RetrogeneDB ID: retro_eeur_500

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_328641:4955..5633(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000015241
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ILF2
• Ensembl ID: ENSEEUG00000013100
• Aliases: None
• Description: interleukin enhancer binding factor 2 [Source:HGNC Symbol;Acc:6037]

Sequence

>retro_eeur_500
GAAGCTGTCGCTGCCTTAGGAAACAAAGTTGTGGAAAGCCTTAGAACACAGGATCCTTCAGAAGTTTTGACCATGTTGAC
CAATGAGACCAGCTTTGAGATTAGCTCCTCTGATGCTACAGTGAAGATTCTTATCACAACAGTACCACCCAATCTCCGAA
AACTGGACCCAGAACTCCATTTGGATATCAAAGTGTTGCAGAGTGCCTTAGCAGCTATCCGGCATGCCCGCTGGTTTGAG
GAAAATGCTTCTCAGTCCACAGTTAAAGTTCTCATCAGACTGTTGAAGGACCTGAGAATTCGTTTTCCTGGTTTTGAGCC
CCTCACACCCTGGATCCTTGACCTACTTGGACATTATGCTGTGATGAACAACCCCACCAGGCAGCCATTGGCCCTAAATG
TGGCATACAGGCGCTGCCTGCAGATTCTGGCTGCAGGGCTGTTCCTGCCAGGGTCAGTAGGTATCACTGACCCCTGTGAG
AGTGGTAACTTCAGAGTACACACAGTGATGACCCTAGAGCAACAGGACATGGTCTGTTACACAGCTCAGACTCTGGTCCG
GATCCTCTCACATGGTGGCTTTAGGAAGATCCTGGGCCAGGAGGGTGATGCCAGTTATCTGGCTTCTGAAATATCTACCT
GGGATGGGGTGATAGTAACTCCTTCAGAAAAGGCATAT

Alignment

ORF - retro_eeur_500 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 99.56 %
• Parental protein coverage: 57.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EAVAALGNKVVESLRTQDPSEVLTMLTNETGFEISSSDATVKILITTVPPNLRKLDPELHLDIKVLQSAL
          EAVAALGNKVVESLRTQDPSEVLTMLTNET.FEISSSDATVKILITTVPPNLRKLDPELHLDIKVLQSAL
Retrocopy EAVAALGNKVVESLRTQDPSEVLTMLTNETSFEISSSDATVKILITTVPPNLRKLDPELHLDIKVLQSAL

Parental  AAIRHARWFEENASQSTVKVLIRLLKDLRIRFPGFEPLTPWILDLLGHYAVMNNPTRQPLALNVAYRRCL
          AAIRHARWFEENASQSTVKVLIRLLKDLRIRFPGFEPLTPWILDLLGHYAVMNNPTRQPLALNVAYRRCL
Retrocopy AAIRHARWFEENASQSTVKVLIRLLKDLRIRFPGFEPLTPWILDLLGHYAVMNNPTRQPLALNVAYRRCL

Parental  QILAAGLFLPGSVGITDPCESGNFRVHTVMTLEQQDMVCYTAQTLVRILSHGGFRKILGQEGDASYLASE
          QILAAGLFLPGSVGITDPCESGNFRVHTVMTLEQQDMVCYTAQTLVRILSHGGFRKILGQEGDASYLASE
Retrocopy QILAAGLFLPGSVGITDPCESGNFRVHTVMTLEQQDMVCYTAQTLVRILSHGGFRKILGQEGDASYLASE

Parental  ISTWDGVIVTPSEKAY
          ISTWDGVIVTPSEKAY
Retrocopy ISTWDGVIVTPSEKAY

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	34.16 RPM	53.98 RPM
SRP017611_kidney	31.69 RPM	49.14 RPM
SRP017611_liver	10.93 RPM	19.78 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_500 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 5 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000013100	1 retrocopy	retro_eeur_500 ,
Macropus eugenii	ENSMEUG00000003651	1 retrocopy	retro_meug_1174,
Myotis lucifugus	ENSMLUG00000001847	3 retrocopies	retro_mluc_1046, retro_mluc_217, retro_mluc_2402,
Macaca mulatta	ENSMMUG00000008149	1 retrocopy	retro_mmul_1516,
Ictidomys tridecemlineatus	ENSSTOG00000000667	1 retrocopy	retro_itri_130,