RetrogeneDB ID: retro_lafr_1102

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_7:80650620..80651434(+)
• Located in intron of: ENSLAFG00000005066

Retrocopy information

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

Parental gene information

• Parental gene symbol: WDR12
• Ensembl ID: ENSLAFG00000011955
• Aliases: None
• Description: None

Sequence

>retro_lafr_1102
AAAAATAGTAATTTGTCTTGCTTACTACTGAGTGCCTCTATGGATCCAACTATTCTCTTACAGGAGTGGAATATAGAGAG
AAACAAAATGACAGCCCTACACTTCTGCATAGGTCATGCTGGAAGTATGGATTCTATAGCTGTTGATAGTACAGGATCTA
AATTTTGCAGTTCCTGGGATAACATGCTAAAGATCTGGTCTACAGTCCCTACAAATGAAGATGAAACAGGAAGAATACAG
AAATCGATCCAGAAAGAAACAGAAAACAGAGCAGTTAGGACTAACAAAAGGACTCCCATGGTGACCCTCTCTGGCCACAA
GGAAGCAATTTCTTCAGTTCTATGGTCAGATGCTGAAGAAATCTGCAGTGCATTTTGGGGCCACAAGATTAGAGCGTGGG
ATGTTGAAACTGGCAGTCTCAAGTCAACTCTGACAGGAAATAAAGTTAATTATGTCTTCTATTCACTACTTCGTAAACAT
TTAGCATCTGGGAGCACAGGTAGGCATATCAGACTGTGGGATCCCCTAACTAAAGATGGATCTGTGGTGTTGCTGTCCCT
AACGTCACATACAGGCTGGCTCACAACAGTAAAGTGGTCTACCCATGAGCAGCAGCTGATCTTAGGTTCTTTAGATAACT
ATGTCAAGCTGTGGGGATACAAGAAGTTATAAAGCTCCTCTCTATGATCTCGCTGCTCATGAAGACAAAGTTCTGGGTGT
AGACTAGACAGACACAGGGTTACTTCTGAGTGGAAGAGCAGACAATAAATTATATTCCTACAGATATTCACCTACCACTT
CCCACGTGAGGGCA

Alignment

ORF - retro_lafr_1102 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.9 %
• Parental protein coverage: 64.78 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KKDNLSCLLLSASMDQTILLWEWNIERNKMKALHCCRGHAGSVDSIAVDSTGTKFCSGSWDKMLKIWSTV
          K..NLSCLLLSASMD.TILL.EWNIERNKM.ALH.C.GHAGS.DSIAVDSTG.KFCS.SWD.MLKIWSTV
Retrocopy KNSNLSCLLLSASMDPTILLQEWNIERNKMTALHFCIGHAGSMDSIAVDSTGSKFCS-SWDNMLKIWSTV

Parental  PTDEED--EMEESINRPRKKQKTEQLGLTRTPIVTLSGHKEAISSVLWSDAEEVCSASWDHTIRVWDIET
          PT.E........SI..............T..P.VTLSGHKEAISSVLWSDAEE.CSA.W.H.IR.WD.ET
Retrocopy PTNEDETGRIQKSIQKETENRAVRTNKRT--PMVTLSGHKEAISSVLWSDAEEICSAFWGHKIRAWDVET

Parental  GSLKSTLTGNKVFNCVSYSPLCKRLASGSTDRHIRLWDPRSKDGSLVSLSLTSHTGWVTSVKWSPTHEQQ
          GSLKSTLTGNKV.N.V.YS.L.K.LASGST.RHIRLWDP..KDGS.V.LSLTSHTGW.T.VKWS.THEQQ
Retrocopy GSLKSTLTGNKV-NYVFYSLLRKHLASGSTGRHIRLWDPLTKDGSVVLLSLTSHTGWLTTVKWS-THEQQ

Parental  LISGSLDNYVKLW-DTRSCKAPLYDLAAHEDKVLGVDWTDSGLLLSGGADNKLYSYRYSPTTSHVGA
          LI.GSLDNYVKLW.DTRS.KAPLYDLAAHEDKVLGVD.TD.GLLLSG.ADNKLYSYRYSPTTSHV.A
Retrocopy LILGSLDNYVKLW>DTRSYKAPLYDLAAHEDKVLGVD*TDTGLLLSGRADNKLYSYRYSPTTSHVRA

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_1102 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000012519	1 retrocopy	retro_cfam_1759,
Choloepus hoffmanni	ENSCHOG00000013851	1 retrocopy	retro_chof_118,
Callithrix jacchus	ENSCJAG00000005171	1 retrocopy	retro_cjac_2690,
Cavia porcellus	ENSCPOG00000008824	1 retrocopy	retro_cpor_1107,
Homo sapiens	ENSG00000138442	1 retrocopy	retro_hsap_1615,
Gorilla gorilla	ENSGGOG00000026073	1 retrocopy	retro_ggor_1222,
Loxodonta africana	ENSLAFG00000011955	1 retrocopy	retro_lafr_1102 ,
Mus musculus	ENSMUSG00000026019	3 retrocopies	retro_mmus_1394, retro_mmus_2649, retro_mmus_2897,
Nomascus leucogenys	ENSNLEG00000007018	1 retrocopy	retro_nleu_2743,
Pongo abelii	ENSPPYG00000013089	1 retrocopy	retro_pabe_1327,
Pan troglodytes	ENSPTRG00000012823	1 retrocopy	retro_ptro_1083,
Tursiops truncatus	ENSTTRG00000001231	1 retrocopy	retro_ttru_1380,