RetrogeneDB ID: retro_lafr_864

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_41:13268126..13268592(+)
• 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_864
AAATGTTTTGCAGATCAAGAGCATCTTTGTGAAGTGTTTAGCATCAGAACTAAAGTGTTAAGAGTTGGGTTGTGTGTTGG
GTTTGATATAGATGAAGTTGTACTGGAAATATTTAATAGAATGTGAAAGAATTAGGCTTTAAAAAAGTTGACATTGTTCA
ATGTGATGTGTGCTTATTATCTAAAAGAAATGTGTAAGTAATTTGATACGGTAGTTAGGAATTCTCCCTTTGGGATCAAA
AATAATAAATGGACAGGTAGTCTTTTCTGATGACTGCTTTGTAAATGGCAAAAAGCAGGAGTACATTCTTTACATAAATT
CTTAACTAGAGAATACATTCAAAAGAAATCTGCAGAATGGAAAATCAAAATAGATATTATCAAGAAGCTGGGACCTTCCA
GCTCCATACCAATCTCATAGAAAGAAGTCAGTGGACATTGAAATGGACATAATTCAATTTCCTTTT

Alignment

ORF - retro_lafr_864 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.26 %
• Parental protein coverage: 75.12 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 5

Retrocopy - Parental Gene Alignment:

Parental  KVVADLGCGCGVLSIGTAMLGAGLCVGFDIDEDALEIFNR-NVEEFELTNVDMVQCDVSSLSNR-MSKSF
          K..AD....C.V.SI.T..L..GLCVGFDIDE..LEIFNR.NV.E.....VD.VQCDV..LS.R.M.K.F
Retrocopy KCFADQEHLCEVFSIRTKVLRVGLCVGFDIDEVVLEIFNR<NVKELGFKKVDIVQCDVCLLSKR>MCK*F

Parental  DTVIMNPPFGTKNNKGTDM-AFLKTALEMART-AVYSLHKSSTREHIQKKAAEWKVKIDI-IAELRYDLP
          DTV..N.PFG.KNNK.T....FL.TAL.MA....V.SLHK..TRE.IQKK.AEW..KI.I.I.....DLP
Retrocopy DTVVRNSPFGIKNNKWTGS<SFLMTAL*MAKS>GVHSLHKFLTREYIQKKSAEW--KIKI>ILSRSWDLP

Parental  ASYKFHKKKSVDIEVDLIRFSF
          A.Y..H.KKSVDIE.D.I.F.F
Retrocopy APYQSHRKKSVDIEMDIIQFPF

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_864 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,