RetrogeneDB ID: retro_lafr_1213

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_9:30765401..30765713(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: METTL5
• Ensembl ID: ENSLAFG00000018044
• Aliases: None
• Description: None

Sequence

>retro_lafr_1213
AAGAAATTAAAGTTTAAGGAACTAGAGAGTTGCCTGCAACAAGTAGATGGATTCAAAAAGCCCAAACTACTTCTAGAACA
GTACCTGACCAGGTCGCACATTGCAGCATGTATGCGCTATACAATCCATAACACATATGATGGTGAAAATAAAGTGGTTG
CAGATTTAGGATGTGGTTGTGGAGTGCCTAGCATGGGAAATGCAATGTTAGCAGCAGGGTTGTATGTTGGATTTGACATA
GATGAAGATGCACTGGAAATATTTAATAGGTATGTGGAAGAGTTTGAGTTAACAAATGTTGACGTGGTTCAA

Alignment

ORF - retro_lafr_1213 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 85.71 %
• Parental protein coverage: 50.24 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KKLKLKELESRLQQVDGFEKPKLLLEQYPTRPHIAACMLYTIHNTYDDIENKVVADLGCGCGVLSIGTAM
          KKLK.KELES.LQQVDGF.KPKLLLEQY.TR.HIAACM.YTIHNTYD..ENKVVADLGCGCGV.S.G.AM
Retrocopy KKLKFKELESCLQQVDGFKKPKLLLEQYLTRSHIAACMRYTIHNTYDG-ENKVVADLGCGCGVPSMGNAM

Parental  LGAGLCVGFDIDEDALEIFNRNVEEFELTNVDMVQ
          L.AGL.VGFDIDEDALEIFNR.VEEFELTNVD.VQ
Retrocopy LAAGLYVGFDIDEDALEIFNRYVEEFELTNVDVVQ

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Loxodonta africana was not studied using RNA-Seq expression data.

ChIP-Seq

Loxodonta africana was not studied using ChIP-Seq data.

EST

Loxodonta africana was not studied using EST data.

TSS

Loxodonta africana was not studied using FANTOM5 data.

Lab

retro_lafr_1213 was not experimentally validated.

Homology

Retrocopy orthology:

Loxodonta africana 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 27 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012438	1 retrocopy	retro_cfam_1726,
Callithrix jacchus	ENSCJAG00000006777	2 retrocopies	retro_cjac_2282, retro_cjac_729,
Cavia porcellus	ENSCPOG00000003343	1 retrocopy	retro_cpor_373,
Dasypus novemcinctus	ENSDNOG00000013460	2 retrocopies	retro_dnov_1043, retro_dnov_773,
Homo sapiens	ENSG00000138382	2 retrocopies	retro_hsap_1365, retro_hsap_2930,
Gorilla gorilla	ENSGGOG00000022484	2 retrocopies	retro_ggor_1064, retro_ggor_2032,
Loxodonta africana	ENSLAFG00000018044	2 retrocopies	retro_lafr_1213 , retro_lafr_864,
Macaca mulatta	ENSMMUG00000023054	3 retrocopies	retro_mmul_1430, retro_mmul_1953, retro_mmul_2193,
Nomascus leucogenys	ENSNLEG00000005018	4 retrocopies	retro_nleu_1070, retro_nleu_1919, retro_nleu_753, retro_nleu_990,
Oryctolagus cuniculus	ENSOCUG00000010405	1 retrocopy	retro_ocun_1440,
Pongo abelii	ENSPPYG00000012916	2 retrocopies	retro_pabe_2281, retro_pabe_2523,
Pan troglodytes	ENSPTRG00000012621	3 retrocopies	retro_ptro_1822, retro_ptro_2062, retro_ptro_938,
Tursiops truncatus	ENSTTRG00000002154	2 retrocopies	retro_ttru_251, retro_ttru_38,