RetrogeneDB ID: retro_eeur_208

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_208759:3600..4081(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TPGS2
• Ensembl ID: ENSEEUG00000005257
• Aliases: None
• Description: tubulin polyglutamylase complex subunit 2 [Source:HGNC Symbol;Acc:24561]

Sequence

>retro_eeur_208
AGTGAGAACCAGCCAGAGAAACCTCATCCGGATTCACACAGTGTGATATTTAAGCCGTATCTTTGCAATGGGCATGGAAA
GGTTTGTCTTGTTTACAAAAGAGGGGCACCAGGATTGGCACAAGGCTCCGAGATCTGGTTCCTAGACAGCACTCTCTACT
GGCATTTTCTCACAAACAACTTTACTGCCTCTTATCGGCTACTTGACACCCACCTAGGCCTGTCCCGGTGACAGTATGCC
TTCAACAGCAATGGCATTAGCCCACAGGCTAAGCAAGGCTTCAACATGTATAAACCCATAACATACAACACAAAGCTGTT
AATGGGAAGGGACTGACTCCTTTGTGAACAAGCTGGATCCCAGAAAAGTATTTAAGAGCAAGAACAACACCTTGGTCCCC
AAGAAGAAAGGGCCTGTTCAGCCTGCCAACAGCCAGAAAGGAACCTCGGTTCTCCCTCACTTCCAAATCTCTGGCTCTGG
A

Alignment

ORF - retro_eeur_208 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.64 %
• Parental protein coverage: 60.61 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  SENQPEKPHFDSRSVIFELDPCSGHGKVCLVYKRGKPGLAQDSEIWFLDRALYWHFLTDTFTAYYRLLVT
          SENQPEKPH.DS.SVIF....C.GHGKVCLVYKRG.PGLAQ.SEIWFLD..LYWHFLT..FTA.YRLL.T
Retrocopy SENQPEKPHPDSHSVIFKPYLCNGHGKVCLVYKRGAPGLAQGSEIWFLDSTLYWHFLTNNFTASYRLLDT

Parental  HLGLPQWQYAFTSYGVSPQAKQWFNMYKPITYNTNLLM-EEADSFVNKLDPSKVFKSKNKTLVPKKKGPV
          HLGL...QYAF.S.G.SPQAKQ.FNMYKPITYNT.LLM.E..DSFVNKLDP.KVFKSKN.TLVPKKKGPV
Retrocopy HLGLSR*QYAFNSNGISPQAKQGFNMYKPITYNTKLLM>EGTDSFVNKLDPRKVFKSKNNTLVPKKKGPV

Parental  QPANSQKGPSSSTSKSSSGSG
          QPANSQKG.S.......SGSG
Retrocopy QPANSQKGTSVLPHFQISGSG

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	52.21 RPM
SRP017611_kidney	0.00 RPM	16.69 RPM
SRP017611_liver	0.00 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_208 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 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000017766	3 retrocopies	retro_cfam_355, retro_cfam_457, retro_cfam_626,
Choloepus hoffmanni	ENSCHOG00000007960	1 retrocopy	retro_chof_1642,
Erinaceus europaeus	ENSEEUG00000005257	3 retrocopies	retro_eeur_208 , retro_eeur_324, retro_eeur_516,
Myotis lucifugus	ENSMLUG00000001739	1 retrocopy	retro_mluc_1194,
Mustela putorius furo	ENSMPUG00000001097	2 retrocopies	retro_mputfur_1622, retro_mputfur_507,
Mus musculus	ENSMUSG00000024269	1 retrocopy	retro_mmus_2648,
Otolemur garnettii	ENSOGAG00000008218	1 retrocopy	retro_ogar_686,
Rattus norvegicus	ENSRNOG00000014957	1 retrocopy	retro_rnor_2961,
Sus scrofa	ENSSSCG00000026953	1 retrocopy	retro_sscr_590,
Tarsius syrichta	ENSTSYG00000005299	2 retrocopies	retro_tsyr_1161, retro_tsyr_512,
Tursiops truncatus	ENSTTRG00000007153	1 retrocopy	retro_ttru_1112,