RetrogeneDB ID: retro_lafr_758

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_36:11243835..11244210(+)
• Located in intron of: ENSLAFG00000006754

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM96A
• Ensembl ID: ENSLAFG00000011114
• Aliases: None
• Description: None

Sequence

>retro_lafr_758
CGGCAGCTTTAGATCATGGAAAAGAAAGCACTAGTAGCTTACAAATTTATTCAAACTACCTGGGACGCAAAGAAGCCCAA
TACTTTAGGAGAACTGGAAGTGATAACACAAAGTTGAGTGGAGGTTCAGGACATAACTGCAGAAGACTATCTGGTTATTA
TCAGGTTCATGCCAACAGTATCTCATTGCTGTCTGGTGACTCTTACTGGGCTGTGCTTCAAAGTAAAATCTGGGTAAGAG
TTTACCTTTTAAACCTGCATTGAATATCTACATTTCTGAATAAACCCACTCAAAAGGACAAGACTTCAACAAGTAGATAA
ACCACAAGAGTGAGTGGCCTGGACTGGAATGGAGATGCCCAACATACTGGAAATC

Alignment

ORF - retro_lafr_758 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 60.63 %
• Parental protein coverage: 77.5 %
• Number of stop codons detected: 5
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  RQSQIMEEKALEVYDLIRNIRDPEKPNTLEELEVVTESCVEVQEINEDDYLVIIRFTPTVPHCSLATLIG
          RQ..IME.KAL..Y..I....D..KPNTL.ELEV.T.S.VEVQ.I...DYLVIIRF.PTV.HC.L.TL.G
Retrocopy RQL*IMEKKALVAYKFIQTTWDAKKPNTLGELEVITQS*VEVQDITAEDYLVIIRFMPTVSHCCLVTLTG

Parental  LCLRVK-LQRCLPFKHKLEIYISEGTHSTEEDINKQINDK-ERVA-AAMENPNLREI
          LC..VK.L...LPFK..L.IYISE.THS...D.NK.IN.K.E.VA...ME.PN..EI
Retrocopy LCFKVK>LGKSLPFKPALNIYISE*THSKGQDFNK*INHK<E*VAWTGMEMPNILEI

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_758 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 21 parental genes, and 37 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000002448	1 retrocopy	retro_amel_1707,
Bos taurus	ENSBTAG00000002012	2 retrocopies	retro_btau_509, retro_btau_984,
Canis familiaris	ENSCAFG00000017035	2 retrocopies	retro_cfam_1450, retro_cfam_439,
Callithrix jacchus	ENSCJAG00000004834	1 retrocopy	retro_cjac_1751,
Equus caballus	ENSECAG00000010303	1 retrocopy	retro_ecab_364,
Erinaceus europaeus	ENSEEUG00000000854	1 retrocopy	retro_eeur_323,
Felis catus	ENSFCAG00000004178	1 retrocopy	retro_fcat_1379,
Homo sapiens	ENSG00000166797	2 retrocopies	retro_hsap_2763, retro_hsap_522,
Gorilla gorilla	ENSGGOG00000016550	2 retrocopies	retro_ggor_1921, retro_ggor_481,
Loxodonta africana	ENSLAFG00000011114	1 retrocopy	retro_lafr_758 ,
Macropus eugenii	ENSMEUG00000005979	2 retrocopies	retro_meug_471, retro_meug_85,
Microcebus murinus	ENSMICG00000011072	1 retrocopy	retro_mmur_233,
Myotis lucifugus	ENSMLUG00000028233	2 retrocopies	retro_mluc_578, retro_mluc_893,
Mustela putorius furo	ENSMPUG00000000605	1 retrocopy	retro_mputfur_722,
Mus musculus	ENSMUSG00000032381	1 retrocopy	retro_mmus_1919,
Nomascus leucogenys	ENSNLEG00000026932	3 retrocopies	retro_nleu_156, retro_nleu_2577, retro_nleu_667,
Ochotona princeps	ENSOPRG00000015229	5 retrocopies	retro_opri_476, retro_opri_522, retro_opri_828, retro_opri_84, retro_opri_999,
Pongo abelii	ENSPPYG00000006544	1 retrocopy	retro_pabe_224,
Pan troglodytes	ENSPTRG00000007153	2 retrocopies	retro_ptro_1870, retro_ptro_390,
Sorex araneus	ENSSARG00000002068	3 retrocopies	retro_sara_54, retro_sara_597, retro_sara_742,
Tarsius syrichta	ENSTSYG00000004186	2 retrocopies	retro_tsyr_195, retro_tsyr_62,