RetrogeneDB ID: retro_lafr_677

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_3:46492722..46493335(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL15
• Ensembl ID: ENSLAFG00000004155
• Aliases: None
• Description: Ribosomal protein L15 [Source:UniProtKB/TrEMBL;Acc:G3STR1]

Sequence

>retro_lafr_677
ATGGGTGCATACAGGTATATCCAGGAGCTGTGGAGGAAGAAGCAGTCCAATGTGATGCGCTTTCTCTTGCGAGTCCGCTG
CTGACAGTACCGCCAGCTCTCTGGGCTGCACAGGGCCCCCCCGCCCCACCCGGCCCAATAAGGCGCGCAGACTGGGGTAC
AAGGCCAAGCAAGGTTATGTCATCTCTCGGATTCATGTACGCCGGGGTGGCCGCAAACGCCCGGTGCCTAAGGGTGCAAC
CTATGGCAAGCCTGTCAATCATGGTGTCAACCAGCTGAAGTTTGCCAGAAGCCTTCAGTCTGTTGCAGAGGCGCGAGCTG
GACGCCACTGTGGGGCTCTGAGGGTCCTGAATTCTTACTGGGTTGGTGAAGATTCCACATACAAATTCTTGGAAGTTATC
CTCATCGATCCATTCCGTAAAGCTATCTGAAGAAACCCTGACACCCAGTGGATCACTAAGCCAGTCCACAAGCACAGGGA
GATGTGCTGGCTGACGTCTGCAGGCCGGAAGAGCCGTGGCCTCTGGAAGGGCCACGAGTTCCACCGCACTATTGGTGGCT
CTCACCGTGCCACTTGGAGACTGCGCAATACTCTCCAGCTCCACCGTTACCGC

Alignment

ORF - retro_lafr_677 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 90.24 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGAYKYIQELWRKKQSDVMRFLLRVRCWQYRQLSALHRAP-RPTRPDKARRLGYKAKQGYVIYRIRVRRG
          MGAY.YIQELWRKKQS.VMRFLLRVRC.QYRQLS.LHRAP.RPTRP.KARRLGYKAKQGYVI.RI.VRRG
Retrocopy MGAYRYIQELWRKKQSNVMRFLLRVRC*QYRQLSGLHRAP>RPTRPNKARRLGYKAKQGYVISRIHVRRG

Parental  GRKRPVPKGATYGKPVNHGVNQLKFARSLQSVAEERAGRHCGALRVLNSYWVGEDSTYKFFEVILIDPFH
          GRKRPVPKGATYGKPVNHGVNQLKFARSLQSVAE.RAGRHCGALRVLNSYWVGEDSTYKF.EVILIDPF.
Retrocopy GRKRPVPKGATYGKPVNHGVNQLKFARSLQSVAEARAGRHCGALRVLNSYWVGEDSTYKFLEVILIDPFR

Parental  KAIRRNPDTQWITKPVHKHREMRGLTSAGRKSRGLGKGHKFHHTIGGSRRAAWRRRNTLQLHRYR
          KAI.RNPDTQWITKPVHKHREM..LTSAGRKSRGL.KGH.FH.TIGGS.RA.WR.RNTLQLHRYR
Retrocopy KAI*RNPDTQWITKPVHKHREMCWLTSAGRKSRGLWKGHEFHRTIGGSHRATWRLRNTLQLHRYR

