RetrogeneDB ID: retro_etel_1468

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_270982:3154..3456(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHOQ
• Ensembl ID: ENSETEG00000019234
• Aliases: None
• Description: ras homolog family member Q [Source:HGNC Symbol;Acc:17736]

Sequence

>retro_etel_1468
AACCCAGTCTCATTCCAAAGGGTGAAAGCGGAGTGGGTACCCAACCTTCAGGGATAGGCATCAAATGTAGCTTTTGATTA
ATAGGAACCCAGGATGATCTCTGAGATGACCCCAAAACTTGAGCCAGACAGAATGATATGAAAGTAAAACTTCCATGGGG
GGAACTTCCAGGACAGAAACTAGCCAAAGAGCCAGGAGCACACCGCTGTACAGAATGTTCACCTTTAACCCAAAAGGGAT
GGAAGGCAGTTTTTAATGAGGCTCTCAGAGCCATTTTCGCTCCAAAGAAACACACAGTAAAA

Alignment

ORF - retro_etel_1468 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 65.69 %
• Parental protein coverage: 63.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  NPASFQNVKEEWVPELKEYAPNVPFL-LIGTQIDLRDDPKTLARLNDMKEK-PVCVEQGQKLAKEIGACC
          NP.SFQ.VK.EWVP.L...A.NV.F..LIGTQ.DL.DDPKT.AR.NDMK.K.P.....GQKLAKE.GA..
Retrocopy NPVSFQRVKAEWVPNLQG*ASNVAFD<LIGTQDDL*DDPKT*ARQNDMKVKLPWGELPGQKLAKEPGAHR

Parental  YVECSALTQKGLKTVFDEAIIAILTPKKHTVK
          ..ECS.LTQKG.K.VF.EA..AI..PKKHTVK
Retrocopy CTECSPLTQKGWKAVFNEALRAIFAPKKHTVK

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_1468 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 12 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000006082	1 retrocopy	retro_amel_383,
Choloepus hoffmanni	ENSCHOG00000000549	3 retrocopies	retro_chof_2030, retro_chof_457, retro_chof_914,
Erinaceus europaeus	ENSEEUG00000015226	1 retrocopy	retro_eeur_129,
Echinops telfairi	ENSETEG00000004443	1 retrocopy	retro_etel_2010,
Echinops telfairi	ENSETEG00000012902	3 retrocopies	retro_etel_1565, retro_etel_1645, retro_etel_42,
Echinops telfairi	ENSETEG00000019234	3 retrocopies	retro_etel_1468 , retro_etel_596, retro_etel_672,
Felis catus	ENSFCAG00000015608	1 retrocopy	retro_fcat_795,
Myotis lucifugus	ENSMLUG00000001567	1 retrocopy	retro_mluc_595,
Pteropus vampyrus	ENSPVAG00000013691	1 retrocopy	retro_pvam_611,
Rattus norvegicus	ENSRNOG00000015415	1 retrocopy	retro_rnor_473,
Sus scrofa	ENSSSCG00000008439	1 retrocopy	retro_sscr_102,
Tursiops truncatus	ENSTTRG00000011892	1 retrocopy	retro_ttru_805,