RetrogeneDB ID: retro_lafr_1186

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_843:13295..13829(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: SRI
• Ensembl ID: ENSLAFG00000027380
• Aliases: None
• Description: None

Sequence

>retro_lafr_1186
GGGACTCCCAGAGGGTCTGCGCTTCCCAGACAAACTCAGGATCCACTGCACGGTTACTTTGCTCCTGTAGCTAGGCAGGA
TAGGCAAATAGATGCCGATGAGCTGCAGAGATGTCTGACAGTCAGGGATTGCCGGAGGGTACAAACCTTTTAGCCTGGAG
ACTTGTTGGCTTATCATTTCAATGCTGGATAGCGGCATGTCTGGCACAATAGGTTTCAATGAATTTAAAGAACCCTGGGC
TGTACTGAATGGCTGGAGACAGCATTTCATCAGTTTTGACAGCTACAGAAGTGGAACAGTGGGTCTTCAAAAATTACAGA
AGGCCCTGACCACTATGGGGTTTAGGTTGCGTCCTCAGGCTTTGAATTCAATTGCAAAGAGGTACAGCACCAATGGAAAG
ATCACTTTTGATGATTGCATTGCCTGCTGCATCAAACTGAGGTCTCTCACAGACAGCTTTCGAAGACAGAGACGGGTCAG
CTAGGTGTTGTGAACTTCCCATATGATGATTTCATTTATTGTGTCATGAATGTT

Alignment

ORF - retro_lafr_1186 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 78.02 %
• Parental protein coverage: 89.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  GAPGGPAFPGQTQDPLYGYFAAVAGQDGQIDADELQRCLT-QSGIAGG-YKPFNLETCRLMVSMLDRDMS
          G.P.G.A.P.QTQDPL.GYFA.VA.QD.QIDADELQRCLT...G...G.YKPF.LETC.L..SMLD..MS
Retrocopy GTPRGSALPRQTQDPLHGYFAPVARQDRQIDADELQRCLT<SQGLPEG<YKPFSLETCWLIISMLDSGMS

Parental  GTMGFNEFKELWSVLNGWRQHFISFDSDRSGTVDPQELQKALTTMGFRLSPQAVNSIAKRYSTNGKITFD
          GT.GFNEFKE.W.VLNGWRQHFISFDS.RSGTV..Q.LQKALTTMGFRL.PQA.NSIAKRYSTNGKITFD
Retrocopy GTIGFNEFKEPWAVLNGWRQHFISFDSYRSGTVGLQKLQKALTTMGFRLRPQALNSIAKRYSTNGKITFD

Parental  DYIACCVKLRALTDSFRRR-DTGQQGVVNFPYDDFIQCVMSV
          D.IACC.KLR.LTDSFRR...TGQ.GVVNFPYDDFI.CVM.V
Retrocopy DCIACCIKLRSLTDSFRRQ<ETGQLGVVNFPYDDFIYCVMNV

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_1186 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 12 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000001855	1 retrocopy	retro_cfam_498,
Cavia porcellus	ENSCPOG00000010096	1 retrocopy	retro_cpor_216,
Latimeria chalumnae	ENSLACG00000000210	1 retrocopy	retro_lcha_89,
Loxodonta africana	ENSLAFG00000027380	2 retrocopies	retro_lafr_1186 , retro_lafr_487,
Monodelphis domestica	ENSMODG00000010355	1 retrocopy	retro_mdom_782,
Mustela putorius furo	ENSMPUG00000018313	1 retrocopy	retro_mputfur_1147,
Pteropus vampyrus	ENSPVAG00000007438	2 retrocopies	retro_pvam_1112, retro_pvam_734,
Rattus norvegicus	ENSRNOG00000049780	1 retrocopy	retro_rnor_1237,
Ictidomys tridecemlineatus	ENSSTOG00000004372	1 retrocopy	retro_itri_607,
Tupaia belangeri	ENSTBEG00000004434	1 retrocopy	retro_tbel_4493,
Tarsius syrichta	ENSTSYG00000014640	1 retrocopy	retro_tsyr_1832,
Xenopus tropicalis	ENSXETG00000008793	1 retrocopy	retro_xtro_25,