RetrogeneDB ID: retro_etel_574

Retrocopy location

• Organism: Lesser hedgehog tenrec (Echinops telfairi)
• Coordinates: GeneScaffold_9121:46302..46763(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MALSU1
• Ensembl ID: ENSETEG00000015566
• Aliases: None
• Description: mitochondrial assembly of ribosomal large subunit 1 [Source:HGNC Symbol;Acc:21721]

Sequence

>retro_etel_574
GAGTCGGGCGCTGCAGATCACACTAGGGCCAAGTTTGACCTCGATATGCTGGTTTCACTTCTGAGGCAAGAAAACGCCAG
AGGCATTTGTGTCATCAGCGTTCCTCCCAAGATGAAATATACAGATTATTTTGTGATTGGGAGGGGCACCTCGACCCGAC
ATTTGCACGCCATGCCCACTACCTTGTGAAAATGCATAAGTTCTCGAAGTGTCAAAAGGACCCTTACGTTAAGATAGAGG
GGAAGGACACCGAGGACTGGCTCTGCATGGACTTCGGCAGCACGGTGCTCCACTTGATGCTTACAGAAACCAGAGAAACC
TACGAATTAGAGAAGCTATGGACCCTACGCTCTTATGATGACCAGTTAGCTCAGATCGCACCTGAGACGTTACCTGAAGA
CTTCATTCTTGGATTAGAAGACGATGCTTCATCCCTGACTCCAGTGGAGTTCAAATGTGAA

Alignment

ORF - retro_etel_574 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.48 %
• Parental protein coverage: 70.64 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  ESGTADHTRAKFDLDMLVSLLRQENARDICVISVPPEMKYTDYFVIGSGTSTRHLHAM-AHYLVKMHKFL
          ESG.ADHTRAKFDLDMLVSLLRQENAR.ICVISVPP.MKYTDYFVIG.GTSTRHLHAM.AHYLVKMHKF.
Retrocopy ESGAADHTRAKFDLDMLVSLLRQENARGICVISVPPKMKYTDYFVIGRGTSTRHLHAM<AHYLVKMHKFS

Parental  KCQKDPYVKIEGKDTEDWLCMDFGSMVLHLMLTETRETYELEKLWTLRSYDDQLAQIAPETLPEDFILGL
          KCQKDPYVKIEGKDTEDWLCMDFGS.VLHLMLTETRETYELEKLWTLRSYDDQLAQIAPETLPEDFILGL
Retrocopy KCQKDPYVKIEGKDTEDWLCMDFGSTVLHLMLTETRETYELEKLWTLRSYDDQLAQIAPETLPEDFILGL

Parental  EDDASSLTPVEFKCE
          EDDASSLTPVEFKCE
Retrocopy EDDASSLTPVEFKCE

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_574 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 7 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000002338	1 retrocopy	retro_chof_1878,
Equus caballus	ENSECAG00000016105	1 retrocopy	retro_ecab_884,
Echinops telfairi	ENSETEG00000015566	1 retrocopy	retro_etel_574 ,
Loxodonta africana	ENSLAFG00000011921	1 retrocopy	retro_lafr_538,
Oryctolagus cuniculus	ENSOCUG00000008972	1 retrocopy	retro_ocun_621,
Otolemur garnettii	ENSOGAG00000017157	1 retrocopy	retro_ogar_2324,
Tursiops truncatus	ENSTTRG00000008920	1 retrocopy	retro_ttru_1715,