RetrogeneDB ID: retro_lafr_866

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_41:19031912..19032305(-)
• Located in intron of: ENSLAFG00000017595

Retrocopy information

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

Parental gene information

• Parental gene symbol: EIF4E1B
• Ensembl ID: ENSLAFG00000027919
• Aliases: None
• Description: None

Sequence

>retro_lafr_866
GAAGAGAAGGGGGCTCTGAACTCTTCCAGAGCTTTGCTGCCTCTGGGGAGGAAGAGCCACGATGAGGGCCCCGTGGAGGT
AGCAGAGGTGGAGCTGGAAGTACACCCTGTGCAGAACAGGTGGGCTCTATGGTTCTTCGAGAATGACTTCAGCTGGGCCT
GGCGGGACAACTTGTATCTGGTTACCAAGTCTGACACCGTGAAGAGCTTCTGGGTGATATACAGTCACATCCAGCTGGCC
AGTAAGCTCTCTTCCGGCTGTGACTACACCCTGTTCAAGGATGGCATCCAGCCCATGTGGGAAGACAGCAGGGATAAGAG
GGGTGGCCACTGGCTGGTCAGCCTCACCAAGCACCAGCACTATAGCAAGCTGGACCTTCTCTGGCTGGAGACA

Alignment

ORF - retro_lafr_866 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.15 %
• Parental protein coverage: 72.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  EEKGDPNSITALLPLRRKARDEGPVEAAEVELELHPLQNKWALWFFKNDFSRAWQDNLHLVTKFDTVEDF
          EEKG..NS..ALLPL.RK..DEGPVE.AEVELE.HP.QN.WALWFF.NDFS.AW.DNL.LVTK.DTV..F
Retrocopy EEKGALNSSRALLPLGRKSHDEGPVEVAEVELEVHPVQNRWALWFFENDFSWAWRDNLYLVTKSDTVKSF

Parental  WAMYSHIQLASKLSSGCDYALFKDGIQPMWEDSRNKRGGRWLVSLAKHQRHSKLDLLWLET
          W..YSHIQLASKLSSGCDY.LFKDGIQPMWEDSR.KRGG.WLVSL.KHQ..SKLDLLWLET
Retrocopy WVIYSHIQLASKLSSGCDYTLFKDGIQPMWEDSRDKRGGHWLVSLTKHQHYSKLDLLWLET

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_866 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 9 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000003103	1 retrocopy	retro_btau_1679,
Erinaceus europaeus	ENSEEUG00000005920	1 retrocopy	retro_eeur_414,
Loxodonta africana	ENSLAFG00000027919	1 retrocopy	retro_lafr_866 ,
Monodelphis domestica	ENSMODG00000005097	3 retrocopies	retro_mdom_1779, retro_mdom_47, retro_mdom_710,
Mus musculus	ENSMUSG00000074895	1 retrocopy	retro_mmus_510,
Nomascus leucogenys	ENSNLEG00000012532	1 retrocopy	retro_nleu_84,
Ochotona princeps	ENSOPRG00000008875	2 retrocopies	retro_opri_1088, retro_opri_21,
Tupaia belangeri	ENSTBEG00000001631	2 retrocopies	retro_tbel_3164, retro_tbel_3690,
Drosophila melanogaster	FBgn0035709	1 retrocopy	retro_dmel_68,