RetrogeneDB ID: retro_eeur_613

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_365121:1039..1313(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSEEUG00000003431
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: SNRPE
• Ensembl ID: ENSEEUG00000006187
• Aliases: None
• Description: small nuclear ribonucleoprotein polypeptide E [Source:HGNC Symbol;Acc:11161]

Sequence

>retro_eeur_613
GCATACCATAGCCAGGGCCAGAAAGGGCAGATAGGTGATGGTACAGCCCATCAACCTCATCTTCAGATACTTGCAAAATA
GATCTTGGATTCAAGTATGGCTTTATGAGCAGGTGAATATGCGGATAGAGGGCTGCATCATTGATTTTGACGAATATATG
AACCTCATATTAGATGACGTAGAAAACATTCATTCCAAAACAAAATCAAGAAAGCAGCTGGGTCGGATCATGTTAAAAGG
AGATAATATCACTCTGCTGCAAAGTGTCTCCAAC

Alignment

ORF - retro_eeur_613 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.26 %
• Parental protein coverage: 98.89 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  AYRGQGQKVQK-VMVQPINLIFRYLQNRSRIQVWLYEQVNMRIEGCIIXXXXXXXXXXXDAE-IHSKTKS
          AY..QGQK.Q..VMVQPINLIFRYLQNRS.IQVWLYEQVNMRIEGCII...........D.E.IHSKTKS
Retrocopy AYHSQGQKGQI>VMVQPINLIFRYLQNRSWIQVWLYEQVNMRIEGCIIDFDEYMNLILDDVENIHSKTKS

Parental  RKQLG-IMLKGDNITLLQSVSN
          RKQLG.IMLKGDNITLLQSVSN
Retrocopy RKQLGRIMLKGDNITLLQSVSN

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	0.48 RPM	1.13 RPM
SRP017611_kidney	1.13 RPM	1.88 RPM
SRP017611_liver	0.00 RPM	1.13 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_613 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 85 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000006735	1 retrocopy	retro_cjac_3163,
Dasypus novemcinctus	ENSDNOG00000004490	24 retrocopies	retro_dnov_1009, retro_dnov_1141, retro_dnov_122, retro_dnov_1223, retro_dnov_1312, retro_dnov_1314, retro_dnov_1362, retro_dnov_1438, retro_dnov_163, retro_dnov_191, retro_dnov_2398, retro_dnov_2671, retro_dnov_360, retro_dnov_414, retro_dnov_513, retro_dnov_579, retro_dnov_796, retro_dnov_828, retro_dnov_898, retro_dnov_900, retro_dnov_902, retro_dnov_93, retro_dnov_967, retro_dnov_983,
Erinaceus europaeus	ENSEEUG00000006187	6 retrocopies	retro_eeur_339, retro_eeur_497, retro_eeur_579, retro_eeur_613 , retro_eeur_85, retro_eeur_92,
Echinops telfairi	ENSETEG00000014015	24 retrocopies	retro_etel_1136, retro_etel_1244, retro_etel_138, retro_etel_1443, retro_etel_1530, retro_etel_1636, retro_etel_1739, retro_etel_1781, retro_etel_1947, retro_etel_2143, retro_etel_234, retro_etel_258, retro_etel_310, retro_etel_377, retro_etel_466, retro_etel_546, retro_etel_56, retro_etel_579, retro_etel_581, retro_etel_582, retro_etel_76, retro_etel_776, retro_etel_799, retro_etel_80,
Gorilla gorilla	ENSGGOG00000000755	7 retrocopies	retro_ggor_1462, retro_ggor_1626, retro_ggor_1700, retro_ggor_2221, retro_ggor_228, retro_ggor_2892, retro_ggor_91,
Myotis lucifugus	ENSMLUG00000013244	8 retrocopies	retro_mluc_1639, retro_mluc_1650, retro_mluc_1994, retro_mluc_2045, retro_mluc_2088, retro_mluc_2326, retro_mluc_85, retro_mluc_919,
Mustela putorius furo	ENSMPUG00000011642	7 retrocopies	retro_mputfur_1078, retro_mputfur_1527, retro_mputfur_1634, retro_mputfur_53, retro_mputfur_638, retro_mputfur_729, retro_mputfur_949,
Pongo abelii	ENSPPYG00000000326	8 retrocopies	retro_pabe_1375, retro_pabe_20, retro_pabe_2023, retro_pabe_228, retro_pabe_3015, retro_pabe_3620, retro_pabe_56, retro_pabe_610,