RetrogeneDB ID: retro_lafr_676

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_3:46045123..46045637(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000027639
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000002512
• Aliases: None
• Description: None

Sequence

>retro_lafr_676
GATGAACTCCTAGAAGGAGCTGTGAAGCCTCCGGCAGGTAAGTATCCTATCTTCTTTTTTGGCACCCAGGAACCTGCATT
TCTAGGTCCCAAAGACCTTTTTCCATATAAGGAATACAAAGACGACTTTGGAAAGTCAAACAAACGGAAAGGATTTAATG
AAGGATTGTGGGAAATAGGAAGTAACCCAGGAGTAAAGTTTACTGGATACCAGGCAATTCAGCAACAGAGCTCTTCGGAA
GCTGAGGGAGTAGGTGGAAATACTGCAGATGCGAGCAGTGAAGGTGACAGAGTAGAAGAGGATGGAAATGGCAAAAGAAA
GAATGAAACAGCAGGCTCAAAATGGAAAAAATCATACACTTCAAAGAAATCCTCTGAACAATCCTGGAAATCTCCAGGGG
ATGAAGATGACAAGGACTGCAAAGAAGAGGAAAACAAAAAGCAGCTCTGAGGGTGGAGATGCCAGCAATGACGCACGAAA
CAGAGCTTCAGACTTGCCGAAAACCAGCAAAGGG

Alignment

ORF - retro_lafr_676 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.78 %
• Parental protein coverage: 98.86 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  DELPEGAVKPPANKYPIFFFGTHETAFLGPKDLFPYKEYKDKFGKSNKRKGFNEGLWEIENNPGVKFTGY
          DEL.EGAVKPPA.KYPIFFFGT.E.AFLGPKDLFPYKEYKD.FGKSNKRKGFNEGLWEI..NPGVKFTGY
Retrocopy DELLEGAVKPPAGKYPIFFFGTQEPAFLGPKDLFPYKEYKDDFGKSNKRKGFNEGLWEIGSNPGVKFTGY

Parental  QAIQQQSSSETEGEGGNTADASSEEEGDRVEEDGKGKRKNEKAGSKRKKSYTSKKSSKQSRKSPGDEDDK
          QAIQQQSSSE.EG.GGNTADASS..EGDRVEEDG.GKRKNE.AGSK.KKSYTSKKSS.QS.KSPGDEDDK
Retrocopy QAIQQQSSSEAEGVGGNTADASS--EGDRVEEDGNGKRKNETAGSKWKKSYTSKKSSEQSWKSPGDEDDK

Parental  DCKEEEN-KSSSEGGDAGNDTRNTTSDLQKTSEG
          DCKEEEN.KSSSEGGDA.ND.RN..SDL.KTS.G
Retrocopy DCKEEEN>KSSSEGGDASNDARNRASDLPKTSKG

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_676 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 8 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000018527	1 retrocopy	retro_btau_1740,
Callithrix jacchus	ENSCJAG00000015775	1 retrocopy	retro_cjac_4165,
Dasypus novemcinctus	ENSDNOG00000003696	2 retrocopies	retro_dnov_619, retro_dnov_819,
Echinops telfairi	ENSETEG00000010466	1 retrocopy	retro_etel_1234,
Loxodonta africana	ENSLAFG00000002512	1 retrocopy	retro_lafr_676 ,
Ictidomys tridecemlineatus	ENSSTOG00000028389	2 retrocopies	retro_itri_292, retro_itri_864,
Tursiops truncatus	ENSTTRG00000004950	1 retrocopy	retro_ttru_1471,
Vicugna pacos	ENSVPAG00000004599	1 retrocopy	retro_vpac_380,