RetrogeneDB ID: retro_etel_1100

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: scaffold_211428:4348..4747(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSETEG00000004305
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPL8
• Ensembl ID: ENSETEG00000007104
• Aliases: None
• Description: ribosomal protein L8 [Source:HGNC Symbol;Acc:10368]

Sequence

>retro_etel_1100
AGAATCTTGGAGACCGAGGCAAGCTACGCCACTGTCATCTCCCACAGCCCTGAAACCAAGAAAACCCGAGTGAAGGTGCC
CTCGGACTCCAAGAAGATTATCTCCTCTGCCAACAGAGCTGTGGTTGGTGTGGTGGCCGGTGGTGGGCACATAGACAAGC
CCATCCTGAAGGCTGGCCGAGCCTGTCACAAGTACAAGGCCACGAGGAGCTGCTGGCCTTGCGTGCAGGTTGTGGGCACA
AGCCCCGTGGAGCCTCCCTTCGGAGGTGGTCACCACCAGCACATGGCAAGCCCTCCACCCTTTTCAGAGATGCCCCTGCT
GGTCGCAAAGTGGGTCTTCTTGCTGCTTGCTGGACTGGACGGCTCCGGGGGAACCAAGACTGTGCAGGAGAAAGAGAAC

Alignment

ORF - retro_etel_1100 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.3 %
• Parental protein coverage: 51.75 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  KLARASGNYATVISHNPETKKTRVKLPSGSKKVISSANRAVVGVVAGGGRIDKPILKAGRAYHKYKARRN
          ........YATVISH.PETKKTRVK.PS.SKK.ISSANRAVVGVVAGGG.IDKPILKAGRA.HKYKA.R.
Retrocopy RILETEASYATVISHSPETKKTRVKVPSDSKKIISSANRAVVGVVAGGGHIDKPILKAGRACHKYKATRS

Parental  CWPRVRGVTMNPVEHPFGGGNHQHI-GKPSTIRRDAPAGRKVGLIAARRTGRLR-GTKTVQEKEN
          CWP.V..V...PVE.PFGGG.HQH..GKPST..RDAPAGRKVGL.AA..TGRLR.GTKTVQEKEN
Retrocopy CWPCVQVVGTSPVEPPFGGGHHQHM<GKPSTLFRDAPAGRKVGLLAACWTGRLR>GTKTVQEKEN

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_1100 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 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Anolis carolinensis	ENSACAG00000017933	1 retrocopy	retro_acar_31,
Ailuropoda melanoleuca	ENSAMEG00000005395	1 retrocopy	retro_amel_241,
Bos taurus	ENSBTAG00000026327	1 retrocopy	retro_btau_96,
Callithrix jacchus	ENSCJAG00000021388	4 retrocopies	retro_cjac_1109, retro_cjac_1169, retro_cjac_1579, retro_cjac_2047,
Dasypus novemcinctus	ENSDNOG00000009300	2 retrocopies	retro_dnov_2505, retro_dnov_503,
Echinops telfairi	ENSETEG00000007104	4 retrocopies	retro_etel_1100 , retro_etel_264, retro_etel_296, retro_etel_916,
Felis catus	ENSFCAG00000026288	1 retrocopy	retro_fcat_570,
Homo sapiens	ENSG00000161016	1 retrocopy	retro_hsap_2851,
Macaca mulatta	ENSMMUG00000013379	2 retrocopies	retro_mmul_1470, retro_mmul_1531,
Mustela putorius furo	ENSMPUG00000006022	1 retrocopy	retro_mputfur_1517,
Oryctolagus cuniculus	ENSOCUG00000024716	1 retrocopy	retro_ocun_146,
Rattus norvegicus	ENSRNOG00000048523	2 retrocopies	retro_rnor_122, retro_rnor_239,
Tursiops truncatus	ENSTTRG00000013858	1 retrocopy	retro_ttru_1147,