RetrogeneDB ID: retro_lafr_475

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_18:14408585..14409113(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: HPRT1
• Ensembl ID: ENSLAFG00000009892
• Aliases: None
• Description: None

Sequence

>retro_lafr_475
GAACCAGGTTACAGCCTGGATTTATTTTGTTTGTCTAATCATTCCACTGAAGATTTACAAAGAGGTTTATTCCTCATGGA
TTAATCACGGACAGGGCAAAATGGCTTCCTCTTGAAATCCTATGAAGGAGATAGGAGGCCACCATACTGTAGCTTTCTGT
GTGCTCCAGGGGCTATAAATTGTTCATTGACAGGCTGAATTATATCACAGCATTGAACAGATGTAGTGCTACATCCGTGC
CTGTGACTGCAGATTTTGTCAGACTGAAGAGCTTCTGTAATGACCAATCAACTGGGGGCATAAAAGTAACTGGTGGAGAT
GGCTTCACAACTTCAGCTGGGAAGAATGCCTTGATTGTTAAAGATACATTCAACACTGGCAAAGCAATGCAAACCTTGCA
TTCATTGGGCAAGTGTCATAATTCAAAGGCAGACAGAGTCGCAAGTGTGCTGGTGAAAGGGACCCCTTCGATCTGTTGGC
TATAGACCAGACCGTATTGGATTTGAAATTCCAGATATGTGTGTAGTA

Alignment

ORF - retro_lafr_475 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.87 %
• Parental protein coverage: 84.21 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  EPGYDLDLFCIPNHYVEDLE-KVFIPHGLIMDRTERLARDVMKEMGGHHIVALCVLKGGYKFFADLLDYI
          EPGY.LDLFC..NH..EDL..K.FIPHGLI.DR...L............I..L.V...GYK.F.D.L.YI
Retrocopy EPGYSLDLFCLSNHSTEDLQ<KRFIPHGLITDRAKWLPLEIL*RR*EATIL*LSVCSRGYKLFIDRLNYI

Parental  KALNRNSDRSIPMTVDFIRLKSYCNDQSTGDIKVIGGDDLATLTGKSFLIFQDIIDTGKTMQTLLSLVRQ
          .ALNR.S..S.P.T.DF.RLKS.CNDQSTG.IKV.GGD...T..GK..LI..D...TGK.MQTL.SL...
Retrocopy TALNRCSATSVPVTADFVRLKSFCNDQSTGGIKVTGGDGFTTSAGKNALIVKDTFNTGKAMQTLHSLGKC

Parental  YNPQMIKVASLLVKRTP-RSVGYRPDFVGFEIPDKFVV
          .N.....VAS.LVK.TP.RSVGYRPD..GFEIPD..VV
Retrocopy HNSKADRVASVLVKGTP>RSVGYRPDRIGFEIPDMCVV

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_475 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 24 parental genes, and 53 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000001339	1 retrocopy	retro_amel_129,
Bos taurus	ENSBTAG00000014685	3 retrocopies	retro_btau_162, retro_btau_179, retro_btau_721,
Canis familiaris	ENSCAFG00000018870	1 retrocopy	retro_cfam_2014,
Cavia porcellus	ENSCPOG00000002512	1 retrocopy	retro_cpor_1299,
Dasypus novemcinctus	ENSDNOG00000008495	5 retrocopies	retro_dnov_1480, retro_dnov_1908, retro_dnov_2057, retro_dnov_255, retro_dnov_763,
Equus caballus	ENSECAG00000017534	1 retrocopy	retro_ecab_734,
Felis catus	ENSFCAG00000004575	2 retrocopies	retro_fcat_104, retro_fcat_1608,
Homo sapiens	ENSG00000165704	1 retrocopy	retro_hsap_917,
Gorilla gorilla	ENSGGOG00000008050	1 retrocopy	retro_ggor_740,
Loxodonta africana	ENSLAFG00000009892	2 retrocopies	retro_lafr_1042, retro_lafr_475 ,
Microcebus murinus	ENSMICG00000006547	1 retrocopy	retro_mmur_1186,
Myotis lucifugus	ENSMLUG00000003591	1 retrocopy	retro_mluc_2107,
Macaca mulatta	ENSMMUG00000008303	1 retrocopy	retro_mmul_1118,
Mustela putorius furo	ENSMPUG00000012699	3 retrocopies	retro_mputfur_1317, retro_mputfur_1638, retro_mputfur_836,
Oryctolagus cuniculus	ENSOCUG00000003186	1 retrocopy	retro_ocun_1082,
Otolemur garnettii	ENSOGAG00000003881	3 retrocopies	retro_ogar_1886, retro_ogar_3298, retro_ogar_3463,
Pongo abelii	ENSPPYG00000020733	2 retrocopies	retro_pabe_3601, retro_pabe_791,
Pan troglodytes	ENSPTRG00000022287	2 retrocopies	retro_ptro_2042, retro_ptro_636,
Rattus norvegicus	ENSRNOG00000031367	2 retrocopies	retro_rnor_1208, retro_rnor_2491,
Sarcophilus harrisii	ENSSHAG00000007965	3 retrocopies	retro_shar_470, retro_shar_513, retro_shar_661,
Tupaia belangeri	ENSTBEG00000000859	5 retrocopies	retro_tbel_1607, retro_tbel_2234, retro_tbel_3627, retro_tbel_4320, retro_tbel_729,
Tarsius syrichta	ENSTSYG00000009579	1 retrocopy	retro_tsyr_2050,
Tursiops truncatus	ENSTTRG00000009954	9 retrocopies	retro_ttru_1007, retro_ttru_1272, retro_ttru_1523, retro_ttru_1598, retro_ttru_1620, retro_ttru_276, retro_ttru_641, retro_ttru_732, retro_ttru_829,
Vicugna pacos	ENSVPAG00000009133	1 retrocopy	retro_vpac_122,