RetrogeneDB ID: retro_lafr_800

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_39:13219608..13219923(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000020646
• Aliases: None
• Description: None

Sequence

>retro_lafr_800
ATGGTGACTGGGGCACCGGATTGGCAAGCACTCTTCAGTCAGTCCATGAAAGGGCTTCTCACAGAGAAGGTGAACACCTG
TGGTACTGATGTGATGGTGCTCACCAAGCAGGTGCTGAAGGGCTCCTGGAGCTCCGAGCTGCTAGGTCAGACAGCTCAAA
ACATGGTACTATAGGAAGATACCATCTTGCACTCAGAAGATAGTTTAAGGAAAACGGCACTAATAACAACACACCTTCAA
TACCAGCAAGAAGCTATTCAGAAGAATGCTGAGCAGTCGTCAGATCTAGAGGACGAGCTGAGTCACATGTTGAAA

Alignment

ORF - retro_lafr_800 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 81.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MATGAPDSQARFGQSVKGLLTEKVNTCGTDVIALTKQVLKGSRSSELLGQAARNMVLQEDAILHSEDSLR
          M.TGAPD.QA.F.QS.KGLLTEKVNTCGTDV..LTKQVLKGS.SSELLGQ.A.NMVL.ED.ILHSEDSLR
Retrocopy MVTGAPDWQALFSQSMKGLLTEKVNTCGTDVMVLTKQVLKGSWSSELLGQTAQNMVL*EDTILHSEDSLR

Parental  KMAIITTHLQYQQEAIQKNVEQSSDLQDQLNHLLK
          K.A.ITTHLQYQQEAIQKN.EQSSDL.D.L.H.LK
Retrocopy KTALITTHLQYQQEAIQKNAEQSSDLEDELSHMLK

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_800 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 5 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000021622	1 retrocopy	retro_cpor_829,
Loxodonta africana	ENSLAFG00000020646	4 retrocopies	retro_lafr_1177, retro_lafr_299, retro_lafr_608, retro_lafr_800 ,
Macropus eugenii	ENSMEUG00000013119	3 retrocopies	retro_meug_112, retro_meug_1350, retro_meug_231,
Otolemur garnettii	ENSOGAG00000032692	1 retrocopy	retro_ogar_1702,
Procavia capensis	ENSPCAG00000000834	1 retrocopy	retro_pcap_87,