RetrogeneDB ID: retro_etel_1830

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_304529:3086..3342(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HYPK
• Ensembl ID: ENSETEG00000007464
• Aliases: None
• Description: huntingtin interacting protein K [Source:HGNC Symbol;Acc:18418]

Sequence

>retro_etel_1830
CCAAAAAGGCCTTGGAAGCCTTATAGGGGGGCAGCAGACCTGAAGGGAGACACTGACTATGCAGAGAAGAAGGAGATCCA
GAGTTCCGACCTGGAGAGGGCCAAGTCCATGACTGGAGACAGACGAAACGGGATAGAAAGCCTAACTGGGACAGGAGAAG
GAACTAGCAAAAGACACCATCGGAAAGGAAGCTCTGGAGCTGATCATGACAGCAGTGGAGATCGCCAGAGCAACAGCAGA
GCGGAGCTTGCAGGAA

Alignment

ORF - retro_etel_1830 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 61.87 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  PEKPRKHDSGAADLERVTDYAEEKEIQSSNLETAMSVIGDRRS-REQKAKQER-EKELAKVTIKKEDLEL
          P..P.K...GAADL...TDYAE.KEIQSS.LE.A.S..GDRR..R..K....R.EKELAK.TI.KE.LEL
Retrocopy PKRPWKPYRGAADLKGDTDYAEKKEIQSSDLERAKSMTGDRRN<RDRKPNWDR<EKELAKDTIGKEALEL

Parental  IMTEMEISRAAAERSLRE
          IMT..EI.RA.AERSL.E
Retrocopy IMTAVEIARATAERSLQE

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_1830 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 13 parental genes, and 19 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002541	2 retrocopies	retro_cjac_1352, retro_cjac_748,
Echinops telfairi	ENSETEG00000007464	3 retrocopies	retro_etel_1504, retro_etel_1616, retro_etel_1830 ,
Gorilla gorilla	ENSGGOG00000014809	1 retrocopy	retro_ggor_2557,
Macropus eugenii	ENSMEUG00000013059	1 retrocopy	retro_meug_1583,
Monodelphis domestica	ENSMODG00000017744	2 retrocopies	retro_mdom_26, retro_mdom_306,
Nomascus leucogenys	ENSNLEG00000005454	1 retrocopy	retro_nleu_2150,
Oryctolagus cuniculus	ENSOCUG00000001161	2 retrocopies	retro_ocun_1395, retro_ocun_967,
Otolemur garnettii	ENSOGAG00000010201	1 retrocopy	retro_ogar_1064,
Pongo abelii	ENSPPYG00000006424	1 retrocopy	retro_pabe_3108,
Pan troglodytes	ENSPTRG00000038721	1 retrocopy	retro_ptro_2582,
Rattus norvegicus	ENSRNOG00000015703	1 retrocopy	retro_rnor_2477,
Ictidomys tridecemlineatus	ENSSTOG00000006916	2 retrocopies	retro_itri_1861, retro_itri_1864,
Tursiops truncatus	ENSTTRG00000003726	1 retrocopy	retro_ttru_1499,