RetrogeneDB ID: retro_lafr_342

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_13:27021129..27021441(+)
• Located in intron of: ENSLAFG00000004994

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000017669
• Aliases: None
• Description: None

Sequence

>retro_lafr_342
ATGACAGTGAAAATGACCCTTCAGAAGGGACAGATCCAGTATGACTTAGCACCTTCCATCTCTACGTGTATCATTAAAGC
CCTCAAGTAAACACCCAGGGATAGAAAGAGGCAGTTACACGTTAAAGACAATATATGTACCACCTTTTACAATATTGTCA
ACAGCATGTGACAGATGTGGTGTGGACTTCTAGCCAGAGAACTCTCCAGAAGCACTAAAGACATCCTGGGGACTGCCCAG
TGGGTGGGCTGCAATGTCAATGGCGTCCATTCTCAAAACATCGAAGATGACATCAACAGTGGTGCGATGGAT

Alignment

ORF - retro_lafr_342 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.81 %
• Parental protein coverage: 63.03 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ITVKLTIQNRQAQIEVVPSASALIIKALKEPPRDRKKQKNIKHSGNITFDEIVGIARQMRHRSLARELSG
          .TVK.T.Q..Q.Q....PS.S..IIKALK..PRDRK.Q...K.....TF..IV....QM....LARELS.
Retrocopy MTVKMTLQKGQIQYDLAPSISTCIIKALK*TPRDRKRQLHVKDNICTTFYNIVNSM*QMWCGLLARELSR

Parental  TIKEILGTAQSVGCNVDGRHPHDIIDDINSGAVE
          ..K.ILGTAQ.VGCNV.G.H...I.DDINSGA..
Retrocopy STKDILGTAQWVGCNVNGVHSQNIEDDINSGAMD

