RetrogeneDB ID: retro_eeur_672

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_39196:317..834(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: LRRC28
• Ensembl ID: ENSEEUG00000006720
• Aliases: None
• Description: leucine rich repeat containing 28 [Source:HGNC Symbol;Acc:28355]

Sequence

>retro_eeur_672
TTAACTGTACCCAAGAGGCTTCACCTGCGCCTTTCTCTGCAGCGCCTCACCGTGAACCGAAATCCTCTATGCTATGTGCA
GCGCCACTTCTGCCAGCTGCCCAGCCTCAATGAGCTCTCCATGGCTGAAAACCATCTTGCATGTTTGCCATGTGATTTAG
GTCGAGCTCAAGAACTACAATATGTATAGGTAGATAACAACGTTCACCTGAAAAGCTTGCCATCCTATCTGGACAGCAAA
GTCATCGGGTGCGGTGGCTATGGGTTGGGCTCCCATTCAAGTTTCTTAGGCGAAGTTGCTGTCCTTTTTTTCATCAGGGC
AACTCACTGTTTTCCTCCCAGCTGAGGTGAAGGTCATCGGGACAGAGAGAGACCACATTCTGCCGCTGCAGGAGCTGACC
ATGTGGAATCTGCATCACACCTGCCACCGCCTCCTGAAGGATTTGAATGTTCTGTCTCCAATCTCATTACCCAGAAGTCT
CCTGGGGCACTGTGACCAGGGTAGCGAGCCCATGTGT

Alignment

ORF - retro_eeur_672 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.29 %
• Parental protein coverage: 55.31 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LTLPERLHLCLSLQYLTVDRNLLWCVPRHLCQLPSLNELSMAGNRLAFLPLDLGRSRELQYVYVDNNIHL
          LT.P.RLHL.LSLQ.LTV.RN.L..V.RH.CQLPSLNELSMA.N.LA.LP.DLGR..ELQYV.VDNN.HL
Retrocopy LTVPKRLHLRLSLQRLTVNRNPLCYVQRHFCQLPSLNELSMAENHLACLPCDLGRAQELQYV*VDNNVHL

Parental  KGLPSYLYNKVI-GCSGCG-APIQVAEVKLLS-FSSGQLTVFLPAEVKAIGTERDHILPLQELAMRSLHH
          K.LPSYL..KVI.G....G.APIQV...KLLS.FSSGQLTVFLPAEVK.IGTERDHILPLQEL.M..LHH
Retrocopy KSLPSYLDSKVI>GAVAMGWAPIQVS*AKLLSFFSSGQLTVFLPAEVKVIGTERDHILPLQELTMWNLHH

Parental  TCHRLLKDLNFLSPISLPRSLLELLHCPLGHCHRC
          TCHRLLKDLN.LSPISLPRSLL...HC..G....C
Retrocopy TCHRLLKDLNVLSPISLPRSLLG--HCDQGSEPMC

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	0.48 RPM	13.86 RPM
SRP017611_kidney	0.56 RPM	13.32 RPM
SRP017611_liver	0.00 RPM	12.70 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_672 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
Callithrix jacchus	ENSCJAG00000016965	1 retrocopy	retro_cjac_2430,
Erinaceus europaeus	ENSEEUG00000006720	1 retrocopy	retro_eeur_672 ,
Monodelphis domestica	ENSMODG00000012729	1 retrocopy	retro_mdom_1822,
Ictidomys tridecemlineatus	ENSSTOG00000004380	1 retrocopy	retro_itri_1866,