RetrogeneDB ID: retro_lafr_228

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_10:42324172..42324444(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000008633
• Aliases: None
• Description: None

Sequence

>retro_lafr_228
GATGCCTGAGAGGAACACAGCTTGGCGCTCTCCACGCTTTCCGCCTAGGATGCAGAATTTGATGCTGTCGTTGGCTCTTT
AGAGGACATGGGTGATGAGTTCCGTTGATCCAGAGAAGTTTCATGGACAAGTACTACTAGAGTTTGAAGACGTGAAAGAG
TATAAACGCACCAAAGTGTCTGTTTTTAACAAGTATTTAGTAAAAATGTATATTGTAGAGCAACTGCTGGAGCGGGTTCC
TTGGAGTTAAAATGGCGGCTTTCACAACATCG

Alignment

ORF - retro_lafr_228 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.27 %
• Parental protein coverage: 58.28 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DALEEESFALSISSASDAEFDAVVGYLEDIIMDDEFQ-LLQRNFMDKYY-QEFEDTEENKLTYTPIFNEY
          DA.EE.S.ALS..SA.DAEFDAVVG.LED..M.DEF..L.QR.FMDKYY..EFED..E.K.T....FN.Y
Retrocopy DA*EEHSLALSTLSA*DAEFDAVVGSLED--MGDEFR<LIQRSFMDKYY<LEFEDVKEYKRTKVSVFNKY

Parental  ISLVEKYIEAQLLERIP-GFNMAAFTTT
          ..LV..YI..QLLER.P.G..MAAFTT.
Retrocopy --LVKMYIVEQLLERVP>GVKMAAFTTS

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_228 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 31 parental genes, and 133 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000004844	1 retrocopy	retro_btau_362,
Canis familiaris	ENSCAFG00000008785	3 retrocopies	retro_cfam_1026, retro_cfam_1235, retro_cfam_1357,
Choloepus hoffmanni	ENSCHOG00000009016	16 retrocopies	retro_chof_1180, retro_chof_1220, retro_chof_1287, retro_chof_1526, retro_chof_1655, retro_chof_1677, retro_chof_1858, retro_chof_1904, retro_chof_2024, retro_chof_2189, retro_chof_2247, retro_chof_2646, retro_chof_2658, retro_chof_408, retro_chof_500, retro_chof_977,
Callithrix jacchus	ENSCJAG00000012116	9 retrocopies	retro_cjac_1766, retro_cjac_1920, retro_cjac_1928, retro_cjac_2548, retro_cjac_2580, retro_cjac_2698, retro_cjac_4074, retro_cjac_625, retro_cjac_689,
Cavia porcellus	ENSCPOG00000011406	5 retrocopies	retro_cpor_1501, retro_cpor_203, retro_cpor_249, retro_cpor_299, retro_cpor_571,
Dipodomys ordii	ENSDORG00000016342	2 retrocopies	retro_dord_227, retro_dord_579,
Equus caballus	ENSECAG00000016621	3 retrocopies	retro_ecab_307, retro_ecab_344, retro_ecab_754,
Felis catus	ENSFCAG00000002937	3 retrocopies	retro_fcat_400, retro_fcat_69, retro_fcat_974,
Homo sapiens	ENSG00000102931	7 retrocopies	retro_hsap_1189, retro_hsap_1846, retro_hsap_3237, retro_hsap_3263, retro_hsap_3270, retro_hsap_4293, retro_hsap_999,
Gorilla gorilla	ENSGGOG00000005471	5 retrocopies	retro_ggor_2159, retro_ggor_2202, retro_ggor_2222, retro_ggor_2868, retro_ggor_927,
Loxodonta africana	ENSLAFG00000008633	3 retrocopies	retro_lafr_103, retro_lafr_228 , retro_lafr_418,
Microcebus murinus	ENSMICG00000012467	6 retrocopies	retro_mmur_1066, retro_mmur_1385, retro_mmur_1444, retro_mmur_1515, retro_mmur_247, retro_mmur_499,
Myotis lucifugus	ENSMLUG00000012680	3 retrocopies	retro_mluc_1338, retro_mluc_1843, retro_mluc_746,
Macaca mulatta	ENSMMUG00000020352	7 retrocopies	retro_mmul_1260, retro_mmul_2037, retro_mmul_2055, retro_mmul_2059, retro_mmul_223, retro_mmul_2232, retro_mmul_2458,
Monodelphis domestica	ENSMODG00000013511	1 retrocopy	retro_mdom_1182,
Mustela putorius furo	ENSMPUG00000004306	2 retrocopies	retro_mputfur_1046, retro_mputfur_1369,
Nomascus leucogenys	ENSNLEG00000002803	7 retrocopies	retro_nleu_1050, retro_nleu_1939, retro_nleu_1946, retro_nleu_2114, retro_nleu_2332, retro_nleu_2428, retro_nleu_955,
Oryctolagus cuniculus	ENSOCUG00000000582	1 retrocopy	retro_ocun_431,
Otolemur garnettii	ENSOGAG00000014535	9 retrocopies	retro_ogar_1448, retro_ogar_1476, retro_ogar_1657, retro_ogar_1658, retro_ogar_1919, retro_ogar_2427, retro_ogar_2475, retro_ogar_3184, retro_ogar_3352,
Ochotona princeps	ENSOPRG00000006931	2 retrocopies	retro_opri_675, retro_opri_98,
Procavia capensis	ENSPCAG00000005664	2 retrocopies	retro_pcap_110, retro_pcap_84,
Pongo abelii	ENSPPYG00000007384	8 retrocopies	retro_pabe_1318, retro_pabe_1348, retro_pabe_1453, retro_pabe_2684, retro_pabe_2704, retro_pabe_3498, retro_pabe_843, retro_pabe_990,
Pan troglodytes	ENSPTRG00000008150	7 retrocopies	retro_ptro_1231, retro_ptro_2189, retro_ptro_2207, retro_ptro_2910, retro_ptro_2948, retro_ptro_752, retro_ptro_816,
Pteropus vampyrus	ENSPVAG00000001391	2 retrocopies	retro_pvam_507, retro_pvam_788,
Rattus norvegicus	ENSRNOG00000016991	1 retrocopy	retro_rnor_780,
Sorex araneus	ENSSARG00000005442	1 retrocopy	retro_sara_190,
Ictidomys tridecemlineatus	ENSSTOG00000010254	1 retrocopy	retro_itri_638,
Tupaia belangeri	ENSTBEG00000014441	1 retrocopy	retro_tbel_2991,
Tarsius syrichta	ENSTSYG00000004923	10 retrocopies	retro_tsyr_1003, retro_tsyr_1066, retro_tsyr_1205, retro_tsyr_1728, retro_tsyr_1755, retro_tsyr_1958, retro_tsyr_2144, retro_tsyr_28, retro_tsyr_298, retro_tsyr_351,
Tursiops truncatus	ENSTTRG00000012794	3 retrocopies	retro_ttru_1403, retro_ttru_325, retro_ttru_973,
Vicugna pacos	ENSVPAG00000005976	2 retrocopies	retro_vpac_242, retro_vpac_554,