RetrogeneDB ID: retro_etel_438

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_7165:196818..197334(-)
• Located in intron of: ENSETEG00000011652

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL18
• Ensembl ID: ENSETEG00000007591
• Aliases: None
• Description: mitochondrial ribosomal protein L18 [Source:HGNC Symbol;Acc:14477]

Sequence

>retro_etel_438
TGGGCATTGTTGCCTGTTTGCGGGAACCCTAAGCGTGGATGTGCGGCCCTCTCAACCAGTTCCCAGCCAGCAACGGATCC
TGAAGTGGCCCCTGTGGATAACGAAGCTGTTGCCCCCAAGTTTCCAAACTGGAATCCCCGGAACCTGGAGCTCTTGGCAG
TAGCGAGGAAAGAAGGAGGTTGGGGAGCAGTGTGACCCTCTGGGACTTCTGGCCCAGATTGCGAGTTATAAGGACTCAAC
ATCATGTGGAAGCATTTGTTGAGCATCGAAATGGCAAGATTGTGGTTTCTGCATCCTCTCGTGAATGGGCTATTAAAAAG
CACCTGTATCGGACCACCAAGGTGGTGGCCTGTGAGAGTGTAGGGAAAATACTGGCAGCGCGTGCTTATGGGCAGGAATC
GATTTCATGGTCTACCAGTCCACCCTTGGGAGGCAGCGTTAGACTCGATCCAGGGACTGCAAAATGCTCTGACAGAAGGT
GGTGCGATGCTAGAGGAACCGCGAAGAATCTCTCAG

Alignment

ORF - retro_etel_438 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.82 %
• Parental protein coverage: 96.11 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  WALLSVCRNPERGCAALSTCSQPARNPEVDPVHNEAVAPEFTNRNPRNLELLAVARKERGWGTVWPSR-E
          WALL.VC.NP.RGCAALST.SQPA..PEV.PV.NEAVAP.F.N.NPRNLELLAVARKE.GWG.V.PS...
Retrocopy WALLPVCGNPKRGCAALSTSSQPATDPEVAPVDNEAVAPKFPNWNPRNLELLAVARKEGGWGAV*PSG<D

Parental  FWHRLRVIRTQHHVEAFVEHRNGKIVVSASTREWAIKKHLYRTTNVVACESVGKILAER-CLRAGINFMV
          FW.RLRVIRTQHHVEAFVEHRNGKIVVSAS.REWAIKKHLYRTT.VVACESVGKILA.R.CL.AGI.FMV
Retrocopy FWPRLRVIRTQHHVEAFVEHRNGKIVVSASSREWAIKKHLYRTTKVVACESVGKILAAR<CLWAGIDFMV

Parental  YQPT-PWEAASDSIQRLQNAMTEGGVTLEEPRRIYQ
          YQ.T.PWEAA.DSIQ.LQNA.TEGG..LEEPRRI.Q
Retrocopy YQST<PWEAALDSIQGLQNALTEGGAMLEEPRRISQ

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_438 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 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000015398	1 retrocopy	retro_amel_1445,
Dipodomys ordii	ENSDORG00000011514	1 retrocopy	retro_dord_741,
Echinops telfairi	ENSETEG00000007591	1 retrocopy	retro_etel_438 ,
Homo sapiens	ENSG00000112110	1 retrocopy	retro_hsap_1664,
Gorilla gorilla	ENSGGOG00000014075	1 retrocopy	retro_ggor_1255,
Macaca mulatta	ENSMMUG00000017037	1 retrocopy	retro_mmul_61,
Mus musculus	ENSMUSG00000057388	1 retrocopy	retro_mmus_1940,
Otolemur garnettii	ENSOGAG00000007327	1 retrocopy	retro_ogar_1660,
Pongo abelii	ENSPPYG00000017147	3 retrocopies	retro_pabe_1416, retro_pabe_1418, retro_pabe_1421,
Pan troglodytes	ENSPTRG00000018761	1 retrocopy	retro_ptro_1128,
Pteropus vampyrus	ENSPVAG00000005322	2 retrocopies	retro_pvam_1480, retro_pvam_252,
Tarsius syrichta	ENSTSYG00000005598	1 retrocopy	retro_tsyr_1847,