RetrogeneDB ID: retro_etel_1543

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_277735:4637..4915(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: POLR3K
• Ensembl ID: ENSETEG00000009989
• Aliases: None
• Description: polymerase (RNA) III (DNA directed) polypeptide K, 12.3 kDa [Source:HGNC Symbol;Acc:14121]

Sequence

>retro_etel_1543
ATGCTGCTCTTCTGCATGAGCTATGGCAACGCACTGATCATGGAGGAAGGCCGGCACTGTCACCACTTCGCCTGCAACAC
CTGTCCCTACGTGCACAGCATCAACCTAAAGATGACAACCCAGAAGTATCCCAAGCTGAAAGAAGTGGATGATGTGCTTG
GAGGAGCAGCTCCCTGAAAGAATGTAGACTCCCCTGCAGAGCCATGTCCTGAATGGGAGAATCCCTGAGCCTATTCATGC
AGCTGCAGACCTGCTCTGCCGATGAGCTAGTGACCACT

Alignment

ORF - retro_etel_1543 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.4 %
• Parental protein coverage: 86.11 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MLLFCPGCGNGLIVEEGQRCHRFACNTCPYVHNITRKVTTRKYPKLKEVDDVLGGAAAWENVDSTAEPCP
          MLLFC...GN.LI.EEG..CH.FACNTCPYVH.I..K.TT.KYPKLKEVDDVLGGAA...NVDS.AEPCP
Retrocopy MLLFCMSYGNALIMEEGRHCHHFACNTCPYVHSINLKMTTQKYPKLKEVDDVLGGAAP*KNVDSPAEPCP

Parental  KCEHPRAY-FMQLQTRSADEPMTT
          ..E.P.AY.FMQLQT.SADE..TT
Retrocopy EWENP*AY<FMQLQTCSADELVTT

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_1543 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 11 parental genes, and 16 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000019715	1 retrocopy	retro_cfam_1881,
Callithrix jacchus	ENSCJAG00000011568	1 retrocopy	retro_cjac_2660,
Echinops telfairi	ENSETEG00000009989	2 retrocopies	retro_etel_1166, retro_etel_1543 ,
Felis catus	ENSFCAG00000009110	2 retrocopies	retro_fcat_1978, retro_fcat_409,
Homo sapiens	ENSG00000161980	1 retrocopy	retro_hsap_1861,
Myotis lucifugus	ENSMLUG00000015593	3 retrocopies	retro_mluc_1565, retro_mluc_1943, retro_mluc_341,
Oryctolagus cuniculus	ENSOCUG00000013608	1 retrocopy	retro_ocun_145,
Otolemur garnettii	ENSOGAG00000002526	2 retrocopies	retro_ogar_1101, retro_ogar_254,
Pan troglodytes	ENSPTRG00000007525	1 retrocopy	retro_ptro_1241,
Pteropus vampyrus	ENSPVAG00000000530	1 retrocopy	retro_pvam_928,
Sus scrofa	ENSSSCG00000007970	1 retrocopy	retro_sscr_1141,