RetrogeneDB ID: retro_lafr_901

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_46:17092912..17093369(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF5A2
• Ensembl ID: ENSLAFG00000013225
• Aliases: None
• Description: None

Sequence

>retro_lafr_901
GATAAAATTGATTTCACTACTGGAGATGCTGGGGCTTCTACCACTTACCCTATGCAGCACTCAGCCCTGCGCAAAAAACG
GCTTGGTGGTGCTCAGAGGATGACCATGCAAAATAGTGCAGATGTCCACTTCCAAAACTGGAAAGCACAGTAATGCCAAG
GTTCGCCTTGTTGGAATTGATATTTTCACATGGAAAAAGCATGAAGATATTTGCCCTTCTACTTAAAACCTGGATATTGC
AAATATTAAAACAAATGGTTATCATCTGATACGCATTCAGGGTGGTTACCTTTCCCTGCTGACAGAAACTGGTGATGTTT
ATGAGGCTCTTAAGTTGCTAGAAGGTGACCTAGGCAATGAGATAGAAGGGAAATACAATTCAGGTAAAGGTGTACAGATG
TCTGTAACATGTGCAGTGAGTGAAGAATAAATAGGCTGTAGTCATAAGCCCTGCAAA

Alignment

ORF - retro_lafr_901 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.2 %
• Parental protein coverage: 98.69 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  EEIDFTTGDAGASSTYPMQCSALRK-NGFVVLKGRPCKIVDMSTSKTGKHGHAKVHLVGIDIFTGKKYED
          ..IDFTTGDAGAS.TYPMQ.SALRK.NG.VVL.G.PCKIV.MSTSKTGKH..AKV.LVGIDIFT.KK.ED
Retrocopy DKIDFTTGDAGASTTYPMQHSALRK>NGLVVLRG*PCKIVQMSTSKTGKHSNAKVRLVGIDIFTWKKHED

Parental  ICPSTHNMDVPNIKRNDYQLICIQDGYLSLLTETGEVREDLKLPEGELGKEIEGKYNAGEDVQVSVMCAM
          ICPST.N.D..NIK.N.Y.LI.IQ.GYLSLLTETG.V.E.LKL.EG.LG.EIEGKYN.G..VQ.SV.CA.
Retrocopy ICPST*NLDIANIKTNGYHLIRIQGGYLSLLTETGDVYEALKLLEGDLGNEIEGKYNSGKGVQMSVTCAV

Parental  SEE-YAVAIKPCK
          SEE......KPCK
Retrocopy SEE*IGCSHKPCK

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_901 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000005363	1 retrocopy	retro_chof_1016,
Cavia porcellus	ENSCPOG00000012594	1 retrocopy	retro_cpor_1060,
Dasypus novemcinctus	ENSDNOG00000014801	2 retrocopies	retro_dnov_1133, retro_dnov_268,
Homo sapiens	ENSG00000163577	1 retrocopy	retro_hsap_1591,
Loxodonta africana	ENSLAFG00000013225	1 retrocopy	retro_lafr_901 ,
Macropus eugenii	ENSMEUG00000007473	2 retrocopies	retro_meug_1619, retro_meug_641,
Nomascus leucogenys	ENSNLEG00000005292	1 retrocopy	retro_nleu_1762,
Oryctolagus cuniculus	ENSOCUG00000016657	1 retrocopy	retro_ocun_65,
Pongo abelii	ENSPPYG00000014294	2 retrocopies	retro_pabe_1308, retro_pabe_1640,
Pan troglodytes	ENSPTRG00000015621	1 retrocopy	retro_ptro_1070,
Ictidomys tridecemlineatus	ENSSTOG00000008130	2 retrocopies	retro_itri_1400, retro_itri_689,