RetrogeneDB ID: retro_lafr_1229

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_9:18919756..18920293(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: TMEM41B
• Ensembl ID: ENSLAFG00000006953
• Aliases: None
• Description: None

Sequence

>retro_lafr_1229
ATGGCTAAAGGCAGAGTTGTGGAAAGATTGCAGATGGGGCACTCCACACGACCCCAACTGAGGACTGAGCAGTGGAGACA
AGGGCTTCCATGGTGCTGGGCAGTGGAGAACACTTGAAAGAGAATGCAAGGGCAGAAGCTGGATCAGCAAGAATTTCACT
CCTTATGTTGGTGCCCATATTCTTATCTGCAGCTTTTGTTATGTTTTTGGTATACAAATATTTTCCCCAGTTTAGTGAAG
AAGAAAGAGTGACTACGAAGGTTCCCAGAGATATGGATAATGTTAAGGGTCTAGGACAAGTTTTATCCAAATATAAGGTC
ACCTTTTATGTACAAGCACTTGTAGCTTATTTTGCTGCATATATTTTCTTGGAAACATTTGCTATTCCAGGCTCTGTATT
TCTCAGTATCCTCTCAGGGTTTCTTTATCCCTTTCTGCTAGCCTTATTCCTTATTTGTTTGTTTTCTGGATTGGGTAACT
CATTCTGCTATATGCTTTCCTGTTTAATTGGGGAAACCAGTTGTAATTTATTTCATG

Alignment

ORF - retro_lafr_1229 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.93 %
• Parental protein coverage: 61.51 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAKGSIAERSQTE-ALPTTPVGDQAARTRAPAAPSSGDHLKEKAREEAGSARMSLLILVSIFLLAAFVMF
          MAKG...ER.Q...AL.TTP..D.A..TRA.....SG.HLKE.AR.EAGSAR.SLL.LV.IFL.AAFVMF
Retrocopy MAKGRVVERLQMG<ALHTTPTED*AVETRASMVLGSGEHLKENARAEAGSARISLLMLVPIFLSAAFVMF

Parental  LVYKNFPQLSEEERVTMKVPRDMDDAKALGKVLSKYKDTFYVQVLVAYFATYIFLQTFAIPGSIFLSILS
          LVYK.FPQ.SEEERVT.KVPRDMD..K.LG.VLSKYK.TFYVQ.LVAYFA.YIFL.TFAIPGS.FLSILS
Retrocopy LVYKYFPQFSEEERVTTKVPRDMDNVKGLGQVLSKYKVTFYVQALVAYFAAYIFLETFAIPGSVFLSILS

Parental  GFLYPFPLALFLVCLCSGLGASFCYMLSYLV-GRPVVYKYL
          GFLYPF.LALFL.CL.SGLG.SFCYMLS.L..G.PVV....
Retrocopy GFLYPFLLALFLICLFSGLGNSFCYMLSCLI>GKPVVIYFM

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_1229 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000026871	1 retrocopy	retro_ecab_122,
Loxodonta africana	ENSLAFG00000006953	1 retrocopy	retro_lafr_1229 ,
Mus musculus	ENSMUSG00000047554	1 retrocopy	retro_mmus_3296,