RetrogeneDB ID: retro_lafr_1000

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_59:6126165..6126321(+)
• Located in intron of: ENSLAFG00000011404

Retrocopy information

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

Parental gene information

• Parental gene symbol: LSM5
• Ensembl ID: ENSLAFG00000029579
• Aliases: None
• Description: LSM5 homolog, U6 small nuclear RNA associated (S. cerevisiae) [Source:HGNC Symbol;Acc:17162]

Sequence

>retro_lafr_1000
CTTCTAGGTTTTGATGACTTTGTCAATATGGTATTGGAAGACGTTACTGAGTTTGAAATCACAGCAGAAGGAAGAAGGAT
TACTAAATTAGATGAGGTTTTGCTAAATGGAAATAATAGAACGGTGCTTGGTCCTGGAGGAGAAGGCCCTGAAGTA

Alignment

ORF - retro_lafr_1000 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 88.46 %
• Parental protein coverage: 57.14 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LLGFDDFVNMVLEDVTEFEITPEGRRITKLDQILLNGNNITMLVPGGEGPEV
          LLGFDDFVNMVLEDVTEFEIT.EGRRITKLD..LLNGNN.T.L.PGGEGPEV
Retrocopy LLGFDDFVNMVLEDVTEFEITAEGRRITKLDEVLLNGNNRTVLGPGGEGPEV

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_1000 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 44 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002332	3 retrocopies	retro_btau_1012, retro_btau_1123, retro_btau_1313,
Callithrix jacchus	ENSCJAG00000009185	3 retrocopies	retro_cjac_1883, retro_cjac_2760, retro_cjac_3068,
Echinops telfairi	ENSETEG00000018068	8 retrocopies	retro_etel_1305, retro_etel_1502, retro_etel_1907, retro_etel_198, retro_etel_2054, retro_etel_2193, retro_etel_454, retro_etel_964,
Loxodonta africana	ENSLAFG00000029579	3 retrocopies	retro_lafr_1000 , retro_lafr_368, retro_lafr_922,
Mus musculus	ENSMUSG00000091625	4 retrocopies	retro_mmus_1568, retro_mmus_423, retro_mmus_826, retro_mmus_837,
Nomascus leucogenys	ENSNLEG00000015268	1 retrocopy	retro_nleu_179,
Otolemur garnettii	ENSOGAG00000013892	3 retrocopies	retro_ogar_2727, retro_ogar_3062, retro_ogar_881,
Pongo abelii	ENSPPYG00000017661	1 retrocopy	retro_pabe_3449,
Pteropus vampyrus	ENSPVAG00000009786	1 retrocopy	retro_pvam_1410,
Rattus norvegicus	ENSRNOG00000042126	3 retrocopies	retro_rnor_1171, retro_rnor_567, retro_rnor_694,
Tupaia belangeri	ENSTBEG00000004876	11 retrocopies	retro_tbel_1043, retro_tbel_1107, retro_tbel_1217, retro_tbel_1323, retro_tbel_1549, retro_tbel_1865, retro_tbel_2203, retro_tbel_2908, retro_tbel_2956, retro_tbel_3330, retro_tbel_4335,
Tursiops truncatus	ENSTTRG00000004237	3 retrocopies	retro_ttru_1521, retro_ttru_1585, retro_ttru_874,