RetrogeneDB ID: retro_eeur_245

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_221905:10634..11104(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPRD1A
• Ensembl ID: ENSEEUG00000007025
• Aliases: None
• Description: regulation of nuclear pre-mRNA domain containing 1A [Source:HGNC Symbol;Acc:25560]

Sequence

>retro_eeur_245
GACACTAAGGAGAGTGTGCAGTCCCTGGCCCTGTGGCTCACCCACCACCACAAGCACTCGTGGCCCACCTCACTGTGTGG
GAGTGGGAGCTGTGCAAAACCAAACCAAACAGGAAGCTTACTTTTCTCTACCTGGCCAATGATGTCATTCAGAACAGTAA
ACAGAAGAGGCCAGAGTTTACACAGGATTTTGCACCACTGATAGTGTTGCCTTTTAAGTATGTTTCAAGTGCAACTGATG
AAAGTAGTAAGAAGTGCCTTGGATGAGTTTTATCTATTTGGGAAGAAAGGTCTGTTTGTGAAAGTGATGTATTAGGGCAG
CTTAAACAAACTCTGTGTGGTGATAAAAAGCCTAGGAAACGAACTTGTAGCCAGATAAAGGTAGATAAGAACGATAACAG
CTCTTTTCTGGGATCACCAAGTGAACCACCAAAAACTTTAGATCTCCTTAGAGCCTTATGAGATCTAGAA

Alignment

ORF - retro_eeur_245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.68 %
• Parental protein coverage: 50.32 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NSQQSVQTLSLWLIHHRKHSRPI-VTVWERELRKAKPNRKLTFLYLANDVIQNSKRKGPEFTKDFAPVIV
          ....SVQ.L.LWL.HH.KHS.P...TVWE.EL.K.KPNRKLTFLYLANDVIQNSK.K.PEFT.DFAP.IV
Retrocopy DTKESVQSLALWLTHHHKHSWPT<LTVWEWELCKTKPNRKLTFLYLANDVIQNSKQKRPEFTQDFAPLIV

Parental  EAFKHVSSETDESCKKHLGRVLSIWEERSVYENDVLEQLKQALYGDKKPRKRTYDQIKVDENENCSSLGS
          ..FK.VSS.TDES.KK.LG.VLSIWEERSV.E.DVL.QLKQ.L.GDKKPRKRT..QIKVD.N.N.S.LGS
Retrocopy LPFKYVSSATDESSKKCLG*VLSIWEERSVCESDVLGQLKQTLCGDKKPRKRTCSQIKVDKNDNSSFLGS

Parental  PSEPPQTLDLVRALQDLE
          PSEPP.TLDL.RAL.DLE
Retrocopy PSEPPKTLDLLRAL*DLE

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	40.93 RPM
SRP017611_kidney	0.00 RPM	23.63 RPM
SRP017611_liver	0.00 RPM	13.02 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_245 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000007025	1 retrocopy	retro_eeur_245 ,
Gorilla gorilla	ENSGGOG00000007369	1 retrocopy	retro_ggor_1237,
Macaca mulatta	ENSMMUG00000018777	1 retrocopy	retro_mmul_1562,
Monodelphis domestica	ENSMODG00000000399	1 retrocopy	retro_mdom_360,
Nomascus leucogenys	ENSNLEG00000006228	1 retrocopy	retro_nleu_1323,
Pongo abelii	ENSPPYG00000009111	1 retrocopy	retro_pabe_1352,
Pan troglodytes	ENSPTRG00000009974	1 retrocopy	retro_ptro_1106,
Vicugna pacos	ENSVPAG00000001641	1 retrocopy	retro_vpac_62,