RetrogeneDB ID: retro_lafr_416

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_15:10497492..10497837(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: GOLT1B
• Ensembl ID: ENSLAFG00000000965
• Aliases: None
• Description: None

Sequence

>retro_lafr_416
ATGATCTCCTTAACAGATACCCAGAAAACTGGAATGGGGTTAACAGGATTTGGAGTGTTTTTCCTGTTCTTTGGAATGAT
TCTCTCTTTTGACAAAGCACTACTGCCTATTGGAAATGTTTAATTTGTAGCTGGCTTGGCTTTTGTAATTGGTTTAGAAA
GAACATTCAGATTTTTCTTTCAAAAACATAAAATGAAAGCTACAGGATTTTTCCTGGGTGATATTTTTGTAGTCCTTGTC
GGTTGGTCTTTCATAGGCATGATCTTCAAAATTTATGGGTTCTTTTTCTTGTTCAGAGGCTTTTTCACTGTGGTTGTTGG
CTTTATTAGAAGAGTGCCCTCCTTG

Alignment

ORF - retro_lafr_416 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.57 %
• Parental protein coverage: 83.33 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MISLTDTQKIGMGLTGFGVFFLFFGMILFFDKALLAIGNVLFVAGLAFVIGLERTFRFFFQKHKMKATGF
          MISLTDTQK.GMGLTGFGVFFLFFGMIL.FDKALL.IGNV.FVAGLAFVIGLERTFRFFFQKHKMKATGF
Retrocopy MISLTDTQKTGMGLTGFGVFFLFFGMILSFDKALLPIGNV*FVAGLAFVIGLERTFRFFFQKHKMKATGF

Parental  FLGGVFVVLVGWPLIGMIFEIYGFFLLFRGFFPVVVGFIRRVPVL
          FLG..FVVLVGW..IGMIF.IYGFF.LFRGFF.VVVGFIRRVP.L
Retrocopy FLGDIFVVLVGWSFIGMIFKIYGFFFLFRGFFTVVVGFIRRVPSL

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_416 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000013576	2 retrocopies	retro_dnov_158, retro_dnov_1730,
Loxodonta africana	ENSLAFG00000000965	1 retrocopy	retro_lafr_416 ,
Tarsius syrichta	ENSTSYG00000009234	1 retrocopy	retro_tsyr_567,