RetrogeneDB ID: retro_eeur_583

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_348901:6086..7502(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PIGN
• Ensembl ID: ENSEEUG00000005812
• Aliases: None
• Description: phosphatidylinositol glycan anchor biosynthesis, class N [Source:HGNC Symbol;Acc:8967]

Sequence

>retro_eeur_583
ATCTCCCTTTGCAAGGAGCTGATTCGTCTTGCACTGGAAGGATTGTCCTACTACCACACTTACGACAGATTCTTTTTGGG
CATCACTGTTGTTCTTGGTTTTGTGGGATGGACATCTTATGCTTCTCTGTTGATCATCAAGTCTCATTCCAACCTCACCA
GAGGTGGTAGTAACAAAATTAAGAAACCAAATCATCTCCTGACATGTACTTTTGTAGCTGTTGGCATTGCAATAGCATTT
TTCCTGCTGATTCAGTCCTGTCCCTGGACTTACTACGTGTACTGTCTGTTGCCGGTGCCAATATGGCATGCGCTTCTGAG
CGAATTTCCAGTGATTGAGGACCTTGTCAAGTCTCTGCTGACCTTTCCCCCTGGTCAATTTATTGGAAGCCTGTTAGTCT
TTGGTCTGGGACTTGAAATACTAGTTCTCAGTTTTTTCTACCGCTATATGCTTACAGCTGGACTTACAGCATTTGCGGGC
TGGCCATTCGTCACTCAGCTGTGGACTCGAGCAAAGAGCACCTCACTGAGTTGGACTTTGTTCTCTTTGCTCCTGGTAGT
GTTTCCACTGATGCCTGTTGTAGGACAGAAGCCAGACATCTCTGTGGTAATGGGAGCAGGCTTGCTGGTTCTTCTTCTGT
CCCTGTTTGTTGTGACATCATATATAAAAAGAAAAGATAATCTCGATGGAGAACTATTTTTGTATCTGCTACAGATACTG
AGCATCATGCTTTCCATGTACACCGTGTATAGCACGCACAGTAGTCTGCAGCGGAAACAAGGACTACCCTTTCTTAATCA
GACCATTAGCTGGATCATATTAGCCTCTTCCTTCATCCTGCCACTTCTGAGTCCCACCATCCTCTTCGAGCGGTTGTTCA
GCATACTCCTTTCCTTGATGTCCACCTACCTGCTTCTAAGCACAGGGTATGAAGCTCTCTTCCCATTAGTGCTGTCATGT
TTGATGTTCATCTGGATACACATGGAACAAGAAACCCTGCAACAATCTGGCTTTTCCTGTAAACAGAAGGTCAACAGTAT
CCAGTTTGCCTACAATATTGATATAACTCAGTATCGAAAGCTCTATCTCGACGACATCCATAGGGCCTTTTTCCTTGTTT
TCTTCTTACTGACAGCATTTTTTGGAACTGGGAATATAGCTTCTATTAACAGCTTTGATCTTGCTTCAGTCTATTGCTTT
GTGACGGTGTTTAGTCCTTTTGTGATGGGAACCCTGATGATGTGGAAGATTTTAATCCCCTTTGTACTTGTGATGTGTGC
TTTTGAAGCAGTTCAGTTAACTACCCAGCTGTCATCAAAAAGCCTTTTTCTCATGGTTCTCGTCATATCAGACATCATGG
CTTTGCACTTTTTCTTCTTGGTCCAGGATTATGGCAGCTGGCTTGATATTGGAACA

Alignment

ORF - retro_eeur_583 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 98.94 %
• Parental protein coverage: 53.03 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ISLCKELIRLALEGLSYYHTYDRFFLGITVVLGFVGWTSYASLLIIKSHSNLTRGGSNKIKKPNHLLTCT
          ISLCKELIRLALEGLSYYHTYDRFFLGITVVLGFVGWTSYASLLIIKSHSNLTRGGSNKIKKPNHLLTCT
Retrocopy ISLCKELIRLALEGLSYYHTYDRFFLGITVVLGFVGWTSYASLLIIKSHSNLTRGGSNKIKKPNHLLTCT

Parental  FVAVGIAIAFFLLIQSCPWTYYVYCLLPVPIWHALLSEFPVIEDLVKSLLTFPPGQFIGSLLVFGLGLEI
          FVAVGIAIAFFLLIQSCPWTYYVYCLLPVPIWHALLSEFPVIEDLVKSLLTFPPGQFIGSLLVFGLGLEI
Retrocopy FVAVGIAIAFFLLIQSCPWTYYVYCLLPVPIWHALLSEFPVIEDLVKSLLTFPPGQFIGSLLVFGLGLEI

Parental  LVLSFFYRYMLTAGLTAFAGWPFVTQLWTRAKSTSLSWTLFSLLLAVFPLMPVVGRKPDISVVMGAGLLV
          LVLSFFYRYMLTAGLTAFAGWPFVTQLWTRAKSTSLSWTLFSLLL.VFPLMPVVG.KPDISVVMGAGLLV
Retrocopy LVLSFFYRYMLTAGLTAFAGWPFVTQLWTRAKSTSLSWTLFSLLLVVFPLMPVVGQKPDISVVMGAGLLV

Parental  LLLSLFVVTSYIKRKDNLDGELFLYLLQILSIMLSMYTVYSTHSSLQRKQGLPLLNQTISWIILASSFIL
          LLLSLFVVTSYIKRKDNLDGELFLYLLQILSIMLSMYTVYSTHSSLQRKQGLP.LNQTISWIILASSFIL
Retrocopy LLLSLFVVTSYIKRKDNLDGELFLYLLQILSIMLSMYTVYSTHSSLQRKQGLPFLNQTISWIILASSFIL

Parental  PLLSPTILFERLFSILLSLMSTYLLLSTGYEALFPLVLSCLMFIWIHMEQETLQQSGFSCKQKVNSIQFA
          PLLSPTILFERLFSILLSLMSTYLLLSTGYEALFPLVLSCLMFIWIHMEQETLQQSGFSCKQKVNSIQFA
Retrocopy PLLSPTILFERLFSILLSLMSTYLLLSTGYEALFPLVLSCLMFIWIHMEQETLQQSGFSCKQKVNSIQFA

Parental  YNIDITQYRKLYLDDIRRAFFLVFFLVTAFFGTGNIASINSFDLASVYCFVTVFSPFVMGTLMMWKILIP
          YNIDITQYRKLYLDDI.RAFFLVFFL.TAFFGTGNIASINSFDLASVYCFVTVFSPFVMGTLMMWKILIP
Retrocopy YNIDITQYRKLYLDDIHRAFFLVFFLLTAFFGTGNIASINSFDLASVYCFVTVFSPFVMGTLMMWKILIP

Parental  FVLVMCAFEAVQLTTQLSSKSLFLMVLVISDIMALHFFFLVQDYGSWLDIGT
          FVLVMCAFEAVQLTTQLSSKSLFLMVLVISDIMALHFFFLVQDYGSWLDIGT
Retrocopy FVLVMCAFEAVQLTTQLSSKSLFLMVLVISDIMALHFFFLVQDYGSWLDIGT

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	2.09 RPM	9.99 RPM
SRP017611_kidney	6.19 RPM	14.44 RPM
SRP017611_liver	2.09 RPM	7.56 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_583 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	ENSEEUG00000005812	1 retrocopy	retro_eeur_583 ,