RetrogeneDB ID: retro_eeur_418

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_292989:316..1135(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RCC1
• Ensembl ID: ENSEEUG00000004565
• Aliases: None
• Description: regulator of chromosome condensation 1 [Source:HGNC Symbol;Acc:1913]

Sequence

>retro_eeur_418
CAGGACAATAATGGTGTGATTGGACTCTTGGAGCCCATGAAGAAAAGCATGGTACCTGTGCAGGTGCAGCTGAGTATGCC
TGTGGTAAAGGTGGCCTCAGGAAGTGACCACTTGGTGATTCTGACAACTGATGGTGACCTCTACACTCTTGGCTATGGGG
AACAGGGCCTGCTGGGCTGTGTGCCTGAATTTTGCAAACCGTGGGGGCCATCAGGGTCTTGAACAACTCCTGGTCCCCAG
TTGTGTGATGCTGAAATCCAGGGGAAGGCAGGGTCATGTGAAATTCCAGGATGCCTTTTGTGGCACCTACTTCACCTTTG
CTATCTCCTATGAGGGTCATGTATATGGTTTCGGTCTTTCCAACTACCATCAGCGAGGAACTTTAGGCACAGACTCTTGC
TTCATATCCCAGAATCTGACATCCTTCAAGAATTCCACCAAGTCATGGGTGGGCTTCTCTGGTGGCCAGCACCATACAGT
CTGCATGGATTCGGAAGAAAAAGCATACAGCTTGGGTGGTGCTGAGTATGGGCAGGCCTTGGGGAGGGTGCTGAAGAGAA
GAGCATACCTACCCTCATCTCCAGGCTTCCTGCTATCTCCTCAGTGGCTTGTGGAGCCTCTGTGGGATATGCTGTGACCA
AAGATGGTCATGTTTTTGCCTGGGGCATGGTCACCAACTACCAGCTGGGCACAGGACAGGAAGAGGATGCATGGAGCCCT
GTGGAGATGACTGGTAAACAGCTGGAGAACTGAGTAGTCTTATCTGTGTCCAGTGGTGGCCAGCACACAGTCTTACTGGT
CAAGGACAAGCAACAGAGC

Alignment

ORF - retro_eeur_418 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.09 %
• Parental protein coverage: 74.53 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KDNNGVIGLLEPMKKSMVPVQVQLSMPVVKVASGNDHLVMLTTDGDLYTLGCGEQGQLGRVPELFANRGG
          .DNNGVIGLLEPMKKSMVPVQVQLSMPVVKVASG.DHLV.LTTDGDLYTLG.GEQG.LG.VPE.F....G
Retrocopy QDNNGVIGLLEPMKKSMVPVQVQLSMPVVKVASGSDHLVILTTDGDLYTLGYGEQGLLGCVPE-FCKPWG

Parental  -RQGLERLLVPKCVMLKSRGSRGHVKFQDAFCGAYFTFAISCEGHVYGFGLSNYHQLGTSGTESCFIPQN
          ..QGLE.LLVP.CVMLKSRG..GHVKFQDAFCG.YFTFAIS.EGHVYGFGLSNYHQ.GT.GT.SCFI.QN
Retrocopy >HQGLEQLLVPSCVMLKSRGRQGHVKFQDAFCGTYFTFAISYEGHVYGFGLSNYHQRGTLGTDSCFISQN

Parental  LTSFKNSTKSWVGFSGGQHHTVCMDSEGKAYSLGRAEYGRLGLG-EGAEEKSIPTLISRLPAVSSVACGA
          LTSFKNSTKSWVGFSGGQHHTVCMDSE.KAYSLG.AEYG...LG.EGAEEKSIPTLISRLPA.SSVACGA
Retrocopy LTSFKNSTKSWVGFSGGQHHTVCMDSEEKAYSLGGAEYGQ-ALG<EGAEEKSIPTLISRLPAISSVACGA

Parental  SVGYAVTKDGRVFAWGMGTNYQLGTGQEEDAWSPVEMTGKQLENRVVLSVSSGGQHTVLLVKDKQQS
          SVGYAVTKDG.VFAWGM.TNYQLGTGQEEDAWSPVEMTGKQLEN.VVLSVSSGGQHTVLLVKDKQQS
Retrocopy SVGYAVTKDGHVFAWGMVTNYQLGTGQEEDAWSPVEMTGKQLEN*VVLSVSSGGQHTVLLVKDKQQS

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	0.64 RPM	8.38 RPM
SRP017611_kidney	1.88 RPM	22.69 RPM
SRP017611_liver	0.96 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_418 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 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000009686	3 retrocopies	retro_cjac_2440, retro_cjac_3424, retro_cjac_3856,
Erinaceus europaeus	ENSEEUG00000004565	1 retrocopy	retro_eeur_418 ,
Myotis lucifugus	ENSMLUG00000017075	1 retrocopy	retro_mluc_2278,
Rattus norvegicus	ENSRNOG00000050106	1 retrocopy	retro_rnor_2886,