RetrogeneDB ID: retro_lafr_426

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_16:17692966..17693467(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPS24
• Ensembl ID: ENSLAFG00000011905
• Aliases: None
• Description: None

Sequence

>retro_lafr_426
ATGGCCACACCTGTGTGCAGTGGGGCATGCCGGCTGTGAGTCCTGGCTGGAAGCCAAGAGCTGCTGTGTGCCTGGTGTGC
CCTGCACGCTTGCTCAGCCTGCAATAAGAACCCAGCAGCCTGAGTCCATGTGGGCAAAAGCGACAAGCCAGTGAAGTAGG
AGGAGGCACACGGCCCACGCTACATTGCCCACTACAAGGGCTGGCTGTTGCTGCACACAGGTGACCTGGATGAGGAGAAC
CACACTGCAGCCCAAACAGTGGAAGAAATCTCCCTTTGCAAGTTCATGCTCGGAATCTTCCCAGGCTGCCTGGCTGACCA
GCTGATCCTAAAGCATTAGGCTAACCAGGCGAAGACCTGTGCCCTGGTGCTGAGACATCTGCCTGCCCCGAAGTTCTACT
TCCTTGTGGGCTCCAGTGAAACTCTGCGGTCCCACTTTTACAAGTGTCCTGTGCTTCTGCACCTCTAAACTGTGCCCTCA
AAGGTGGTGTATAAGTACATC

Alignment

ORF - retro_lafr_426 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.86 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAAPVCGGGFRLRVLAGSRQLLCAWRALHTSSAWAKNRAARVRVGKGDKPVTYGEAHAPHYIAHRKGWLS
          MA.PVC.G..RL.VLAGS..LLCAW.ALH..SA..KN.AA.V.VGK.DKPV...EAH.P.YIAH.KGWL.
Retrocopy MATPVCSGACRL*VLAGSQELLCAWCALHACSACNKNPAA*VHVGKSDKPVK*EEAHGPRYIAHYKGWLL

Parental  LHTGNLDGEDHAAARTVEDVFLRKFMWGTFPGCLADQVILKRRANQLEICALVLRQLPAHKFYFLVGYSE
          LHTG.LD.E.H.AA.TVE...L.KFM.G.FPGCLADQ.ILK..ANQ...CALVLR.LPA.KFYFLVG.SE
Retrocopy LHTGDLDEENHTAAQTVEEISLCKFMLGIFPGCLADQLILKH*ANQAKTCALVLRHLPAPKFYFLVGSSE

Parental  TLLSHFYKCPVRLHLQTVPSKVVYKYL
          TL.SHFYKCPV.LHL.TVPSKVVYKY.
Retrocopy TLRSHFYKCPVLLHL*TVPSKVVYKYI

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_426 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
Ailuropoda melanoleuca	ENSAMEG00000017491	1 retrocopy	retro_amel_1126,
Bos taurus	ENSBTAG00000007398	1 retrocopy	retro_btau_411,
Choloepus hoffmanni	ENSCHOG00000003106	1 retrocopy	retro_chof_2334,
Dasypus novemcinctus	ENSDNOG00000016853	3 retrocopies	retro_dnov_1195, retro_dnov_153, retro_dnov_2049,
Echinops telfairi	ENSETEG00000016782	1 retrocopy	retro_etel_1350,
Homo sapiens	ENSG00000062582	1 retrocopy	retro_hsap_836,
Gorilla gorilla	ENSGGOG00000005692	1 retrocopy	retro_ggor_687,
Loxodonta africana	ENSLAFG00000011905	1 retrocopy	retro_lafr_426 ,
Macaca mulatta	ENSMMUG00000002405	1 retrocopy	retro_mmul_1089,
Monodelphis domestica	ENSMODG00000013889	1 retrocopy	retro_mdom_1785,
Pan troglodytes	ENSPTRG00000019127	1 retrocopy	retro_ptro_583,
Pteropus vampyrus	ENSPVAG00000015911	4 retrocopies	retro_pvam_1129, retro_pvam_1360, retro_pvam_180, retro_pvam_978,
Tursiops truncatus	ENSTTRG00000002938	1 retrocopy	retro_ttru_1860,