RetrogeneDB ID: retro_eeur_38

Retrocopy location

• Organism: Hedgehog (Erinaceus europaeus)
• Coordinates: GeneScaffold_2397:97916..98295(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CALM2
• Ensembl ID: ENSEEUG00000000040
• Aliases: None
• Description: calmodulin 2 (phosphorylase kinase, delta) [Source:HGNC Symbol;Acc:1445]

Sequence

>retro_eeur_38
GCTGACCAACTGACCAAAGAGCAGATTGCAAAATTCAAAGAAGCTTTTTCACTATTTGACAAGGATGGGGATTGAACTAT
AGCAACAAAAGAATTGAGAACTGTAATGAGGTCTCTTGGGCAAAATCCTACAGAAGCAGAATTGTAGGACATGATTAATG
AAGTAGATGCTGATGGTAATGGCACAATCGATTTCCCAGAATTTATGACAATGATGGGAAGAAAAATGAAAGGTACAGAC
AGTGAAGAAGAAATTAGAGAAGCGTTCCTGTGTGTTTGATAAGGATGGTAATGGTTATAATAGTGCAGCTGAGCTTCGCC
ACATGATGACAAACCTTGGAGAGGAGTTACAGATGAAGAGGTTGGATGAGATGATCAGG

Alignment

ORF - retro_eeur_38 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.04 %
• Parental protein coverage: 85.14 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLT
          ADQLT.EQIA.FKEAFSLFDKDGD.TI.TKEL.TVMRSLGQNPTEAEL.DMINEVDADGNGTIDFPEF.T
Retrocopy ADQLTKEQIAKFKEAFSLFDKDGD*TIATKELRTVMRSLGQNPTEAEL*DMINEVDADGNGTIDFPEFMT

Parental  MMARKMKDTDSEEEIREAFR-VFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIR
          MM.RKMK.TDSEEEIREAF..VFDKDGNGY.SAAELRH.MTNLGE.L.....DEMIR
Retrocopy MMGRKMKGTDSEEEIREAFL>VFDKDGNGYNSAAELRHMMTNLGEELQMKRLDEMIR

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	33.52 RPM	484.56 RPM
SRP017611_kidney	11.81 RPM	169.91 RPM
SRP017611_liver	2.25 RPM	26.21 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_38 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 20 parental genes, and 62 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000015712	1 retrocopy	retro_acar_45,
Choloepus hoffmanni	ENSCHOG00000008245	6 retrocopies	retro_chof_1940, retro_chof_2261, retro_chof_367, retro_chof_735, retro_chof_833, retro_chof_965,
Cavia porcellus	ENSCPOG00000012181	3 retrocopies	retro_cpor_1012, retro_cpor_87, retro_cpor_89,
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,
Echinops telfairi	ENSETEG00000018667	16 retrocopies	retro_etel_1032, retro_etel_1075, retro_etel_108, retro_etel_1164, retro_etel_1184, retro_etel_1507, retro_etel_1650, retro_etel_1683, retro_etel_1903, retro_etel_2139, retro_etel_22, retro_etel_539, retro_etel_687, retro_etel_864, retro_etel_902, retro_etel_951,
Ficedula albicollis	ENSFALG00000012828	1 retrocopy	retro_falb_16,
Gadus morhua	ENSGMOG00000009342	1 retrocopy	retro_gmor_23,
Latimeria chalumnae	ENSLACG00000005059	1 retrocopy	retro_lcha_53,
Loxodonta africana	ENSLAFG00000009865	1 retrocopy	retro_lafr_655,
Myotis lucifugus	ENSMLUG00000029016	6 retrocopies	retro_mluc_13, retro_mluc_1732, retro_mluc_18, retro_mluc_19, retro_mluc_2207, retro_mluc_2258,
Macaca mulatta	ENSMMUG00000017466	1 retrocopy	retro_mmul_256,
Monodelphis domestica	ENSMODG00000009222	1 retrocopy	retro_mdom_1126,
Otolemur garnettii	ENSOGAG00000008824	6 retrocopies	retro_ogar_1126, retro_ogar_1196, retro_ogar_1432, retro_ogar_1535, retro_ogar_209, retro_ogar_2326,
Petromyzon marinus	ENSPMAG00000003323	1 retrocopy	retro_pmar_12,
Pongo abelii	ENSPPYG00000012430	5 retrocopies	retro_pabe_1068, retro_pabe_1133, retro_pabe_115, retro_pabe_45, retro_pabe_599,
Pelodiscus sinensis	ENSPSIG00000013173	1 retrocopy	retro_psin_9,
Sus scrofa	ENSSSCG00000008433	1 retrocopy	retro_sscr_228,
Taeniopygia guttata	ENSTGUG00000002581	1 retrocopy	retro_tgut_6,