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_342 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 11 parental genes, and 264 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000006732	32 retrocopies	retro_chof_1081, retro_chof_129, retro_chof_145, retro_chof_1469, retro_chof_147, retro_chof_1531, retro_chof_156, retro_chof_1666, retro_chof_1724, retro_chof_1843, retro_chof_1886, retro_chof_197, retro_chof_1992, retro_chof_2080, retro_chof_2152, retro_chof_2169, retro_chof_2279, retro_chof_2318, retro_chof_249, retro_chof_2599, retro_chof_2614, retro_chof_2656, retro_chof_295, retro_chof_310, retro_chof_354, retro_chof_386, retro_chof_484, retro_chof_592, retro_chof_677, retro_chof_831, retro_chof_916, retro_chof_925,
Dasypus novemcinctus	ENSDNOG00000008412	48 retrocopies	retro_dnov_1021, retro_dnov_1039, retro_dnov_1105, retro_dnov_1111, retro_dnov_1291, retro_dnov_1292, retro_dnov_1339, retro_dnov_1355, retro_dnov_1383, retro_dnov_1387, retro_dnov_1408, retro_dnov_1636, retro_dnov_1658, retro_dnov_1695, retro_dnov_1711, retro_dnov_1884, retro_dnov_2053, retro_dnov_2055, retro_dnov_2058, retro_dnov_210, retro_dnov_2165, retro_dnov_2196, retro_dnov_2199, retro_dnov_2222, retro_dnov_231, retro_dnov_2370, retro_dnov_2430, retro_dnov_2452, retro_dnov_2485, retro_dnov_2490, retro_dnov_260, retro_dnov_2603, retro_dnov_2637, retro_dnov_2639, retro_dnov_330, retro_dnov_343, retro_dnov_368, retro_dnov_387, retro_dnov_395, retro_dnov_455, retro_dnov_552, retro_dnov_560, retro_dnov_590, retro_dnov_597, retro_dnov_614, retro_dnov_634, retro_dnov_654, retro_dnov_677,
Latimeria chalumnae	ENSLACG00000015373	3 retrocopies	retro_lcha_31, retro_lcha_87, retro_lcha_92,
Loxodonta africana	ENSLAFG00000017669	10 retrocopies	retro_lafr_1, retro_lafr_193, retro_lafr_204, retro_lafr_286, retro_lafr_342 , retro_lafr_41, retro_lafr_8, retro_lafr_802, retro_lafr_830, retro_lafr_984,
Macropus eugenii	ENSMEUG00000007380	12 retrocopies	retro_meug_1102, retro_meug_1107, retro_meug_1199, retro_meug_1357, retro_meug_1426, retro_meug_1611, retro_meug_1634, retro_meug_1691, retro_meug_1953, retro_meug_265, retro_meug_479, retro_meug_493,
Monodelphis domestica	ENSMODG00000004571	9 retrocopies	retro_mdom_1061, retro_mdom_1177, retro_mdom_1192, retro_mdom_1526, retro_mdom_1719, retro_mdom_1871, retro_mdom_1947, retro_mdom_309, retro_mdom_925,
Otolemur garnettii	ENSOGAG00000000597	120 retrocopies	retro_ogar_1002, retro_ogar_1010, retro_ogar_1049, retro_ogar_1069, retro_ogar_1106, retro_ogar_1117, retro_ogar_1137, retro_ogar_1140, retro_ogar_1181, retro_ogar_1188, retro_ogar_1189, retro_ogar_1192, retro_ogar_1230, retro_ogar_1247, retro_ogar_1263, retro_ogar_1295, retro_ogar_1331, retro_ogar_1341, retro_ogar_1408, retro_ogar_1409, retro_ogar_1427, retro_ogar_1457, retro_ogar_1464, retro_ogar_1489, retro_ogar_1503, retro_ogar_1534, retro_ogar_1536, retro_ogar_1550, retro_ogar_1569, retro_ogar_1570, retro_ogar_1579, retro_ogar_1606, retro_ogar_1621, retro_ogar_1709, retro_ogar_1717, retro_ogar_1739, retro_ogar_1789, retro_ogar_1803, retro_ogar_1810, retro_ogar_1825, retro_ogar_1836, retro_ogar_1881, retro_ogar_1885, retro_ogar_1916, retro_ogar_1923, retro_ogar_1937, retro_ogar_1941, retro_ogar_1948, retro_ogar_1969, retro_ogar_1975, retro_ogar_1987, retro_ogar_2055, retro_ogar_2115, retro_ogar_2134, retro_ogar_2172, retro_ogar_2179, retro_ogar_2180, retro_ogar_2208, retro_ogar_2209, retro_ogar_2230, retro_ogar_2291, retro_ogar_2323, retro_ogar_2387, retro_ogar_2483, retro_ogar_2495, retro_ogar_2511, retro_ogar_2570, retro_ogar_2620, retro_ogar_2622, retro_ogar_2624, retro_ogar_2749, retro_ogar_2768, retro_ogar_2809, retro_ogar_2904, retro_ogar_2935, retro_ogar_2945, retro_ogar_2953, retro_ogar_2980, retro_ogar_3004, retro_ogar_3017, retro_ogar_303, retro_ogar_3035, retro_ogar_3128, retro_ogar_3135, retro_ogar_3164, retro_ogar_3394, retro_ogar_3489, retro_ogar_395, retro_ogar_398, retro_ogar_412, retro_ogar_427, retro_ogar_452, retro_ogar_480, retro_ogar_512, retro_ogar_513, retro_ogar_538, retro_ogar_560, retro_ogar_587, retro_ogar_624, retro_ogar_636, retro_ogar_653, retro_ogar_655, retro_ogar_667, retro_ogar_668, retro_ogar_669, retro_ogar_683, retro_ogar_700, retro_ogar_734, retro_ogar_737, retro_ogar_744, retro_ogar_747, retro_ogar_775, retro_ogar_818, retro_ogar_853, retro_ogar_868, retro_ogar_901, retro_ogar_927, retro_ogar_956, retro_ogar_962, retro_ogar_964,
Procavia capensis	ENSPCAG00000007469	3 retrocopies	retro_pcap_135, retro_pcap_253, retro_pcap_306,
Rattus norvegicus	ENSRNOG00000016220	4 retrocopies	retro_rnor_166, retro_rnor_236, retro_rnor_247, retro_rnor_312,
Sarcophilus harrisii	ENSSHAG00000017864	8 retrocopies	retro_shar_140, retro_shar_266, retro_shar_284, retro_shar_335, retro_shar_346, retro_shar_453, retro_shar_508, retro_shar_646,
Tursiops truncatus	ENSTTRG00000015700	15 retrocopies	retro_ttru_1215, retro_ttru_1328, retro_ttru_1356, retro_ttru_1373, retro_ttru_1390, retro_ttru_1449, retro_ttru_1685, retro_ttru_1847, retro_ttru_187, retro_ttru_1942, retro_ttru_342, retro_ttru_421, retro_ttru_536, retro_ttru_65, retro_ttru_774,