RetrogeneDB ID: retro_lafr_1158

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_8:21880713..21881143(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ENOPH1
• Ensembl ID: ENSLAFG00000008619
• Aliases: None
• Description: None

Sequence

>retro_lafr_1158
AGAGTGGCATTCACAGCTAGAGGCATGATAGCAGAGTTCTTTGAAGATGTAGTTCCAGCAGTCAGGAAATGGAAAGAGGC
TGGAATGAAGGCGTATATCTATTTTTTGGTAAGTATAGAGACACAGAAACTATTATTTGGGCATTCCACAGAGGGTGTTA
TTTTTGAGATTTTTGATGGTCACCTTGATACCAAGATTGGACACAGAGTGGAGACTGAGAGTTATGGGAAGATTGCAAAC
AGCGCCGATTGCTTAACCCACATCCTGTTTCTGACAGACGTTACTGTAGAGGTCAGTGCTGCCGAGGAAGTGGACATGCA
AGTAGCTGTGGTGGTGGTGAGGCTGGGAAATGTGGGACTAACTGATAACGAAAAGACTTAACTACAGCCTCATCACATCC
TTCAGCAAGCTCTACCTGCCTGCCTCAACC

Alignment

ORF - retro_lafr_1158 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.17 %
• Parental protein coverage: 54.79 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  RAAFTAGLMKAEFFEDVVPAVRKWREAGMKVYIYSSGSVEAQKLLFGHSTEGDILELFDGHFDTKIGHKV
          R.AFTA..M.AEFFEDVVPAVRKW.EAGMK.YIY...S.E.QKLLFGHSTEG.I.E.FDGH.DTKIGH.V
Retrocopy RVAFTARGMIAEFFEDVVPAVRKWKEAGMKAYIYFLVSIETQKLLFGHSTEGVIFEIFDGHLDTKIGHRV

Parental  ESESYRKIANSIGCSTNNILFLTDVTLEASAAEEAEVHVA-VVVRPGNAGLTDDEKT-YYSLITSFSELY
          E.ESY.KIANS..C.T..ILFLTDVT.E.SAAEE....VA.VVVR.GN.GLTD.EKT..YSLITSFS.LY
Retrocopy ETESYGKIANSADCLT-HILFLTDVTVEVSAAEEVDMQVAVVVVRLGNVGLTDNEKT>NYSLITSFSKLY

Parental  LPAST
          LPAST
Retrocopy LPAST

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_1158 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 15 parental genes, and 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005140	2 retrocopies	retro_amel_1186, retro_amel_930,
Choloepus hoffmanni	ENSCHOG00000003283	4 retrocopies	retro_chof_2150, retro_chof_470, retro_chof_486, retro_chof_596,
Callithrix jacchus	ENSCJAG00000015251	2 retrocopies	retro_cjac_1376, retro_cjac_2375,
Equus caballus	ENSECAG00000019612	1 retrocopy	retro_ecab_164,
Erinaceus europaeus	ENSEEUG00000004274	1 retrocopy	retro_eeur_563,
Homo sapiens	ENSG00000145293	1 retrocopy	retro_hsap_2900,
Gorilla gorilla	ENSGGOG00000003719	1 retrocopy	retro_ggor_2010,
Loxodonta africana	ENSLAFG00000008619	1 retrocopy	retro_lafr_1158 ,
Macropus eugenii	ENSMEUG00000011458	1 retrocopy	retro_meug_1125,
Myotis lucifugus	ENSMLUG00000014460	1 retrocopy	retro_mluc_2504,
Otolemur garnettii	ENSOGAG00000002502	1 retrocopy	retro_ogar_1549,
Pongo abelii	ENSPPYG00000014887	1 retrocopy	retro_pabe_2399,
Pan troglodytes	ENSPTRG00000016218	1 retrocopy	retro_ptro_1960,
Ictidomys tridecemlineatus	ENSSTOG00000013987	2 retrocopies	retro_itri_1067, retro_itri_1587,
Tursiops truncatus	ENSTTRG00000001800	1 retrocopy	retro_ttru_1231,