RetrogeneDB ID: retro_eeur_623

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_368772:68387..69023(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LIX1L
• Ensembl ID: ENSEEUG00000015291
• Aliases: None
• Description: Lix1 homolog (mouse)-like [Source:HGNC Symbol;Acc:28715]

Sequence

>retro_eeur_623
GATATAATAAATGAAGGCCTGGTGGTCTATGAGTCGCTACCATCCCCTGGACCTCCCTTTGTGAGTTATGTCACCCTCCC
AGGGGGAAGCTGTTTTGGCAACTTTCAGTGCTGCCTAAGTAGAGCAGAGGCCAGACGGGATGCAGCTAAAGTGGCTCTAA
TCAACTCCCTCTTCAACGAGCTGCCCTCTCGCAGGATCACCAAGGAATTCATTATGGAGAGTGTGCAGGAAGCCGTTGCT
TCCACCAGTGGTACCCTAGATGATGCTGATGACCCCAGTACCAGCATTGGAGCCTATCACTACATGCTGGAGTCAAACAT
GGGGAAGACCATGTTAGAGTTTCAGGAACTGATGACCATTTTCCAGCTCTTGCACTGGAATGGCAGCCTTAAAGCTCTTC
GTGAAACAAAGTGTTCCCGACAGGAAGTCATCTCCTATTATTCCCAGTATTCCCTAGATGAAAAAATGCGCAGTCACATG
GCCCTGGATTGGATTACAAAGGAGCGAGAATCACCAGGAATTCTCTCGCAAGAGCTATGAATGGCCCTGAGAGAGTTGGA
GGAAGCAAGGAAAGCAGGACAAGAACTGAGATTTTACAAAGAAAAGAAAGAAATCCTGAGTTTAGCCCTGACTCAG

Alignment

ORF - retro_eeur_623 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.62 %
• Parental protein coverage: 63.47 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DLKNGALVVYEMVPSNSPPYVCYVTLPGGSCFGSFQFCPTKAEARRSAAKIALMNSVFNEHPSRRITDEF
          D..N..LVVYE..PS..PP.V.YVTLPGGSCFG.FQ.C...AEARR.AAK.AL.NS.FNE.PSRRIT.EF
Retrocopy DIINEGLVVYESLPSPGPPFVSYVTLPGGSCFGNFQCCLSRAEARRDAAKVALINSLFNELPSRRITKEF

Parental  IEKSVSEALASFNGNREEADNPNTGIGAFRFMLESNKGKSMLEFQELMTVFQLLHWNGSLKAMRERQCSR
          I..SV.EA.AS..G....AD.P.T.IGA...MLESN.GK.MLEFQELMT.FQLLHWNGSLKA.RE..CSR
Retrocopy IMESVQEAVASTSGTLDDADDPSTSIGAYHYMLESNMGKTMLEFQELMTIFQLLHWNGSLKALRETKCSR

Parental  QEVLAHYSHRALDDDIRHQMALDWVSREQSVPGALSRELASTEQELDEARLAGKELRFHKEKKDILMLAA
          QEV...YS...LD...R..MALDW...E...PG.LS.EL.....EL.EAR.AG.ELRF.KEKK.IL.LA.
Retrocopy QEVISYYSQYSLDEKMRSHMALDWITKERESPGILSQEL*MALRELEEARKAGQELRFYKEKKEILSLAL

Parental  GQ
          .Q
Retrocopy TQ

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	0.97 RPM	6.45 RPM
SRP017611_kidney	2.06 RPM	3.75 RPM
SRP017611_liver	0.00 RPM	2.25 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_623 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000015291	1 retrocopy	retro_eeur_623 ,