RetrogeneDB ID: retro_lafr_673

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_3:26300202..26300787(-)
• Located in intron of: ENSLAFG00000007070

Retrocopy information

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

Parental gene information

• Parental gene symbol: LFNG
• Ensembl ID: ENSLAFG00000018428
• Aliases: None
• Description: None

Sequence

>retro_lafr_673
ACCTTCACCTTCACTGACGGAGATGACCCCGAGCTACAGCTCCAGGGGGGCGGTCATGTCATCAACACCAACCGCTCCGC
TGTGCACACCCACCAGGCGCTCTGCTGCAAGATGGGAATTAATACGACACGTTCTTCATCGAGTCGGGGCGCAGGTGGTT
CTGCCACGTGGATGATGACAACTAGGTGAACCCCGGAAGCCTGCTGCGGCTGCTGGCCTTCTCACCCAGCCAGGACGTGT
ACCTGGGGCGGTCCAGCCTGGACCACCCCATCGAGGCCACTGAGCAGGCCCCAGGGGGTGGCACTGTCACCACGGTCAAG
TTCTGGTTTGCCACCGGTGGGGCTGGATTCTGCCTCAGCGGAGGCCTCGCCCTCAAGATGAGCCCGTGGGCTGGTCTGGG
CAGCTTCATGTGCACGGCTGAGCGGGTGCGGCTCCGGGACTACTGTACCCGCGGGCTACATCGTGGAGGGGCTCCTGGGC
ACGCATCTGCTGCACAGCCCACTTTTCCACTCACACCTGGAGAACCTGCTGCGGCTGCCAGCCGATGCTGTGCTCCAGCA
GGTCAGCTTGAGCTATGGGGGTCCA

Alignment

ORF - retro_lafr_673 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.64 %
• Parental protein coverage: 73.66 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TFIFTDEED-EVLARHTGNVINTNCSAAHSRQALSCKMAVE-YD-HFIESGRKWFCHVDDDNYVNVRALL
          TF.FTD..D.E......G.VINTN.SA.H..QAL.CKM....YD..FIESGR.WFCHVDDDN.VN...LL
Retrocopy TFTFTDGDDPELQLQGGGHVINTNRSAVHTHQALCCKMGIN<YDTFFIESGRRWFCHVDDDN*VNPGSLL

Parental  RLLASYPHKQDVYLGKPSLDRPIQATERV-GEGEVRPVHFWFATGGAGFCISRGLALKMSPWASGGHFLS
          RLLA..P..QDVYLG..SLD.PI.ATE...G.G.V..V.FWFATGGAGFC.S.GLALKMSPWA..G.F..
Retrocopy RLLAFSP-SQDVYLGRSSLDHPIEATEQAPGGGTVTTVKFWFATGGAGFCLSGGLALKMSPWAGLGSFMC

Parental  TAERIRLPDDCT-IGYIVEALLGVPLTRSGLFHSHLENLQQVPASELHEQVGLSPGQP
          TAER.RL.D.CT..GYIVE.LLG..L..S.LFHSHLENL...PA.....QV.LS.G.P
Retrocopy TAERVRLRDYCT>AGYIVEGLLGTHLLHSPLFHSHLENLLRLPADAVLQQVSLSYGGP

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_673 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 1 parental gene, and 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000018428	1 retrocopy	retro_lafr_673 ,