RetrogeneDB ID: retro_lafr_439

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_16:25109111..25109478(-)
• Located in intron of: ENSLAFG00000006150

Retrocopy information

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

Parental gene information

• Parental gene symbol: RPS24
• Ensembl ID: ENSLAFG00000027878
• Aliases: None
• Description: 40S ribosomal protein S24 [Source:UniProtKB/TrEMBL;Acc:G3UL73]

Sequence

>retro_lafr_439
AACAATATGGTAAGTATCTGGACCAAGAAGTTCATAAACAACTGACCAGTTCAGTGGAAACAAATAGTCATCAGTGTGCT
TCACGCTGGGAAGGCAAAGGTACTTACGATAGAAATTCTGGAAAAACTGGCCAAAATGTAAAGACCACACCAGAGGTCAT
CTTTGTGCTTGGATTCAGAACCGATTTTGGTGGAGGCAAAACAACTGGCTTTGGCATGACACATGACTTACTATGCTTGG
ATTAGCAAAAAAAAATGAACCCAAACACAAACTTGCAGAATATAGCCCGTATAAGAAGAAAAAGAGCTCAAGAAAACAGC
GAAAAGAACCCAAAAACAGAATGAAGAAAGTCAGGGAGACGGCAAAG

Alignment

ORF - retro_lafr_439 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.2 %
• Parental protein coverage: 93.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  NDTVTIRTRKFMTNRLLQRKQMVIDVLHPGKATVPKTEIREKLAKM-YKTTPDVIFVFGFRTHFGGGKTT
          N..V.I.T.KF..N...Q.KQ.VI.VLH.GKA.V...EI.EKLAKM..KTTP.VIFV.GFRT.FGGGKTT
Retrocopy NNMVSIWTKKFINN*PVQWKQIVISVLHAGKAKVLTIEILEKLAKM<VKTTPEVIFVLGFRTDFGGGKTT

Parental  GFGMIYD--SLDYAKK-NEPKHRLARHGLYEKKKTSRKQRKERKNRMKKVRGTAK
          GFGM..D...LD..KK.NEPKH.LA....Y.KKK.SRKQRKE.KNRMKKVR.TAK
Retrocopy GFGMTHDLLCLD*QKK<NEPKHKLAEYSPYKKKKSSRKQRKEPKNRMKKVRETAK

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_439 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 85 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017818	17 retrocopies	retro_amel_1043, retro_amel_1258, retro_amel_1303, retro_amel_1397, retro_amel_145, retro_amel_1814, retro_amel_1832, retro_amel_225, retro_amel_24, retro_amel_251, retro_amel_328, retro_amel_331, retro_amel_515, retro_amel_718, retro_amel_768, retro_amel_81, retro_amel_886,
Bos taurus	ENSBTAG00000013264	9 retrocopies	retro_btau_1137, retro_btau_1311, retro_btau_1562, retro_btau_285, retro_btau_467, retro_btau_577, retro_btau_586, retro_btau_788, retro_btau_980,
Cavia porcellus	ENSCPOG00000020096	3 retrocopies	retro_cpor_1333, retro_cpor_14, retro_cpor_923,
Dipodomys ordii	ENSDORG00000000189	4 retrocopies	retro_dord_248, retro_dord_498, retro_dord_717, retro_dord_766,
Felis catus	ENSFCAG00000000849	3 retrocopies	retro_fcat_19, retro_fcat_772, retro_fcat_85,
Homo sapiens	ENSG00000138326	3 retrocopies	retro_hsap_1511, retro_hsap_526, retro_hsap_658,
Gadus morhua	ENSGMOG00000012595	1 retrocopy	retro_gmor_15,
Loxodonta africana	ENSLAFG00000027878	10 retrocopies	retro_lafr_1017, retro_lafr_190, retro_lafr_303, retro_lafr_340, retro_lafr_439 , retro_lafr_558, retro_lafr_596, retro_lafr_669, retro_lafr_854, retro_lafr_995,
Myotis lucifugus	ENSMLUG00000024102	1 retrocopy	retro_mluc_260,
Mustela putorius furo	ENSMPUG00000003778	1 retrocopy	retro_mputfur_10,
Mus musculus	ENSMUSG00000025290	13 retrocopies	retro_mmus_1101, retro_mmus_1462, retro_mmus_1589, retro_mmus_1592, retro_mmus_1599, retro_mmus_2134, retro_mmus_2332, retro_mmus_2497, retro_mmus_2984, retro_mmus_3162, retro_mmus_321, retro_mmus_3233, retro_mmus_602,
Oryctolagus cuniculus	ENSOCUG00000012472	1 retrocopy	retro_ocun_16,
Otolemur garnettii	ENSOGAG00000011005	3 retrocopies	retro_ogar_1000, retro_ogar_2, retro_ogar_2130,
Pan troglodytes	ENSPTRG00000002666	10 retrocopies	retro_ptro_1023, retro_ptro_1114, retro_ptro_1257, retro_ptro_1555, retro_ptro_1885, retro_ptro_2376, retro_ptro_362, retro_ptro_393, retro_ptro_478, retro_ptro_983,
Rattus norvegicus	ENSRNOG00000010189	1 retrocopy	retro_rnor_206,
Ictidomys tridecemlineatus	ENSSTOG00000013000	4 retrocopies	retro_itri_167, retro_itri_376, retro_itri_528, retro_itri_728,
Tarsius syrichta	ENSTSYG00000006715	1 retrocopy	retro_tsyr_1919,