RetrogeneDB ID: retro_lafr_1245

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_94:809450..809654(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: UBL5
• Ensembl ID: ENSLAFG00000012892
• Aliases: None
• Description: None

Sequence

>retro_lafr_1245
ATCGAGGTGGTTTGCACCAATCATCTGGGGAAGCAGCTGTCTGTCAAATGCAACATGAATGATACCATCCGGGACACTAA
GAAATGGACGACAGCCCAAACTGGCACCATTGGAACAAGACTGTCCTGAAGAAGTGGTACACCATTTTTAAGGACCACGT
GTGTCTGGGCAAGCTATAGAGATAGAGATGACATGGATATAGAT

Alignment

ORF - retro_lafr_1245 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 64.29 %
• Parental protein coverage: 93.15 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  IEVVCNDRLGKKVRVKCNPDDTIGDLKKLIAAQTGT-RWNKIVLKKWYTIFKDHVCLG-DYEIHDGMNLE
          IEVVC...LGK...VKCN..DTI.D.KK...AQTGT..WNK.VLKKWYTIFKDHVCLG..Y...D.M...
Retrocopy IEVVCTNHLGKQLSVKCNMNDTIRDTKKWTTAQTGT<HWNKTVLKKWYTIFKDHVCLG>SYRDRDDMDID

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_1245 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 22 parental genes, and 49 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000012371	2 retrocopies	retro_amel_1796, retro_amel_314,
Canis familiaris	ENSCAFG00000032630	5 retrocopies	retro_cfam_1482, retro_cfam_1733, retro_cfam_1953, retro_cfam_2125, retro_cfam_801,
Callithrix jacchus	ENSCJAG00000006097	1 retrocopy	retro_cjac_1394,
Dasypus novemcinctus	ENSDNOG00000006384	5 retrocopies	retro_dnov_1858, retro_dnov_196, retro_dnov_2470, retro_dnov_2590, retro_dnov_860,
Dipodomys ordii	ENSDORG00000006499	6 retrocopies	retro_dord_122, retro_dord_124, retro_dord_132, retro_dord_444, retro_dord_514, retro_dord_534,
Homo sapiens	ENSG00000198258	3 retrocopies	retro_hsap_1821, retro_hsap_2798, retro_hsap_3154,
Gorilla gorilla	ENSGGOG00000005999	1 retrocopy	retro_ggor_173,
Loxodonta africana	ENSLAFG00000012892	2 retrocopies	retro_lafr_1245 , retro_lafr_699,
Macropus eugenii	ENSMEUG00000015506	2 retrocopies	retro_meug_300, retro_meug_304,
Myotis lucifugus	ENSMLUG00000027369	2 retrocopies	retro_mluc_1516, retro_mluc_1766,
Macaca mulatta	ENSMMUG00000007877	2 retrocopies	retro_mmul_1437, retro_mmul_1996,
Mus musculus	ENSMUSG00000084786	1 retrocopy	retro_mmus_98,
Oryctolagus cuniculus	ENSOCUG00000029004	2 retrocopies	retro_ocun_1465, retro_ocun_755,
Ochotona princeps	ENSOPRG00000013412	2 retrocopies	retro_opri_228, retro_opri_687,
Pongo abelii	ENSPPYG00000009536	3 retrocopies	retro_pabe_1489, retro_pabe_2226, retro_pabe_2814,
Pan troglodytes	ENSPTRG00000010451	3 retrocopies	retro_ptro_1170, retro_ptro_1895, retro_ptro_2280,
Pteropus vampyrus	ENSPVAG00000008628	1 retrocopy	retro_pvam_1461,
Rattus norvegicus	ENSRNOG00000020442	1 retrocopy	retro_rnor_786,
Sarcophilus harrisii	ENSSHAG00000010974	1 retrocopy	retro_shar_753,
Sus scrofa	ENSSSCG00000023331	2 retrocopies	retro_sscr_544, retro_sscr_608,
Ictidomys tridecemlineatus	ENSSTOG00000005286	1 retrocopy	retro_itri_966,
Tursiops truncatus	ENSTTRG00000008535	1 retrocopy	retro_ttru_166,