RetrogeneDB ID: retro_eeur_528

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_338950:3527..3824(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHEBL1
• Ensembl ID: ENSEEUG00000008514
• Aliases: None
• Description: Ras homolog enriched in brain like 1 [Source:HGNC Symbol;Acc:21166]

Sequence

>retro_eeur_528
CTTTTGTATTCTGTCACATCTCTGCATAGTTTCCAAATCATTGAGAGCCTGTACCAAAAACTGCATTAAGTTCATGGCAA
AATTTGGCTGCCACTGGTGCTAGCAGGGAATAAGGCAGATCTCTCACTGGAAAGGGAGGTGCAGGGAGCTGAAGCAAAGA
AGTTGGCAGAATCCTGGGGTGCAATATATATAGAGAGAGTTCAAGAGAATCAGTTGACTCATGTCTATTTCACCAAAATC
ATCCAGATTAGCCAGCTGGAGAATTCCTATGGACAAGAATGCCACTGCCGTCTCATG

Alignment

ORF - retro_eeur_528 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.21 %
• Parental protein coverage: 55.19 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LVYSVTSLHSFQIIESLYQKLHEVHGKIRLPVVLVGNKADLSLEREVQAVEGKKLAESWGAIYMESSARK
          L.YSVTSLHSFQIIESLYQKLH.VHGKI.LP.VL.GNKADLSLEREVQ..E.KKLAESWGAIY.E.....
Retrocopy LLYSVTSLHSFQIIESLYQKLH*VHGKIWLPLVLAGNKADLSLEREVQGAEAKKLAESWGAIYIE-RVQE

Parental  NQMTHAVFTKIIQEISRVENSYGQKCHCRLM
          NQ.TH..FTKIIQ.IS..ENSYGQ.CHCRLM
Retrocopy NQLTHVYFTKIIQ-ISQLENSYGQECHCRLM

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	0.64 RPM
SRP017611_kidney	0.00 RPM	0.94 RPM
SRP017611_liver	0.00 RPM	0.00 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_528 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000002998	1 retrocopy	retro_cpor_1328,
Erinaceus europaeus	ENSEEUG00000008514	2 retrocopies	retro_eeur_338, retro_eeur_528 ,
Oryctolagus cuniculus	ENSOCUG00000016881	1 retrocopy	retro_ocun_1802,
Otolemur garnettii	ENSOGAG00000013477	1 retrocopy	retro_ogar_2338,
Pan troglodytes	ENSPTRG00000004897	1 retrocopy	retro_ptro_115,
Rattus norvegicus	ENSRNOG00000021571	1 retrocopy	retro_rnor_2059,