RetrogeneDB ID: retro_lafr_547

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_20:37805164..37805591(-)
• Located in intron of: ENSLAFG00000002742

Retrocopy information

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

Parental gene information

• Parental gene symbol: RWDD2B
• Ensembl ID: ENSLAFG00000004504
• Aliases: None
• Description: None

Sequence

>retro_lafr_547
ATAACTGAAATTGAGCAGGCAGAAGCCCAGCCCCCCGAGTTAGAACTGCTGGCCGTTATGTTCCCCAGTAACAAGTTCAT
AGTTCCTGATCAGCTAGCTTTAGCCGAATTGAAAGATAATATTGAAAAGAAGACCATAGAGGGACGATCCTCAAAAATTT
ACTGTCAGTATCAACCTTGATGTGTCTGAGGAAGCAATGGTGATGTTTTCACTGACCTGTATTCTTTTCAAATACCCTGC
AGTTCGGCCTGAAATTACTGTCAGATCAATATTATTAAGTAGATCCCAGCAGTCTCAGCTGAACACAGATCTGAATGCAT
ACTTGGAAAAGAACTGTTACGGAGATGTCTGTATACTGAATGCCACAGAGCTATGTCAGCAGAGACACCACATCTTCTGC
CACCATAGGAAGTACAGCGCTACCACT

Alignment

ORF - retro_lafr_547 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.03 %
• Parental protein coverage: 50.34 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTELEQAEAQLSELELLASMFPSEKEFVVNDQLALAELKDCVEKKTTEGRSSKIY-FTVNINLDVSEEAM
          .TE.EQAEAQ..ELELLA.MFPS.K.F.V.DQLALAELKD..EKKT.EGRSSKIY....N...DVSEEAM
Retrocopy ITEIEQAEAQPPELELLAVMFPSNK-FIVPDQLALAELKDNIEKKTIEGRSSKIY>VSINL--DVSEEAM

Parental  VTFSLACVLPFKYPAVLPEITVRSVFLSRSQQTQLNTDLHAYLQKNCCGDVCILNATDWVREHASGYVSR
          V.FSL.C.L.FKYPAV.PEITVRS..LSRSQQ.QLNTDL.AYL.KNC.GDVCILNAT.............
Retrocopy VMFSLTCIL-FKYPAVRPEITVRSILLSRSQQSQLNTDLNAYLEKNCYGDVCILNATELCQQRHHIFCHH

Parental  DATSSTT
          ...S.TT
Retrocopy RKYSATT

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_547 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000004504	1 retrocopy	retro_lafr_547 ,
Ictidomys tridecemlineatus	ENSSTOG00000027590	1 retrocopy	retro_itri_907,