RetrogeneDB ID: retro_eeur_468

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: scaffold_315107:12729..13013(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CALM3
• Ensembl ID: ENSEEUG00000000140
• Aliases: None
• Description: calmodulin 3 (phosphorylase kinase, delta) [Source:HGNC Symbol;Acc:1449]

Sequence

>retro_eeur_468
TTGGGAACTGTCATGAGATCTCTTGGGCAGAATCCCCCAGAAACAGAGTTATATAGGACATGGTTCATGAAGTAGATGTT
GATGGTAATGGCATGATCGACTTCCCAGAATTTCTGACCATGATGGCAAGAAACATGAAAGATACAGACAGTGAAGAAGA
AATGAGAGAAGCATTCCGTGTGTTTGAGAAGGATGGCGATGGTCATATGAGTGTAGCTGAGCTTTGCCATGGGATGACAG
ACCTTGGAGAGAAGTTAACAGATGAAGTTCATGAAATGGTCAGA

Alignment

ORF - retro_eeur_468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.16 %
• Parental protein coverage: 69.34 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  LGTVMRS-LG-QNPTEAELQDMINEVDADGNGTIDFPEFLTMMARKMKDTDSEEEIREAFRVFDKDGNGY
          LGTVMRS.LG...P......DM..EVD.DGNG.IDFPEFLTMMAR.MKDTDSEEE.REAFRVF.KDG.G.
Retrocopy LGTVMRS>LG>ESPRNRVI*DMVHEVDVDGNGMIDFPEFLTMMARNMKDTDSEEEMREAFRVFEKDGDGH

Parental  ISAAELRHVMTNLGEKLTDEEVDEMIR
          .S.AEL.H.MT.LGEKLTD.EV.EM.R
Retrocopy MSVAELCHGMTDLGEKLTD-EVHEMVR

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	343.88 RPM
SRP017611_kidney	0.38 RPM	86.08 RPM
SRP017611_liver	0.00 RPM	35.69 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_468 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 24 parental genes, and 54 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015712	1 retrocopy	retro_acar_45,
Ailuropoda melanoleuca	ENSAMEG00000008565	3 retrocopies	retro_amel_1209, retro_amel_1562, retro_amel_421,
Bos taurus	ENSBTAG00000014583	2 retrocopies	retro_btau_113, retro_btau_135,
Canis familiaris	ENSCAFG00000029151	4 retrocopies	retro_cfam_121, retro_cfam_164, retro_cfam_225, retro_cfam_68,
Cavia porcellus	ENSCPOG00000001612	1 retrocopy	retro_cpor_1316,
Erinaceus europaeus	ENSEEUG00000000040	3 retrocopies	retro_eeur_38, retro_eeur_561, retro_eeur_671,
Erinaceus europaeus	ENSEEUG00000000140	1 retrocopy	retro_eeur_468 ,
Echinops telfairi	ENSETEG00000009377	5 retrocopies	retro_etel_1062, retro_etel_1542, retro_etel_1812, retro_etel_587, retro_etel_854,
Felis catus	ENSFCAG00000004995	1 retrocopy	retro_fcat_1726,
Homo sapiens	ENSG00000160014	3 retrocopies	retro_hsap_1255, retro_hsap_1785, retro_hsap_59,
Gorilla gorilla	ENSGGOG00000000212	4 retrocopies	retro_ggor_187, retro_ggor_2234, retro_ggor_522, retro_ggor_988,
Loxodonta africana	ENSLAFG00000001155	5 retrocopies	retro_lafr_100, retro_lafr_156, retro_lafr_631, retro_lafr_646, retro_lafr_86,
Microcebus murinus	ENSMICG00000013180	3 retrocopies	retro_mmur_1032, retro_mmur_1447, retro_mmur_501,
Myotis lucifugus	ENSMLUG00000010528	1 retrocopy	retro_mluc_2477,
Monodelphis domestica	ENSMODG00000009222	1 retrocopy	retro_mdom_1126,
Mustela putorius furo	ENSMPUG00000005261	1 retrocopy	retro_mputfur_404,
Mus musculus	ENSMUSG00000019370	3 retrocopies	retro_mmus_2879, retro_mmus_3448, retro_mmus_454,
Nomascus leucogenys	ENSNLEG00000002752	2 retrocopies	retro_nleu_1407, retro_nleu_3097,
Otolemur garnettii	ENSOGAG00000014764	2 retrocopies	retro_ogar_2085, retro_ogar_3311,
Procavia capensis	ENSPCAG00000005751	1 retrocopy	retro_pcap_7,
Petromyzon marinus	ENSPMAG00000003323	1 retrocopy	retro_pmar_12,
Pongo abelii	ENSPPYG00000010154	4 retrocopies	retro_pabe_1106, retro_pabe_1466, retro_pabe_3238, retro_pabe_3676,
Pelodiscus sinensis	ENSPSIG00000013173	1 retrocopy	retro_psin_9,
Ictidomys tridecemlineatus	ENSSTOG00000014352	1 retrocopy	retro_itri_1018,