RetrogeneDB ID: retro_lafr_1123

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_71:8986368..8986611(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPL37
• Ensembl ID: ENSLAFG00000030052
• Aliases: None
• Description: Ribosomal protein L37 [Source:UniProtKB/TrEMBL;Acc:G3U3B7]

Sequence

>retro_lafr_1123
ACGTTGTGCCGCCGCTATGGCTGTAAGGCCTACCACCTTCAGAGGTCAACCTGTGGCAAATGTGGCTGCCCTGCCAAGTG
CAAGAGGAAGTCTAATTAGAGTGCCAAGGCTAAAAGATGAAAGACCACTGGTACTGGTTGAATGAGACACCTAAAAATTG
TATACTGCAGATTCAGTCACGGATTCTGTGAAGGAACAACATCTAAACCCAAGAGGGCAGCTGTTGCAGCATCCAGTTCA
TCT

Alignment

ORF - retro_lafr_1123 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 82.72 %
• Parental protein coverage: 83.51 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TLCRRCGSKAYHLQKSTCGKCGYPAKRKRKYNWSAKAKRRNTTGTGRMRHLKIVYRRFRHGFREGTTPKP
          TLCRR.G.KAYHLQ.STCGKCG.PAK.KRK.N.SAKAKR..TTGTG.MRHLKIVY.RF.HGF.EGTT.KP
Retrocopy TLCRRYGCKAYHLQRSTCGKCGCPAKCKRKSN*SAKAKR*KTTGTG*MRHLKIVYCRFSHGFCEGTTSKP

Parental  KRAAVAASSSS
          KRAAVAASSSS
Retrocopy KRAAVAASSSS

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_1123 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 17 parental genes, and 181 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005142	6 retrocopies	retro_btau_1430, retro_btau_1502, retro_btau_1575, retro_btau_1670, retro_btau_181, retro_btau_243,
Callithrix jacchus	ENSCJAG00000007388	10 retrocopies	retro_cjac_107, retro_cjac_1443, retro_cjac_169, retro_cjac_2091, retro_cjac_2443, retro_cjac_247, retro_cjac_2495, retro_cjac_2654, retro_cjac_2956, retro_cjac_332,
Homo sapiens	ENSG00000145592	21 retrocopies	retro_hsap_1277, retro_hsap_1424, retro_hsap_156, retro_hsap_1747, retro_hsap_1763, retro_hsap_2009, retro_hsap_2120, retro_hsap_2239, retro_hsap_2265, retro_hsap_2499, retro_hsap_2515, retro_hsap_2923, retro_hsap_343, retro_hsap_3610, retro_hsap_3901, retro_hsap_3958, retro_hsap_4685, retro_hsap_537, retro_hsap_795, retro_hsap_887, retro_hsap_953,
Latimeria chalumnae	ENSLACG00000002787	1 retrocopy	retro_lcha_6,
Loxodonta africana	ENSLAFG00000030052	13 retrocopies	retro_lafr_1101, retro_lafr_1123 , retro_lafr_1125, retro_lafr_1136, retro_lafr_215, retro_lafr_374, retro_lafr_448, retro_lafr_507, retro_lafr_532, retro_lafr_619, retro_lafr_775, retro_lafr_985, retro_lafr_986,
Myotis lucifugus	ENSMLUG00000001565	10 retrocopies	retro_mluc_1037, retro_mluc_1334, retro_mluc_1441, retro_mluc_1651, retro_mluc_1897, retro_mluc_1917, retro_mluc_2006, retro_mluc_454, retro_mluc_738, retro_mluc_959,
Macaca mulatta	ENSMMUG00000023807	6 retrocopies	retro_mmul_1602, retro_mmul_1672, retro_mmul_206, retro_mmul_329, retro_mmul_976, retro_mmul_997,
Monodelphis domestica	ENSMODG00000020301	3 retrocopies	retro_mdom_130, retro_mdom_1843, retro_mdom_942,
Mus musculus	ENSMUSG00000041841	28 retrocopies	retro_mmus_1333, retro_mmus_1360, retro_mmus_1425, retro_mmus_1560, retro_mmus_1717, retro_mmus_1732, retro_mmus_1804, retro_mmus_1813, retro_mmus_2067, retro_mmus_2379, retro_mmus_2385, retro_mmus_2513, retro_mmus_2559, retro_mmus_2575, retro_mmus_2691, retro_mmus_2811, retro_mmus_2838, retro_mmus_3090, retro_mmus_3222, retro_mmus_3343, retro_mmus_3345, retro_mmus_3364, retro_mmus_3455, retro_mmus_3493, retro_mmus_3503, retro_mmus_3504, retro_mmus_3674, retro_mmus_438,
Nomascus leucogenys	ENSNLEG00000016508	4 retrocopies	retro_nleu_1841, retro_nleu_2065, retro_nleu_2407, retro_nleu_77,
Oryctolagus cuniculus	ENSOCUG00000029674	11 retrocopies	retro_ocun_1063, retro_ocun_1269, retro_ocun_1476, retro_ocun_1491, retro_ocun_1514, retro_ocun_1870, retro_ocun_295, retro_ocun_683, retro_ocun_771, retro_ocun_879, retro_ocun_956,
Otolemur garnettii	ENSOGAG00000034300	7 retrocopies	retro_ogar_127, retro_ogar_1308, retro_ogar_1662, retro_ogar_1667, retro_ogar_2670, retro_ogar_662, retro_ogar_76,
Pongo abelii	ENSPPYG00000015422	26 retrocopies	retro_pabe_1058, retro_pabe_1180, retro_pabe_1443, retro_pabe_1532, retro_pabe_1643, retro_pabe_1705, retro_pabe_1756, retro_pabe_1840, retro_pabe_1851, retro_pabe_1865, retro_pabe_1951, retro_pabe_1967, retro_pabe_1985, retro_pabe_212, retro_pabe_2403, retro_pabe_2432, retro_pabe_2962, retro_pabe_3180, retro_pabe_3260, retro_pabe_353, retro_pabe_3549, retro_pabe_3638, retro_pabe_466, retro_pabe_634, retro_pabe_707, retro_pabe_813,
Pan troglodytes	ENSPTRG00000016822	20 retrocopies	retro_ptro_1208, retro_ptro_1219, retro_ptro_1338, retro_ptro_1451, retro_ptro_1460, retro_ptro_152, retro_ptro_1552, retro_ptro_1584, retro_ptro_1605, retro_ptro_1978, retro_ptro_2440, retro_ptro_2654, retro_ptro_2687, retro_ptro_273, retro_ptro_403, retro_ptro_553, retro_ptro_613, retro_ptro_660, retro_ptro_873, retro_ptro_974,
Rattus norvegicus	ENSRNOG00000012538	6 retrocopies	retro_rnor_171, retro_rnor_181, retro_rnor_220, retro_rnor_246, retro_rnor_321, retro_rnor_325,
Sarcophilus harrisii	ENSSHAG00000013969	4 retrocopies	retro_shar_295, retro_shar_350, retro_shar_395, retro_shar_715,
Sus scrofa	ENSSSCG00000025883	5 retrocopies	retro_sscr_1004, retro_sscr_1220, retro_sscr_1221, retro_sscr_767, retro_sscr_872,