RetrogeneDB ID: retro_eeur_413

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_291294:696..1065(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NT5C3B
• Ensembl ID: ENSEEUG00000013493
• Aliases: None
• Description: 5'-nucleotidase, cytosolic IIIB [Source:HGNC Symbol;Acc:28300]

Sequence

>retro_eeur_413
ATTGAGATCGATCCGCATATGACCGTAGAAGATAAGTTCCCTTACATGGTTGAGTGGTATACTAAGTCGCATGGTTTGCT
GGTTGAGCAAGGGATCCCAAAAGCTAAAATTCAAGAAGTTGTGACAGAATCTGACATTATGCTCAAGGAAGGATGTGGGA
ATTTCTTCGATAAGCTCCACCAACGTGACATCCCCATGTTCATCTTTTCGGCTGGAATTTGCGATGTCCTGGAGGAGGTG
ATCAGGCAGGCTGGTGTCTATCATTCCAATGTGAAAGTAGTTTCCAACTTCATGGATTTTGACGACAATAGGGTAGTGAA
AGGATTTAAAGGAGAACTAATTCACGTATTTAACAAACATGGTGCCTTG

Alignment

ORF - retro_eeur_413 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.47 %
• Parental protein coverage: 54.91 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IEIDPQRSIKEKLPHMVEWWTKAHNLLCQQKIQKFQIAQMVRESSVMLREGYKAFFNTLYQNNIPLFIFS
          IEIDP......K.P.MVEW.TK.H.LL..Q.I.K..I...V.ES..ML.EG...FF..L.Q..IP.FIFS
Retrocopy IEIDPHMTVEDKFPYMVEWYTKSHGLLVEQGIPKAKIQEVVTESDIMLKEGCGNFFDKLHQRDIPMFIFS

Parental  AGVGDVLEEIIRQMKVFHSNIHIVSNYMDFDEDGILQGFKGQLIHTYNKNSSV
          AG..DVLEE.IRQ..V.HSN...VSN.MDFD......GFKG.LIH..NK....
Retrocopy AGICDVLEEVIRQAGVYHSNVKVVSNFMDFDDNRVVKGFKGELIHVFNKHGAL

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	19.82 RPM	69.78 RPM
SRP017611_kidney	31.32 RPM	40.70 RPM
SRP017611_liver	10.29 RPM	14.63 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_413 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 7 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005754	1 retrocopy	retro_amel_1542,
Erinaceus europaeus	ENSEEUG00000013493	1 retrocopy	retro_eeur_413 ,
Felis catus	ENSFCAG00000023499	1 retrocopy	retro_fcat_1017,
Mustela putorius furo	ENSMPUG00000010759	2 retrocopies	retro_mputfur_1354, retro_mputfur_1594,
Pan troglodytes	ENSPTRG00000009181	1 retrocopy	retro_ptro_2082,
Pteropus vampyrus	ENSPVAG00000010634	1 retrocopy	retro_pvam_233,
Sorex araneus	ENSSARG00000006434	1 retrocopy	retro_sara_505,