RetrogeneDB ID: retro_eeur_442

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_305426:18484..19006(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CSNK2A2
• Ensembl ID: ENSEEUG00000000930
• Aliases: None
• Description: casein kinase 2, alpha prime polypeptide [Source:HGNC Symbol;Acc:2459]

Sequence

>retro_eeur_442
CTGAGACTGATAGACTGGGGTCTAGCAGAGTTCTGTCATCCTGCTCAGGAATACAATGTCCGTGTAGCCTTAAGCTACTT
CAAAGGGCCAGAGCTCCTTGTGGACTATGAGATGTAGAATTATAGTTTGGACATGTGGAGTTTAGGTTGTACATGAGCAA
GCATGATCTTTAGAAAGGAATCCTTCTTCCATGGACAGGACAACTATGACCAGCTTGCTCACATTGCCAAGGTTCTGGGT
ACAGAGGAGGTGTATGGGTATTTGAAGAAGTATCCCATAGAACTAGATCCACACTTCCATGATATCCTGGGGCAACATTC
ACGGAAAATCTGGGGAAACTTTACACATAGTGAGAACAGACATCTTGTCAGCCCTGAGGTCCTAGATCTTCTGGACAAGC
TTCAACAAAGATTGACTGCCAAAGAGGCCATTGAGCACCCATACTTCTACCCCGTAGTGAAGGCACAGTCCCAGCCCTGT
GCAGATAATGCTATGCTTTCTAGTGGTCTCATGGTAGCCCAA

Alignment

ORF - retro_eeur_442 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.89 %
• Parental protein coverage: 56.83 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LRLIDWGLAEFYHPAQEYNVRVASRYFKGPELLVDYQMYDYSLDMWSLGCMLASMIFRKEPFFHGQDNYD
          LRLIDWGLAEF.HPAQEYNVRVA..YFKGPELLVDY.M..YSLDMWSLGC..ASMIFRKE.FFHGQDNYD
Retrocopy LRLIDWGLAEFCHPAQEYNVRVALSYFKGPELLVDYEM*NYSLDMWSLGCT*ASMIFRKESFFHGQDNYD

Parental  QLVRIAKVLGTDELYGYLKKYHIDLDPHFNDILGQHSRKRWENFIHSENRHLVSPEALDLLDKLLRYDHQ
          QL..IAKVLGT.E.YGYLKKY.I.LDPHF.DILGQHSRK.W.NF.HSENRHLVSP.....LD.L.....Q
Retrocopy QLAHIAKVLGTEEVYGYLKKYPIELDPHFHDILGQHSRKIWGNFTHSENRHLVSP---EVLDLLDKL--Q

Parental  QRLTAKEAMEHPYFYPVVKEQSQPCADNAVLSSGLTAAR
          QRLTAKEA.EHPYFYPVVK.QSQPCADNA.LSSGL..A.
Retrocopy QRLTAKEAIEHPYFYPVVKAQSQPCADNAMLSSGLMVAQ

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	40.12 RPM
SRP017611_kidney	0.00 RPM	30.19 RPM
SRP017611_liver	0.00 RPM	20.90 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_442 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 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Erinaceus europaeus	ENSEEUG00000000930	1 retrocopy	retro_eeur_442 ,
Macropus eugenii	ENSMEUG00000013416	1 retrocopy	retro_meug_1470,
Myotis lucifugus	ENSMLUG00000000283	2 retrocopies	retro_mluc_1999, retro_mluc_2562,
Mustela putorius furo	ENSMPUG00000004713	1 retrocopy	retro_mputfur_1121,
Ochotona princeps	ENSOPRG00000011847	2 retrocopies	retro_opri_149, retro_opri_723,
Ictidomys tridecemlineatus	ENSSTOG00000003538	1 retrocopy	retro_itri_1769,