RetrogeneDB ID: retro_eeur_63

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_3369:96542..96865(+)
• Located in intron of: ENSEEUG00000000601

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000013363
• Aliases: None
• Description: None

Sequence

>retro_eeur_63
CTTCTCTTGATGGCGGCTTCAGCGATGGTCCGAAGCGACGCCTGGACCAGTCTGGGCTGCGGGCGGGCAAGAGGCTAAAA
ATGCAGTATGCCACTGGCCGGCTGCTCAAGTTCCAGATTTGTGTTTCCTGAGGTTATAGGCAGGTGTTTGAGGAGTACAT
GCGGGTTATTAGCCAGCAGTACCCAGACATCCGCATTGAAGGAGAGAATTACCTCCCTCAACCAATATACAGACACATAG
CCTCTTTCCTGTCAGTCTTCAAACTAGTATTAATAGGCTTAATAATTGTGGGCAAGGATCCACTTGCTTTCTTTGGCATG
CAA

Alignment

ORF - retro_eeur_63 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.24 %
• Parental protein coverage: 55.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  LLLMAASAMVRSDASTNL-GGVPGKRLKMQYATGPLLKFQIXXXXXYRRVFEEYMRVISQRYPDIRIEGE
          LLLMAASAMVRSDA.T.L.G...GKRLKMQYATG.LLKFQI.....YR.VFEEYMRVISQ.YPDIRIEGE
Retrocopy LLLMAASAMVRSDAWTSL<GLRAGKRLKMQYATGRLLKFQICVS*GYRQVFEEYMRVISQQYPDIRIEGE

Parental  NYLPQPIYRHIASFLSVFKLVLIGLIIVGKDPFAFFGMQ
          NYLPQPIYRHIASFLSVFKLVLIGLIIVGKDP.AFFGMQ
Retrocopy NYLPQPIYRHIASFLSVFKLVLIGLIIVGKDPLAFFGMQ

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	0.00 RPM	31.75 RPM
SRP017611_kidney	0.56 RPM	61.33 RPM
SRP017611_liver	0.48 RPM	31.35 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_63 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 6 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002576	1 retrocopy	retro_cpor_459,
Erinaceus europaeus	ENSEEUG00000013363	2 retrocopies	retro_eeur_63 , retro_eeur_697,
Monodelphis domestica	ENSMODG00000021273	1 retrocopy	retro_mdom_467,
Oryctolagus cuniculus	ENSOCUG00000013866	9 retrocopies	retro_ocun_1080, retro_ocun_1229, retro_ocun_1783, retro_ocun_1803, retro_ocun_1831, retro_ocun_327, retro_ocun_328, retro_ocun_557, retro_ocun_779,
Pongo abelii	ENSPPYG00000029483	1 retrocopy	retro_pabe_3478,
Tursiops truncatus	ENSTTRG00000007522	2 retrocopies	retro_ttru_1556, retro_ttru_694,