RetrogeneDB ID: retro_lafr_471

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_18:37004719..37005242(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RHEB
• Ensembl ID: ENSLAFG00000000691
• Aliases: None
• Description: None

Sequence

>retro_lafr_471
ATGCCGCAGTCCACCTCCCGAAAGATCACCATTCTGGGCTACTAGTCTGTAGGGAAATCCTTATTGAGGATTAAATTTGT
TGAAGGCCAGTTTGTTGATTCCTATGATCCAACCATAAAAGACACTTTTGCAAAACTGATCACAGGAAATATCATCAACT
GGTGAACACAGCTGGGCAGGATGAATATTCCATCTTTTCCTCAGACATACTCTATAGATATTAAGGGTTATATTCTTGCA
GACTCTGTTACATCAATCAAAAGTTTTAAGTGCCTCAAGTTATCCATAGCAAATTGTTGGATCTGGTGGGGAAAGTTTAA
ATATCTATTATGCTGGTGGGAAATAAAAAAGACCTACATATAGAAAGGGTGATCAATTATGAAGAAAGGAAATTTTAGCA
GAATCTTGGAATGCAGCTTTTTTGGAATCTTCTGCTAAAGAAAATCAGGCTGTTGTGGATGTTTTTAGAAAGATAATTTT
ACAGGCAGAAAAAATTCACAAGACAGCTTCACAAGGAATATCT

Alignment

ORF - retro_lafr_471 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.38 %
• Parental protein coverage: 97.28 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MPQSKSRKIAILGYRSVGKSSLTIQFVEGQFVDSYDPTIENTFTKLITVNGQEYHLQLVDTAGQDEYSIF
          MPQS.SRKI.ILGY.SVGKS.L.I.FVEGQFVDSYDPTI..TF.KLIT.N......QL....G......F
Retrocopy MPQSTSRKITILGY*SVGKSLLRIKFVEGQFVDSYDPTIKDTFAKLITGNIINW*TQL----GRMNIPSF

Parental  PQTYSIDINGYILVYSVTSIKSFEVIK-VIHGKLLDMVGKVQIPIMLVGNKKDLHMERVISYEEGK-ALA
          PQTYSIDI.GYIL..SVTSIKSF...K.VIH.KLLD.VGKV.I.IMLVGNKKDLH.ERVI.YEE.K..LA
Retrocopy PQTYSIDIKGYILADSVTSIKSFKCLK<VIHSKLLDLVGKV*ISIMLVGNKKDLHIERVINYEERK<ILA

Parental  ESWNAAFLESSAKENQTAVDVFRRIILEAEKIDGAASQGKS
          ESWNAAFLESSAKENQ..VDVFR.IIL.AEKI...ASQG.S
Retrocopy ESWNAAFLESSAKENQAVVDVFRKIILQAEKIHKTASQGIS

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_471 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 13 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000031861	1 retrocopy	retro_btau_373,
Callithrix jacchus	ENSCJAG00000020414	1 retrocopy	retro_cjac_1694,
Cavia porcellus	ENSCPOG00000007541	2 retrocopies	retro_cpor_287, retro_cpor_787,
Dasypus novemcinctus	ENSDNOG00000016493	1 retrocopy	retro_dnov_2542,
Homo sapiens	ENSG00000106615	2 retrocopies	retro_hsap_568, retro_hsap_570,
Gorilla gorilla	ENSGGOG00000014675	1 retrocopy	retro_ggor_149,
Loxodonta africana	ENSLAFG00000000691	1 retrocopy	retro_lafr_471 ,
Macropus eugenii	ENSMEUG00000011774	1 retrocopy	retro_meug_172,
Myotis lucifugus	ENSMLUG00000004309	2 retrocopies	retro_mluc_2140, retro_mluc_857,
Mus musculus	ENSMUSG00000028945	1 retrocopy	retro_mmus_1779,
Oryctolagus cuniculus	ENSOCUG00000013173	1 retrocopy	retro_ocun_1309,
Ictidomys tridecemlineatus	ENSSTOG00000004544	2 retrocopies	retro_itri_1251, retro_itri_1357,
Tarsius syrichta	ENSTSYG00000001286	2 retrocopies	retro_tsyr_1174, retro_tsyr_1848,