RetrogeneDB ID: retro_lafr_616

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_25:24690016..24690386(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000031860
• Aliases: None
• Description: None

Sequence

>retro_lafr_616
ATGGGCCACCGCCCTACCTCATGTTACCAGTATTATAAAAATAAGCCCTACCCAAAGTTTTGCTTCTACCAAGGTATGCC
TGATACCAAGATTTGCATCTTTGACCTGGGTTGGAAGAAGGCAAAAGTGGATGAGTTCCCACTCTGTGGCCACTTGGTCA
GATGAATATGAGCAGCTCTCCTCAGAAGCCCTGGAGGCTGCCGGTATTTATGCCAACAAGTCCATGGTGAAAAGTTGTGG
CAAAGATGGCTTTCACATCCGACTGTGGCTCCATCCCTCCCATGCCATTTGTATCAACAAGATGTTGATCTGTGCTGGGG
CTGACAGGCTCCAGACAGGTATGCTAGGTGCCTTTGGAAAACCCAAAGGT

Alignment

ORF - retro_lafr_616 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.19 %
• Parental protein coverage: 57.55 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGRRPARWLRYCKNKP-PKTPFCRDVPDAKIRIFDLGRKKAKVDEFPLCHMV-SDEYEQLSSEALEAARI
          MG.RP.....Y.KNKP.PK..F....PD.KI.IFDLG.KKAKVDEFPLC....SDEYEQLSSEALEAA.I
Retrocopy MGHRPTSCYQYYKNKPYPKFCFYQGMPDTKICIFDLGWKKAKVDEFPLCGHL>SDEYEQLSSEALEAAGI

Parental  CANKYMVKSCGKDGFHIRVRLHPFHVIRINKMLSCAGADRLQTGMRGAFGKPQG
          .ANK.MVKSCGKDGFHIR..LHP.H.I.INKML.CAGADRLQTGM.GAFGKP.G
Retrocopy YANKSMVKSCGKDGFHIRLWLHPSHAICINKMLICAGADRLQTGMLGAFGKPKG

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_616 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 21 retrocopies.

Species	Parental gene accession	Retrocopies number
Echinops telfairi	ENSETEG00000001712	10 retrocopies	retro_etel_1073, retro_etel_1284, retro_etel_1517, retro_etel_1654, retro_etel_249, retro_etel_338, retro_etel_403, retro_etel_47, retro_etel_538, retro_etel_631,
Loxodonta africana	ENSLAFG00000031860	1 retrocopy	retro_lafr_616 ,
Macropus eugenii	ENSMEUG00000013163	3 retrocopies	retro_meug_1839, retro_meug_5, retro_meug_547,
Macaca mulatta	ENSMMUG00000005494	5 retrocopies	retro_mmul_1506, retro_mmul_1654, retro_mmul_307, retro_mmul_335, retro_mmul_906,
Monodelphis domestica	ENSMODG00000008731	2 retrocopies	retro_mdom_177, retro_mdom_829,