RetrogeneDB ID: retro_lafr_430

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_16:42865230..42865611(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: RAB6B
• Ensembl ID: ENSLAFG00000009905
• Aliases: None
• Description: None

Sequence

>retro_lafr_430
GCAGTAAGGAAGATATCCATCATCACTCACTTCATGTATGACAGCCTTGACTGCGCCTGCCAGACAACCGTTGGAACTGA
CTTCCTGTCTAAGATAATGTACTTGGAGGATTGAACAGTTCAGCTACAGCTATGGAACACAGCTGACCAGGAGCATTTTT
GAAGCCTATTTCCTAGATACATTTGTGATTCAGCTATTACAGTGGTTGTCTATGACATCATGAACAGTAGTTCTTTCAGG
AAGACAGATAAATGGATAGAGGATGTACAAGCCGAAAGAGTTGATGATACCATCATGTTGGTGGGTAACAAGAATGATCT
GAACAACAAAAGACCAGTCTCTGCAGAGAAAGGGGAAGAAAAACCCAGAGACCTCAACATA

Alignment

ORF - retro_lafr_430 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 58.59 %
• Parental protein coverage: 67.72 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SVGKTSLITRFMYDSFDNTYQATIGIDFLSKTMYLEDRTVRLQLWDTAGQERFRSLIPSYIRDSTVAVVV
          .V.K.S.IT.FMYDS.D...Q.T.G.DFLSK.MYLED.TV.LQLW.TA.QE.F.SL.P.YI.DS...VVV
Retrocopy AVRKISIITHFMYDSLDCACQTTVGTDFLSKIMYLED*TVQLQLWNTADQEHF*SLFPRYICDSAITVVV

Parental  YDITNLNSFQQTSKWIDDVRTERGSDVIIMLVGNKTDLADKRQITIEEGEQRAKELSV
          YDI.N..SF..T.KWI.DV..ER..D..IMLVGNK.DL..KR....E.GE.....L..
Retrocopy YDIMNSSSFRKTDKWIEDVQAERVDDT-IMLVGNKNDLNNKRPVSAEKGEEKPRDLNI

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_430 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 5 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000009412	1 retrocopy	retro_etel_1486,
Loxodonta africana	ENSLAFG00000009905	1 retrocopy	retro_lafr_430 ,
Ornithorhynchus anatinus	ENSOANG00000031623	1 retrocopy	retro_oana_94,
Ochotona princeps	ENSOPRG00000001164	5 retrocopies	retro_opri_1098, retro_opri_20, retro_opri_606, retro_opri_797, retro_opri_993,
Pongo abelii	ENSPPYG00000003663	3 retrocopies	retro_pabe_2097, retro_pabe_2191, retro_pabe_3537,