RetrogeneDB ID: retro_lafr_1157

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_8:20721233..20721604(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: MRPL51
• Ensembl ID: ENSLAFG00000002106
• Aliases: None
• Description: None

Sequence

>retro_lafr_1157
AGCAGAGGGGCAGGCAGGGGCCCGTGGGGCTGGGTGTCCCTGGCCTGCAGAACCTTTTCTCTGGGCATTCCTGGACTGCC
CCATGTAAGGCTTACCCTCCCACCCCCTGAAGTTGTTAAATCATTGGAACAAGAAGAGAGCTGTGTTTGAGCTGTATGGC
AACACTGGGATCCTGGATAACTCTGAAAGGCACCCCAAAGAACTGATCAAGGACCCCAAATGGCTTCGGGGTTGGAATGG
GAATGAACTACAGCATTGTATCAGAAAAGAAGAAAATAGCTAGGAATCGCATGTTCCTGGATGACCTGCAAAAACTTAAC
AAACGCATAAACTGTCTTTACAAACACTTTATTCAACATAGACAGTACCGG

Alignment

ORF - retro_lafr_1157 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.8 %
• Parental protein coverage: 96.09 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SWGASRVLWGWVPLTCRSFSLGVPGLSRVRLTLPPPKVV-DRWNEKRAMFGVYDNIGILGNFEKHPKELI
          S.GA.R..WGWV.L.CR.FSLG.PGL..VRLTLPPP.VV...WN.KRA.F..Y.N.GIL.N.E.HPKELI
Retrocopy SRGAGRGPWGWVSLACRTFSLGIPGLPHVRLTLPPPEVV>NHWNKKRAVFELYGNTGILDNSERHPKELI

Parental  KGPRWLRGWKGNELQRCIR-KKKMVGNRMFLDDLHNLNKRISYLYKHFNRHGKYR
          K.P.WLRGW.GNELQ.CIR.KKK...NRMFLDDL..LNKRI..LYKHF..H..YR
Retrocopy KDPKWLRGWNGNELQHCIR>KKKIARNRMFLDDLQKLNKRINCLYKHFIQHRQYR

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_1157 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 8 parental genes, and 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014729	1 retrocopy	retro_btau_1609,
Callithrix jacchus	ENSCJAG00000018232	1 retrocopy	retro_cjac_548,
Cavia porcellus	ENSCPOG00000008478	1 retrocopy	retro_cpor_1082,
Loxodonta africana	ENSLAFG00000002106	2 retrocopies	retro_lafr_1157 , retro_lafr_845,
Mus musculus	ENSMUSG00000030335	2 retrocopies	retro_mmus_1967, retro_mmus_2607,
Pteropus vampyrus	ENSPVAG00000012566	1 retrocopy	retro_pvam_534,
Rattus norvegicus	ENSRNOG00000019165	2 retrocopies	retro_rnor_2582, retro_rnor_926,
Tupaia belangeri	ENSTBEG00000000936	2 retrocopies	retro_tbel_3219, retro_tbel_3408,