RetrogeneDB ID: retro_lafr_636

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_27:16460843..16461084(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NME1-NME2
• Ensembl ID: ENSLAFG00000007784
• Aliases: None
• Description: None

Sequence

>retro_lafr_636
GTGCGGCGCAGCCCACTGGGCGAGATCGTCAAGCACTTAGAGCCAAAGGGATTCCGCCTCGTGGTCATGAAGTTCCTTGG
GCCTGCAAGAAACACCTGCAGCAACACTATGTTAACCTGAAAGACTGCCCATTCTTCCCAGGGCTGAAGTACGTGAACTC
AGAACCAGTTGTGGCCATGGTATGGGAGGACTGAAGGTAGTGAAGACAGGTCAAGTGATGCGTGGGGAGACCAATCCAGC
A

Alignment

ORF - retro_lafr_636 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.86 %
• Parental protein coverage: 53.95 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  VQRGLVGDIIKRFEQKGFRLVAMKFVQ-ASEEHLKQHYIDLKDRPFFPGLVKYMNSGPVVAMVWE-GLNV
          V.R...G.I.K..E.KGFRLV.MKF...A...HL.QHY..LKD.PFFPGL.KY.NS.PVVAMVWE.GL.V
Retrocopy VRRSPLGEIVKHLEPKGFRLVVMKFLG<ACKKHLQQHYVNLKDCPFFPGL-KYVNSEPVVAMVWE<GLKV

Parental  VKTGRVMLGETNPA
          VKTG.VM.GETNPA
Retrocopy VKTGQVMRGETNPA

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_636 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 15 parental genes, and 39 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000008022	3 retrocopies	retro_amel_1573, retro_amel_390, retro_amel_538,
Bos taurus	ENSBTAG00000047186	1 retrocopy	retro_btau_1329,
Equus caballus	ENSECAG00000021658	1 retrocopy	retro_ecab_404,
Erinaceus europaeus	ENSEEUG00000003783	2 retrocopies	retro_eeur_156, retro_eeur_5,
Felis catus	ENSFCAG00000006742	5 retrocopies	retro_fcat_1083, retro_fcat_1117, retro_fcat_1475, retro_fcat_216, retro_fcat_663,
Homo sapiens	ENSG00000011052	1 retrocopy	retro_hsap_1063,
Loxodonta africana	ENSLAFG00000007784	1 retrocopy	retro_lafr_636 ,
Myotis lucifugus	ENSMLUG00000016929	3 retrocopies	retro_mluc_1422, retro_mluc_1882, retro_mluc_637,
Macaca mulatta	ENSMMUG00000001940	1 retrocopy	retro_mmul_1827,
Mustela putorius furo	ENSMPUG00000015573	4 retrocopies	retro_mputfur_1236, retro_mputfur_1590, retro_mputfur_327, retro_mputfur_912,
Mus musculus	ENSMUSG00000020857	1 retrocopy	retro_mmus_221,
Rattus norvegicus	ENSRNOG00000002671	8 retrocopies	retro_rnor_1129, retro_rnor_1610, retro_rnor_1708, retro_rnor_1784, retro_rnor_1966, retro_rnor_2646, retro_rnor_2951, retro_rnor_628,
Sus scrofa	ENSSSCG00000017591	1 retrocopy	retro_sscr_854,
Tupaia belangeri	ENSTBEG00000013053	6 retrocopies	retro_tbel_1271, retro_tbel_1386, retro_tbel_2497, retro_tbel_294, retro_tbel_4620, retro_tbel_820,
Tursiops truncatus	ENSTTRG00000007433	1 retrocopy	retro_ttru_1821,