RetrogeneDB ID: retro_eeur_302

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_247066:4452..4691(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSEEUG00000015895
• Aliases: None
• Description: None

Sequence

>retro_eeur_302
GTGGCGCACAGACAGACTCCTTAGTCAGACAGATACGACAAGGAGGAGGAGTTTGGGTACCGGCATGTCATATTGCCAAG
GACATAGCCAAGCTGGCCCCTAAAACCCATCTGATGTCCGAGTCTGAATGGAGGAATCTCGGTGTTGAGCAGAGTCAGGG
CTGGCTCCATTATATCATCCACGAGCCAGAGCCTCACATCTCGCTGTTCCGCTGGCCACTGCCAAAGAAGCCCAAGACA

Alignment

ORF - retro_eeur_302 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.78 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MSHKQIYYSDKYD-DEEFEYRHVMLP-KDIAKLVPKTHLMSESEWRNLGVQQSQGWVHYMIHEPEPHILL
          ..H.Q...SD.YD..EEF.YRHV.LP.KDIAKL.PKTHLMSESEWRNLGV.QSQGW.HY.IHEPEPHI.L
Retrocopy VAHRQTP*SDRYDKEEEFGYRHVILP<KDIAKLAPKTHLMSESEWRNLGVEQSQGWLHYIIHEPEPHISL

Parental  FRRPLPKKPKT
          FR.PLPKKPKT
Retrocopy FRWPLPKKPKT

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	0.32 RPM	0.48 RPM
SRP017611_kidney	0.56 RPM	0.94 RPM
SRP017611_liver	0.00 RPM	0.80 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_302 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 8 parental genes, and 31 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000033635	10 retrocopies	retro_cjac_13, retro_cjac_1441, retro_cjac_1478, retro_cjac_1779, retro_cjac_2040, retro_cjac_2212, retro_cjac_2649, retro_cjac_276, retro_cjac_57, retro_cjac_876,
Dipodomys ordii	ENSDORG00000003764	6 retrocopies	retro_dord_25, retro_dord_290, retro_dord_599, retro_dord_64, retro_dord_647, retro_dord_739,
Erinaceus europaeus	ENSEEUG00000004384	7 retrocopies	retro_eeur_183, retro_eeur_255, retro_eeur_293, retro_eeur_551, retro_eeur_632, retro_eeur_639, retro_eeur_640,
Erinaceus europaeus	ENSEEUG00000015895	1 retrocopy	retro_eeur_302 ,
Homo sapiens	ENSG00000173207	1 retrocopy	retro_hsap_27,
Gorilla gorilla	ENSGGOG00000013419	4 retrocopies	retro_ggor_10, retro_ggor_1070, retro_ggor_2739, retro_ggor_659,
Rattus norvegicus	ENSRNOG00000042561	1 retrocopy	retro_rnor_97,
Sarcophilus harrisii	ENSSHAG00000004796	1 retrocopy	retro_shar_786,