RetrogeneDB ID: retro_eeur_516

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_333675:18116..18560(+)
• 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_516
AGTGAAAACCAGCCAGAGAAGCCTCACTTTGATTCATATAGTGTGATTTTTGAGCTGGGTCCTTGTAATGGACATGGGAA
CGTTTGTCTTGTCTACAAAAGAGGGAAACCAGAATTGGCATAAGACAATGAGATCTGGTTCCTTGACAGAGCACTCTACT
GGCATTTCATTACAGACAACTTTACTGCCCATAATTGTCTGCTTGTCACCCACCTAGGCCTGTCCCAGAGGCAGTCTGCC
TTCACCAGCTATGGCATTAGCCCACAGGCTAAACAATGATTCAACATGTACAAAGCTATAACATACAACACAAACCTGTT
AACAGAAGAAACTGACTCCTTTGAGAAGCTGGATCCTAGCAAAATGTTTAAGAGAAAGAATAAGATCTTGGTCCCCAAGA
AGAAAAGGCCTGTTCGGCTTGCCAGCAGCTAGAAAAGACCCTCA

Alignment

ORF - retro_eeur_516 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.19 %
• Parental protein coverage: 56.44 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SENQPEKPHFDSRSVIFELDPCSGHGKVCLVYKRGKPGLAQDSEIWFLDRALYWHFLTDTFTAYYRLLVT
          SENQPEKPHFDS.SVIFEL.PC.GHG.VCLVYKRGKP.LA.D.EIWFLDRALYWHF.TD.FTA...LLVT
Retrocopy SENQPEKPHFDSYSVIFELGPCNGHGNVCLVYKRGKPELA*DNEIWFLDRALYWHFITDNFTAHNCLLVT

Parental  HLGLPQWQYAFTSYGVSPQAKQWFNMYKPITYNTNLLMEEADSFVNKLDPSKVFKSKNKTLVPKKKGPVQ
          HLGL.Q.Q.AFTSYG.SPQAKQ.FNMYK.ITYNTNLL.EE.DSF..KLDPSK.FK.KNK.LVPKKK.PV.
Retrocopy HLGLSQRQSAFTSYGISPQAKQ*FNMYKAITYNTNLLTEETDSF-EKLDPSKMFKRKNKILVPKKKRPVR

Parental  PANSQKGPS
          .A.S.K.PS
Retrocopy LASS*KRPS

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	1.13 RPM	52.21 RPM
SRP017611_kidney	0.38 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_516 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,