RetrogeneDB ID: retro_lafr_999

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_59:4462668..4463258(+)
• Located in intron of: ENSLAFG00000003535

Retrocopy information

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

Parental gene information

• Parental gene symbol: EI24
• Ensembl ID: ENSLAFG00000010888
• Aliases: None
• Description: None

Sequence

>retro_lafr_999
CTTTGGGTGCTTAGCGAAGTTGTCAGTGCTATTTGGTTCCAAGATGTAGCTGATCTAACATCTGAGGTAGCAGGGAGGAA
GCCTCACCCACTCCCTAGTGTCAGCAAAGTAACCACTGAGAAGCTCTTCAGCCTTTTGCTGCAGCATCTTTTCTTTCTCC
CAGGGATGTTTATAAGTCTCTTCCCCACCCATCTTGCTGGTCAGCTCTTAGTCTCCTCATGTGTTCCTTCTGCATTCACT
GGACTGCTTTGAATACCGCTGATTCAATAAGGTAACTGAAACATACCAGTGGCTGTCAGACACAGAAAGGAACGGGACTT
ACTACTTTGGATTGGTTTGCCTTTGGCTTTCCTCACAGCCATGCATTTCTCACACATTATCAGTGGCTGCCTCTTTCCTT
TACTCATTATCAGCACCAATGAAGCAAAGACCCCCTTATTTCAGTTGCGCCTCTATTCCTTGGTGGTCTTCTCAAGCAAC
AGCCTCTTCTACAAGACGGTCTACCTGCAGTCTGCTCTGAGTAGCTCAACCTCTGCAGGAAGTTCCCATCACCACATCCA
TCTCCTGCCAAGCTGAAGGCTGCTGCAGGC

Alignment

ORF - retro_lafr_999 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.38 %
• Parental protein coverage: 58.03 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  LFVLSKVVNAIWFQDIADLAFEVSGRKPHPFPSVSKIIADMLFNLLLQALFLLQGMFVSLFPIHLVGQL-
          L.VLS.VV.AIWFQD.ADL..EV.GRKPHP.PSVSK.....LF.LLLQ.LF.L.GMF.SLFP.HL.GQL.
Retrocopy LWVLSEVVSAIWFQDVADLTSEVAGRKPHPLPSVSKVTTEKLFSLLLQHLFFLPGMFISLFPTHLAGQL<

Parental  VSLL-HMSLLYSLYCFEYRWFNKGIEMHQRLSNIERNWPYYFG-FGLPLAFLTAMQSSYIISGCLFSILF
          .SLL.H..LL.SL.CFEYR.FNK..E..Q.LS..ERN..YYFG..GLPLAFLTAM..S.IISGCLF....
Retrocopy LSLL<HVFLLHSLDCFEYR*FNKVTETYQWLSDTERNGTYYFG<IGLPLAFLTAMHFSHIISGCLF----

Parental  PLFIISANEAKTPGKAYLFQLRLFSLVVFLSNRLFHKTVYLQSALSSSTSA-EKFPSPHPSPAKLKAAAG
          PL.IIS.NEAKTP....LFQLRL.SLVVF.SN.LF.KTVYLQSALSSSTSA..KFPSPHPSPAKLKAAAG
Retrocopy PLLIISTNEAKTP----LFQLRLYSLVVFSSNSLFYKTVYLQSALSSSTSA<RKFPSPHPSPAKLKAAAG

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_999 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 26 parental genes, and 69 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000990	2 retrocopies	retro_amel_1449, retro_amel_1681,
Bos taurus	ENSBTAG00000007202	2 retrocopies	retro_btau_1242, retro_btau_443,
Canis familiaris	ENSCAFG00000010898	1 retrocopy	retro_cfam_1829,
Choloepus hoffmanni	ENSCHOG00000012669	3 retrocopies	retro_chof_1433, retro_chof_1994, retro_chof_804,
Cavia porcellus	ENSCPOG00000007272	2 retrocopies	retro_cpor_132, retro_cpor_929,
Dasypus novemcinctus	ENSDNOG00000002362	4 retrocopies	retro_dnov_1083, retro_dnov_1421, retro_dnov_2143, retro_dnov_2345,
Equus caballus	ENSECAG00000015861	1 retrocopy	retro_ecab_1022,
Erinaceus europaeus	ENSEEUG00000003274	1 retrocopy	retro_eeur_435,
Felis catus	ENSFCAG00000015100	1 retrocopy	retro_fcat_1754,
Homo sapiens	ENSG00000149547	3 retrocopies	retro_hsap_236, retro_hsap_2782, retro_hsap_3804,
Loxodonta africana	ENSLAFG00000010888	15 retrocopies	retro_lafr_262, retro_lafr_263, retro_lafr_264, retro_lafr_265, retro_lafr_394, retro_lafr_395, retro_lafr_396, retro_lafr_397, retro_lafr_398, retro_lafr_399, retro_lafr_566, retro_lafr_589, retro_lafr_626, retro_lafr_627, retro_lafr_999 ,
Microcebus murinus	ENSMICG00000003023	3 retrocopies	retro_mmur_398, retro_mmur_498, retro_mmur_632,
Myotis lucifugus	ENSMLUG00000001583	1 retrocopy	retro_mluc_1249,
Macaca mulatta	ENSMMUG00000010009	3 retrocopies	retro_mmul_1443, retro_mmul_1653, retro_mmul_2244,
Nomascus leucogenys	ENSNLEG00000007451	3 retrocopies	retro_nleu_2149, retro_nleu_684, retro_nleu_853,
Oryctolagus cuniculus	ENSOCUG00000014670	1 retrocopy	retro_ocun_1578,
Otolemur garnettii	ENSOGAG00000001838	6 retrocopies	retro_ogar_1055, retro_ogar_1379, retro_ogar_2700, retro_ogar_2701, retro_ogar_659, retro_ogar_799,
Ochotona princeps	ENSOPRG00000013491	2 retrocopies	retro_opri_106, retro_opri_1130,
Procavia capensis	ENSPCAG00000012762	1 retrocopy	retro_pcap_452,
Pongo abelii	ENSPPYG00000004033	3 retrocopies	retro_pabe_2234, retro_pabe_3107, retro_pabe_416,
Pan troglodytes	ENSPTRG00000004444	4 retrocopies	retro_ptro_1202, retro_ptro_1883, retro_ptro_206, retro_ptro_2581,
Pteropus vampyrus	ENSPVAG00000004532	1 retrocopy	retro_pvam_1124,
Rattus norvegicus	ENSRNOG00000030391	1 retrocopy	retro_rnor_2605,
Sarcophilus harrisii	ENSSHAG00000017333	1 retrocopy	retro_shar_433,
Ictidomys tridecemlineatus	ENSSTOG00000004299	2 retrocopies	retro_itri_1343, retro_itri_1373,
Tarsius syrichta	ENSTSYG00000004747	2 retrocopies	retro_tsyr_1238, retro_tsyr_1423,