM	54.95 RPM
SRP017611_kidney	1.50 RPM	56.26 RPM
SRP017611_liver	0.48 RPM	26.37 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_450 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000014384	1 retrocopy	retro_eeur_450 ,
Homo sapiens	ENSG00000141101	1 retrocopy	retro_hsap_2984,
Gorilla gorilla	ENSGGOG00000025456	1 retrocopy	retro_ggor_2067,
Pan troglodytes	ENSPTRG00000008285	1 retrocopy	retro_ptro_2019,