RetrogeneDB ID: retro_eeur_218

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_212186:1706..2282(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: PCBP1
• Ensembl ID: ENSEEUG00000001077
• Aliases: None
• Description: poly(rC) binding protein 1 [Source:HGNC Symbol;Acc:8647]

Sequence

>retro_eeur_218
ATGGACACCGGTGTGATTGAAGGTAGATTAAATGTCACTCTCACCATCCGACTACTTATGCATGGAAAGGAAGTTGTCAG
TATCATCGGAAAGAAAGGAGAATCAGTTAAGAAGATGCGTGAAGAGGGTGCACGAATCAACATCTCAGAAGGGAATTGTC
CTGAGAGAATTATCACCTTGGCTGGACCCACTAATGCCATCTTCAAAGCTTTTGCTATGATCACTGACAAACTGGAAGAG
GACATCAGCAGCTCTCTGACAAAAAGCACAGCTGCCGGTAGACCCCCAGTCACCCTGAGGCTGGTGGTCCCTGCTAGTCA
GTGTGGCTCTCTCATCAGAAAAGGTGGTTGCAAGATCAAGGAAATACGAGAGAGTACAGGGGCTCAGGTCCAAGTGGCCG
GGGATATGCTTCCCAATTCAACTCAGCAAACCATTACTATTGCTGGCATTCCGCAATCCATCATTGAGTGAGTGAAACGG
ATTTGCGTGGTCATGTTGGAGTCCCCCCTGAAGGGCGTGACCATCCCCTACTGGCCCCAGCCATCCAGTTCTCCAGTCAT
CTTTGCAGATGGTCAG

Alignment

ORF - retro_eeur_218 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.83 %
• Parental protein coverage: 54.12 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNTGVIEGGLNVTLTIRLLMHGKEVGSIIGKKGESVKKMREESGARINISEGNCPERIITLAGPTNAIFK
          M.TGVIEG.LNVTLTIRLLMHGKEV.SIIGKKGESVKKMREE.GARINISEGNCPERIITLAGPTNAIFK
Retrocopy MDTGVIEGRLNVTLTIRLLMHGKEVVSIIGKKGESVKKMREE-GARINISEGNCPERIITLAGPTNAIFK

Parental  AFAMIIDKLEEDISSSMTNSTAASRPPVTLRLVVPASQCGSLIGKGGCKIKEIRESTGAQVQVAGDMLPN
          AFAMI.DKLEEDISSS.T.STAA.RPPVTLRLVVPASQCGSLI.KGGCKIKEIRESTGAQVQVAGDMLPN
Retrocopy AFAMITDKLEEDISSSLTKSTAAGRPPVTLRLVVPASQCGSLIRKGGCKIKEIRESTGAQVQVAGDMLPN

Parental  STERAITIAGIPQSIIECVKQICVVMLEFILFSPPKGVTIPYRPKPSSSPVIFAGGQ
          ST...ITIAGIPQSIIE.VK.ICVVMLE....SP.KGVTIPY.P.PSSSPVIFA.GQ
Retrocopy STQQTITIAGIPQSIIE*VKRICVVMLE----SPLKGVTIPYWPQPSSSPVIFADGQ

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	1.77 RPM	167.11 RPM
SRP017611_kidney	2.06 RPM	322.00 RPM
SRP017611_liver	1.77 RPM	143.25 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_218 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 7 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000000967	2 retrocopies	retro_cpor_193, retro_cpor_97,
Equus caballus	ENSECAG00000022389	1 retrocopy	retro_ecab_67,
Erinaceus europaeus	ENSEEUG00000001077	2 retrocopies	retro_eeur_218 , retro_eeur_655,
Homo sapiens	ENSG00000197111	2 retrocopies	retro_hsap_4077, retro_hsap_83,
Microcebus murinus	ENSMICG00000011651	2 retrocopies	retro_mmur_1226, retro_mmur_1228,
Macaca mulatta	ENSMMUG00000006608	2 retrocopies	retro_mmul_1263, retro_mmul_1994,
Oryctolagus cuniculus	ENSOCUG00000022490	3 retrocopies	retro_ocun_10, retro_ocun_1622, retro_ocun_898,