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_677 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 20 parental genes, and 143 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000003497	6 retrocopies	retro_amel_1281, retro_amel_1470, retro_amel_1519, retro_amel_516, retro_amel_548, retro_amel_712,
Bos taurus	ENSBTAG00000033080	2 retrocopies	retro_btau_152, retro_btau_201,
Callithrix jacchus	ENSCJAG00000003810	23 retrocopies	retro_cjac_1052, retro_cjac_1270, retro_cjac_1316, retro_cjac_1553, retro_cjac_1578, retro_cjac_1625, retro_cjac_1668, retro_cjac_1741, retro_cjac_2143, retro_cjac_2330, retro_cjac_2518, retro_cjac_2532, retro_cjac_2599, retro_cjac_2821, retro_cjac_2907, retro_cjac_3807, retro_cjac_4185, retro_cjac_506, retro_cjac_585, retro_cjac_712, retro_cjac_734, retro_cjac_783, retro_cjac_890,
Cavia porcellus	ENSCPOG00000002253	4 retrocopies	retro_cpor_620, retro_cpor_807, retro_cpor_900, retro_cpor_978,
Equus caballus	ENSECAG00000010157	1 retrocopy	retro_ecab_38,
Felis catus	ENSFCAG00000026237	6 retrocopies	retro_fcat_1820, retro_fcat_285, retro_fcat_306, retro_fcat_610, retro_fcat_930, retro_fcat_985,
Gorilla gorilla	ENSGGOG00000024274	13 retrocopies	retro_ggor_1327, retro_ggor_1611, retro_ggor_1716, retro_ggor_1989, retro_ggor_2029, retro_ggor_2125, retro_ggor_2314, retro_ggor_2473, retro_ggor_39, retro_ggor_524, retro_ggor_552, retro_ggor_654, retro_ggor_771,
Loxodonta africana	ENSLAFG00000004155	1 retrocopy	retro_lafr_677 ,
Myotis lucifugus	ENSMLUG00000013809	15 retrocopies	retro_mluc_1357, retro_mluc_1709, retro_mluc_1720, retro_mluc_2052, retro_mluc_2142, retro_mluc_2454, retro_mluc_425, retro_mluc_623, retro_mluc_701, retro_mluc_714, retro_mluc_748, retro_mluc_749, retro_mluc_907, retro_mluc_943, retro_mluc_99,
Macaca mulatta	ENSMMUG00000006353	1 retrocopy	retro_mmul_209,
Mustela putorius furo	ENSMPUG00000012148	7 retrocopies	retro_mputfur_1011, retro_mputfur_1252, retro_mputfur_1291, retro_mputfur_314, retro_mputfur_346, retro_mputfur_658, retro_mputfur_669,
Mus musculus	ENSMUSG00000012405	2 retrocopies	retro_mmus_118, retro_mmus_8,
Nomascus leucogenys	ENSNLEG00000003580	1 retrocopy	retro_nleu_80,
Oryctolagus cuniculus	ENSOCUG00000010961	2 retrocopies	retro_ocun_215, retro_ocun_228,
Otolemur garnettii	ENSOGAG00000013056	13 retrocopies	retro_ogar_1066, retro_ogar_1129, retro_ogar_1182, retro_ogar_1453, retro_ogar_1483, retro_ogar_1629, retro_ogar_1809, retro_ogar_2378, retro_ogar_270, retro_ogar_3058, retro_ogar_3096, retro_ogar_3349, retro_ogar_903,
Procavia capensis	ENSPCAG00000011995	1 retrocopy	retro_pcap_265,
Pongo abelii	ENSPPYG00000014065	18 retrocopies	retro_pabe_1073, retro_pabe_1201, retro_pabe_1480, retro_pabe_1896, retro_pabe_2049, retro_pabe_2377, retro_pabe_2433, retro_pabe_2467, retro_pabe_2562, retro_pabe_3004, retro_pabe_3028, retro_pabe_3098, retro_pabe_561, retro_pabe_597, retro_pabe_642, retro_pabe_705, retro_pabe_801, retro_pabe_816,
Rattus norvegicus	ENSRNOG00000008140	17 retrocopies	retro_rnor_1046, retro_rnor_1409, retro_rnor_1497, retro_rnor_1685, retro_rnor_1690, retro_rnor_1785, retro_rnor_2042, retro_rnor_2249, retro_rnor_2313, retro_rnor_2451, retro_rnor_2473, retro_rnor_2786, retro_rnor_2997, retro_rnor_428, retro_rnor_66, retro_rnor_710, retro_rnor_844,
Sus scrofa	ENSSSCG00000028079	5 retrocopies	retro_sscr_1219, retro_sscr_1225, retro_sscr_448, retro_sscr_968, retro_sscr_997,
Tursiops truncatus	ENSTTRG00000007244	5 retrocopies	retro_ttru_1305, retro_ttru_1358, retro_ttru_280, retro_ttru_920, retro_ttru_987,