RetrogeneDB ID: retro_lafr_1223

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_9:66906966..66907547(+)
• Located in intron of: ENSLAFG00000015781

Retrocopy information

• Ensembl ID: ENSLAFG00000015787
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: RPS7
• Ensembl ID: ENSLAFG00000015087
• Aliases: None
• Description: None

Sequence

>retro_lafr_1223
GTGCTCAGTTCAAGCATGAAGATTGTCAAGTCCAATGGCGAAAAGCCGGATGAATTCGAGTCTGGCATTTTTCAAGCGCT
GCTTGAACTGGAGATGAACTTGGACTTAAAGGCTCAGTTGAGGGAGCTGAATATAACCGCAGCCAAGGAAATTGAAGTTG
GTGGTGGCAGGAAAGCTATTATAATCTTTGTTCCCGTTCCTCAACTGAAGTCTTTCCAGAAAATCCAAGTCAGGCTAGTA
CACGAACTGGAGAAAAAGTTCAGTGGAAAGCATGTTGTCTTTATTGCTCAGAGGAGAATTCTGCCTAAACCAACTCGAAA
AAGTCATACAAAAAATAAGCAGAAGCGTCCCAGGAGCCGTACTCTGACAGCCGTACGTGACGCAACCCTTGAAGACTTGG
TCTTCCCAAGTGAGATTGTGTGCAAGAGAATCCATGTAAAACTGGACGGCAGCCGGCTTATCAAAGTGCATTTGGACAAG
CACAGCAGACCAATGTAGAACACAAGGTTGAAACTTTTTCTGGTGTGTATAAGAAGCTCACGGGCAAGGATGTTAATTTT
GAATTCCCAGAGTTTCAATTG

Alignment

ORF - retro_lafr_1223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 92.82 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MFSSSAKIVKPNGEKPDEFESGISQALLELEMNSDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLK
          ..SSS.KIVK.NGEKPDEFESGI.QALLELEMN.DLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLK
Retrocopy VLSSSMKIVKSNGEKPDEFESGIFQALLELEMNLDLKAQLRELNITAAKEIEVGGGRKAIIIFVPVPQLK

Parental  SFQKIQVRLVRELEKKFSGKHVVFIAQRRILPKPTRKSRTKNKQKRPRSRTLTAVHDAILEDLVFPSEIV
          SFQKIQVRLV.ELEKKFSGKHVVFIAQRRILPKPTRKS.TKNKQKRPRSRTLTAV.DA.LEDLVFPSEIV
Retrocopy SFQKIQVRLVHELEKKFSGKHVVFIAQRRILPKPTRKSHTKNKQKRPRSRTLTAVRDATLEDLVFPSEIV

Parental  GKRIRVKLDGSRLIKVHLDK-AQQNNVEHKVETFSGVYKKLTGKDVNFEFPEFQL
          .KRI.VKLDGSRLIKVHLDK.AQQ.NVEHKVETFSGVYKKLTGKDVNFEFPEFQL
Retrocopy CKRIHVKLDGSRLIKVHLDK<AQQTNVEHKVETFSGVYKKLTGKDVNFEFPEFQL

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_1223 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 22 parental genes, and 109 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000018435	2 retrocopies	retro_amel_391, retro_amel_914,
Bos taurus	ENSBTAG00000016224	5 retrocopies	retro_btau_1016, retro_btau_1046, retro_btau_1351, retro_btau_448, retro_btau_997,
Canis familiaris	ENSCAFG00000003263	1 retrocopy	retro_cfam_1798,
Callithrix jacchus	ENSCJAG00000016462	2 retrocopies	retro_cjac_16, retro_cjac_2287,
Cavia porcellus	ENSCPOG00000009795	2 retrocopies	retro_cpor_1139, retro_cpor_773,
Dasypus novemcinctus	ENSDNOG00000013285	14 retrocopies	retro_dnov_1091, retro_dnov_1351, retro_dnov_1388, retro_dnov_1459, retro_dnov_1688, retro_dnov_1849, retro_dnov_1940, retro_dnov_1970, retro_dnov_238, retro_dnov_2409, retro_dnov_558, retro_dnov_582, retro_dnov_623, retro_dnov_791,
Equus caballus	ENSECAG00000020253	2 retrocopies	retro_ecab_276, retro_ecab_396,
Homo sapiens	ENSG00000171863	14 retrocopies	retro_hsap_111, retro_hsap_112, retro_hsap_1242, retro_hsap_1737, retro_hsap_1837, retro_hsap_2907, retro_hsap_2925, retro_hsap_329, retro_hsap_3635, retro_hsap_404, retro_hsap_4711, retro_hsap_4760, retro_hsap_528, retro_hsap_703,
Loxodonta africana	ENSLAFG00000015087	11 retrocopies	retro_lafr_1223 , retro_lafr_160, retro_lafr_217, retro_lafr_318, retro_lafr_319, retro_lafr_413, retro_lafr_514, retro_lafr_720, retro_lafr_786, retro_lafr_964, retro_lafr_970,
Myotis lucifugus	ENSMLUG00000006121	1 retrocopy	retro_mluc_1118,
Macaca mulatta	ENSMMUG00000011870	7 retrocopies	retro_mmul_1831, retro_mmul_1846, retro_mmul_1929, retro_mmul_23, retro_mmul_2403, retro_mmul_2540, retro_mmul_357,
Monodelphis domestica	ENSMODG00000014495	2 retrocopies	retro_mdom_662, retro_mdom_810,
Mus musculus	ENSMUSG00000061477	2 retrocopies	retro_mmus_271, retro_mmus_53,
Nomascus leucogenys	ENSNLEG00000015407	10 retrocopies	retro_nleu_1505, retro_nleu_1771, retro_nleu_1783, retro_nleu_2278, retro_nleu_2346, retro_nleu_2510, retro_nleu_2892, retro_nleu_3080, retro_nleu_817, retro_nleu_835,
Oryctolagus cuniculus	ENSOCUG00000008507	2 retrocopies	retro_ocun_203, retro_ocun_230,
Otolemur garnettii	ENSOGAG00000028165	1 retrocopy	retro_ogar_133,
Pongo abelii	ENSPPYG00000025872	12 retrocopies	retro_pabe_1033, retro_pabe_1555, retro_pabe_2506, retro_pabe_2982, retro_pabe_2983, retro_pabe_31, retro_pabe_313, retro_pabe_360, retro_pabe_3659, retro_pabe_3803, retro_pabe_499, retro_pabe_524,
Pan troglodytes	ENSPTRG00000011615	3 retrocopies	retro_ptro_202, retro_ptro_3132, retro_ptro_58,
Rattus norvegicus	ENSRNOG00000008551	2 retrocopies	retro_rnor_39, retro_rnor_391,
Sus scrofa	ENSSSCG00000027353	5 retrocopies	retro_sscr_136, retro_sscr_137, retro_sscr_240, retro_sscr_364, retro_sscr_956,
Ictidomys tridecemlineatus	ENSSTOG00000024830	3 retrocopies	retro_itri_1147, retro_itri_1161, retro_itri_1215,
Tursiops truncatus	ENSTTRG00000001616	6 retrocopies	retro_ttru_1422, retro_ttru_1659, retro_ttru_1706, retro_ttru_301, retro_ttru_323, retro_ttru_773,