RetrogeneDB ID: retro_etel_1754

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_292056:4827..5292(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL11
• Ensembl ID: ENSETEG00000015216
• Aliases: None
• Description: mitochondrial ribosomal protein L11 [Source:HGNC Symbol;Acc:14042]

Sequence

>retro_etel_1754
CCAATCCTGGGTCAGCGAGGCATTTCCATCAACCAGTACTGCAAGGACTTCAATGAGATGACAGACATCAAAGAAGGCAT
CCTTCTGCCTACCAATATTTTTGTGAAACCACGCAGGACATATGAATTCAAGGTTGGCTAATCCACCGTTTCCTACTTTC
TGAAGGCAGCTGCTGAGACTGAGAAGGGACCCCGGAACACAGACAAAGTGGTGGCAGACCTGGTGACCTTGAAGCTCGTA
TATGAGATTTCCTGAGTCAAAGCTCAGGAGGACGCCTTTGGCCTGTAGGATGTGGCCTTGTCCTCCGTTGTCTGTTCCCT
CATCGGCTCAGATCGGTCTCTGGGCATCTGAGTGGTGAAGGACCTCAGTTCCGAGGAGCTGGAAGCATTCCAGAAGGAGT
GAGTTATGTTCCTGGCTGCTCAGAAACAGGCAGACTTGTCAGCCTAGGCAGAAGCTGTCAAGAAG

Alignment

ORF - retro_etel_1754 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.79 %
• Parental protein coverage: 81.15 %
• Number of stop codons detected: 6
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  PILGQRGVSINQFCKEFNEKTKDLKEGIPLPTKIFVKPDRTFEFKIGQPTVSYFLKAAAGIEKGARETGK
          PILGQRG.SINQ.CK.FNE.T.D.KEGI.LPT.IFVKP.RT.EFK.G..TVSYFLKAAA..EKG.R.T.K
Retrocopy PILGQRGISINQYCKDFNEMT-DIKEGILLPTNIFVKPRRTYEFKVG*STVSYFLKAAAETEKGPRNTDK

Parental  EVTGM-TLKHVYEIAQVKAQDDAFALQNVPLSSVVRSIIGSARSLGIRVVKDLSSEELAAFQKERAVFLA
          .V....TLK.VYEI..VKAQ.DAF.L..V.LSSVV.S.IGS.RSLGI.VVKDLSSEEL.AFQKE...FLA
Retrocopy VVADLVTLKLVYEIS*VKAQEDAFGL*DVALSSVVCSLIGSDRSLGI*VVKDLSSEELEAFQKE*VMFLA

Parental  AQKEADLAAQEEAAKK
          AQK.ADL.A..EA.KK
Retrocopy AQKQADLSA*AEAVKK

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_1754 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 15 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012706	1 retrocopy	retro_cfam_761,
Callithrix jacchus	ENSCJAG00000001470	1 retrocopy	retro_cjac_803,
Dasypus novemcinctus	ENSDNOG00000004111	2 retrocopies	retro_dnov_1607, retro_dnov_566,
Echinops telfairi	ENSETEG00000015216	2 retrocopies	retro_etel_1754 , retro_etel_333,
Homo sapiens	ENSG00000174547	1 retrocopy	retro_hsap_3390,
Gorilla gorilla	ENSGGOG00000001300	1 retrocopy	retro_ggor_2296,
Myotis lucifugus	ENSMLUG00000004047	1 retrocopy	retro_mluc_2131,
Mus musculus	ENSMUSG00000024902	1 retrocopy	retro_mmus_2118,
Nomascus leucogenys	ENSNLEG00000006111	1 retrocopy	retro_nleu_1705,
Otolemur garnettii	ENSOGAG00000010448	2 retrocopies	retro_ogar_1143, retro_ogar_3159,
Pongo abelii	ENSPPYG00000003025	1 retrocopy	retro_pabe_2786,
Pan troglodytes	ENSPTRG00000003924	1 retrocopy	retro_ptro_2305,
Ictidomys tridecemlineatus	ENSSTOG00000025971	1 retrocopy	retro_itri_941,
Tarsius syrichta	ENSTSYG00000008712	1 retrocopy	retro_tsyr_1095,
Tursiops truncatus	ENSTTRG00000002678	1 retrocopy	retro_ttru_431,