RetrogeneDB ID: retro_etel_539

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_8916:49505..49949(+)
• Located in intron of: ENSETEG00000004135

Retrocopy information

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

Parental gene information

• Parental gene symbol: CALM2
• Ensembl ID: ENSETEG00000018667
• Aliases: None
• Description: calmodulin 2 (phosphorylase kinase, delta) [Source:HGNC Symbol;Acc:1445]

Sequence

>retro_etel_539
GCCGATCAGCTGACCGAAGAGCAGATTGCCGAGTTCAGGGAGGCTTTCTCCCTAATCGATAAAGATGGCGACGGCTCCAT
CACAAGAAAGGAGTTTGGAACTGTCCTGAGGTCCCTGGGTCACAACCCAACCGAAGCTGAGCTGCAGGATATGGCCAACG
AGGTGGACGCCGAGGGTCAAGGCACCATTGATTTCCCAGGGTTTTTGACCGTGATGGCTCGAAAAATGAAAGACACGGAC
AGCGAGGAAGAAATCCGCAGGGCATTCCGAATCTTTGACAAGGATGGCCGTGGCCTCATCAGTGTGGCCGAGCTGCGCCA
CGTCATGACCAACTTAGGAGAAAAACTAACAGACGAAGAAATAAATGAAATGATCACAGAAGCAGACATAGACGGCAACG
GAGAAGTCAACTATGAAGAATTCGTACGGAGGATGATTTTAAAA

Alignment

ORF - retro_etel_539 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.43 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ADQLTEEQIAEFKEAFSLFDKDGDGTITTKELGTVMRSLGQNPTEAELQDMINEVDADGNGTIDFPEFLT
          ADQLTEEQIAEF.EAFSL.DKDGDG.IT.KE.GTV.RSLG.NPTEAELQDM.NEVDA.G.GTIDFP.FLT
Retrocopy ADQLTEEQIAEFREAFSLIDKDGDGSITRKEFGTVLRSLGHNPTEAELQDMANEVDAEGQGTIDFPGFLT

Parental  MMARKMKDTDSEEEIREAFRVFDKDGNGYISAAELRHVMTNLGEKLTDEEVDEMIREADIDGDGQVNYEE
          .MARKMKDTDSEEEIR.AFR.FDKDG.G.IS.AELRHVMTNLGEKLTDEE..EMI.EADIDG.G.VNYEE
Retrocopy VMARKMKDTDSEEEIRRAFRIFDKDGRGLISVAELRHVMTNLGEKLTDEEINEMITEADIDGNGEVNYEE

Parental  FVQMMTAK
          FV..M..K
Retrocopy FVRRMILK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Echinops telfairi was not studied using RNA-Seq expression data.

ChIP-Seq

Echinops telfairi was not studied using ChIP-Seq data.

EST

Echinops telfairi was not studied using EST data.

TSS

Echinops telfairi was not studied using FANTOM5 data.

Lab

retro_etel_539 was not experimentally validated.

Homology

Retrocopy orthology:

Echinops telfairi 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 19 parental genes, and 61 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,
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,