RetrogeneDB ID: retro_lafr_1237

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_9:75844512..75844759(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS21
• Ensembl ID: ENSLAFG00000015793
• Aliases: None
• Description: 40S ribosomal protein S21 [Source:UniProtKB/TrEMBL;Acc:G3TFU7]

Sequence

>retro_lafr_1237
GTGCAGAATAACGCCAGCAAGTTCGTGGACCTGGATGTGTCACGTAAATGCTCCACCAGCAACTGCATCATGACCACCAA
GGACCACGCATTCATCCAGATGAACGTGGCTGAGCTTGACAAGGTCACTGTCAGGTTCAACGGCCTATGAAGACCTACGC
TATCTACAGGGTCATTCACAGGATGGTGAGTCAGATGATTCTATTCTCTGACTGGCCAAGGCCGACGGCATTGTCTCAGA
GAACTTC

Alignment

ORF - retro_lafr_1237 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 71.76 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MQNDAGEFVDLYVPRKCSASNRIIGAKDHASIQMNVAEVDKVTGRFNG-QFKTYAICGAIRRM-GESDDS
          .QN.A..FVDL.V.RKCS.SN.I...KDHA.IQMNVAE.DKVT.RFNG...KTYAI...I.RM.GESDDS
Retrocopy VQNNASKFVDLDVSRKCSTSNCIMTTKDHAFIQMNVAELDKVTVRFNG<PMKTYAIYRVIHRM<GESDDS

Parental  ILRLAKADGIVSKNF
          IL.LAKADGIVS.NF
Retrocopy IL*LAKADGIVSENF

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_1237 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 73 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017399	2 retrocopies	retro_amel_1783, retro_amel_87,
Bos taurus	ENSBTAG00000020795	2 retrocopies	retro_btau_174, retro_btau_1780,
Canis familiaris	ENSCAFG00000012676	4 retrocopies	retro_cfam_1055, retro_cfam_1687, retro_cfam_1896, retro_cfam_28,
Callithrix jacchus	ENSCJAG00000014195	5 retrocopies	retro_cjac_2266, retro_cjac_2572, retro_cjac_629, retro_cjac_82, retro_cjac_884,
Erinaceus europaeus	ENSEEUG00000004573	2 retrocopies	retro_eeur_235, retro_eeur_501,
Gorilla gorilla	ENSGGOG00000023745	7 retrocopies	retro_ggor_131, retro_ggor_1380, retro_ggor_1647, retro_ggor_2043, retro_ggor_2089, retro_ggor_2875, retro_ggor_917,
Latimeria chalumnae	ENSLACG00000012753	1 retrocopy	retro_lcha_124,
Loxodonta africana	ENSLAFG00000015793	4 retrocopies	retro_lafr_1055, retro_lafr_1237 , retro_lafr_352, retro_lafr_499,
Macropus eugenii	ENSMEUG00000015832	2 retrocopies	retro_meug_1221, retro_meug_466,
Microcebus murinus	ENSMICG00000012997	5 retrocopies	retro_mmur_110, retro_mmur_1388, retro_mmur_264, retro_mmur_55, retro_mmur_965,
Macaca mulatta	ENSMMUG00000005006	8 retrocopies	retro_mmul_1006, retro_mmul_1043, retro_mmul_1138, retro_mmul_1279, retro_mmul_1331, retro_mmul_1948, retro_mmul_588, retro_mmul_633,
Ochotona princeps	ENSOPRG00000000937	1 retrocopy	retro_opri_996,
Pongo abelii	ENSPPYG00000011205	8 retrocopies	retro_pabe_1562, retro_pabe_157, retro_pabe_2446, retro_pabe_2505, retro_pabe_3503, retro_pabe_365, retro_pabe_710, retro_pabe_986,
Pan troglodytes	ENSPTRG00000013708	1 retrocopy	retro_ptro_42,
Pteropus vampyrus	ENSPVAG00000003548	2 retrocopies	retro_pvam_1362, retro_pvam_1368,
Rattus norvegicus	ENSRNOG00000006325	2 retrocopies	retro_rnor_128, retro_rnor_172,
Sus scrofa	ENSSSCG00000021825	1 retrocopy	retro_sscr_7,
Ictidomys tridecemlineatus	ENSSTOG00000001029	5 retrocopies	retro_itri_1027, retro_itri_1487, retro_itri_637, retro_itri_82, retro_itri_849,
Tarsius syrichta	ENSTSYG00000007061	5 retrocopies	retro_tsyr_105, retro_tsyr_123, retro_tsyr_1502, retro_tsyr_2157, retro_tsyr_951,
Tursiops truncatus	ENSTTRG00000011105	6 retrocopies	retro_ttru_1058, retro_ttru_1418, retro_ttru_1707, retro_ttru_1749, retro_ttru_1773, retro_ttru_674,