RetrogeneDB ID: retro_lafr_493

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_19:35334671..35335070(-)
• Located in intron of: ENSLAFG00000006600

Retrocopy information

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

Parental gene information

• Parental gene symbol: GMFB
• Ensembl ID: ENSLAFG00000004659
• Aliases: None
• Description: None

Sequence

>retro_lafr_493
AGTGATTGTTTGGTGGTTTGTGATGTTGCTGAAGATTTAGTGGAAAAGCTGAGAAAGTTTCATTTTTGCAAAGAAACCAA
CAATGCTGCCATTATAGTGAATACTGACAAAGATAAACGCCTGGTGGTACTGAATGGGGAGCTTGAGGGCCTTTCAGCAG
ATGAACTTAAAGACCAACTACCTGAATGACAACCTCACTTCATTGTTTATAGTTATAAATATCAACATGATGATGAAGTT
TCATGTGCTTTTTTGTCCTTTATTTTCTCCAGTCCTGTTGGATATAAGCCTGAACAACAGATGATGCATGCTGGGAGTAA
GAATAAACTAGTCCAAACAGCTGAACTAACCAAGGTACTTGAAGTAAGAAATACTGAAGGCATAACTGAAGACTGGTTA

Alignment

ORF - retro_lafr_493 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.36 %
• Parental protein coverage: 94.37 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SESLVVCDVAEDLVEKLRKFRFRKETNNAAIIMKIDKDKRLVVLDEELEGISPDELKDELPERQPRTFIV
          S..LVVCDVAEDLVEKLRKF.F.KETNNAAII...DKDKRLVVL..ELEG.S.DELKD.LPE.QP..FIV
Retrocopy SDCLVVCDVAEDLVEKLRKFHFCKETNNAAIIVNTDKDKRLVVLNGELEGLSADELKDQLPE*QPH-FIV

Parental  YSYKYQHDDGRVSYPLCFIFSSPVGCKPEQQMMYAGSKNKLVQTAELTKVFEIRNTEDLTEEWL
          YSYKYQHDD......L.FIFSSPVG.KPEQQMM.AGSKNKLVQTAELTKV.E.RNTE..TE.WL
Retrocopy YSYKYQHDDEVSCAFLSFIFSSPVGYKPEQQMMHAGSKNKLVQTAELTKVLEVRNTEGITEDWL

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_493 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 8 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000007312	1 retrocopy	retro_cjac_736,
Cavia porcellus	ENSCPOG00000004207	1 retrocopy	retro_cpor_240,
Homo sapiens	ENSG00000197045	1 retrocopy	retro_hsap_2818,
Loxodonta africana	ENSLAFG00000004659	1 retrocopy	retro_lafr_493 ,
Macaca mulatta	ENSMMUG00000012326	1 retrocopy	retro_mmul_1498,
Nomascus leucogenys	ENSNLEG00000012717	1 retrocopy	retro_nleu_1197,
Oryctolagus cuniculus	ENSOCUG00000004488	2 retrocopies	retro_ocun_1849, retro_ocun_1881,
Pongo abelii	ENSPPYG00000005830	1 retrocopy	retro_pabe_2209,