RetrogeneDB ID: retro_lafr_450

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_17:22837357..22837700(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG12
• Ensembl ID: ENSLAFG00000015307
• Aliases: None
• Description: None

Sequence

>retro_lafr_450
GAAGCTGTCACCACTGAGCCTCCTACTTCTGCTGCAGTCCCCCCAGGGCCAAGGAACCTACCCGAGACACCAGAAAAAAA
TTTTTTTTTTCATCCTGCTAAAGGCTGTGGGAGACACTCCTATTATGAAAACAGTGGAGTGGGCTATAGAGGGAACCCGA
ACCATCCAAGGATTCATTGACTTCATCAAAAAGTTCCTTAAACTTGTGGCCTCAGAATAGTTGTTTACTTATGTGTATCA
GTCCTTTGTCCCTACCCTAGACCAGGAAATTGAAACACTCTATGGGTGTTTTGGCAGTGATGGTAAAATGGTCCTACATT
ACTGCAAATCTCAGGCTTGGGGA

Alignment

ORF - retro_lafr_450 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.07 %
• Parental protein coverage: 80.58 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  ETVTPEPP-SAAVSPG-SEEPTGDTK-KKID--ILLKAVGDTPIMKTKKWAVERTRTIQGLIDFIKKFLK
          E.VT.EPP.SAAV.PG...EPT.DT..KKI...ILLKAVGDTPIMKT..WA.E.TRTIQG.IDFIKKFLK
Retrocopy EAVTTEPPTSAAVPPG<AKEPTRDTR<KKIFFFILLKAVGDTPIMKTVEWAIEGTRTIQGFIDFIKKFLK

Parental  LVASEQLFIYVNQSFAPSPDQEVGTLYECFGSDGKLVLHYCKSQAWG
          LVASE.LF.YV.QSF.P..DQE..TLY.CFGSDGK.VLHYCKSQAWG
Retrocopy LVASE*LFTYVYQSFVPTLDQEIETLYGCFGSDGKMVLHYCKSQAWG

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_450 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 12 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000004464	1 retrocopy	retro_chof_1745,
Cavia porcellus	ENSCPOG00000007187	2 retrocopies	retro_cpor_865, retro_cpor_944,
Equus caballus	ENSECAG00000012452	1 retrocopy	retro_ecab_883,
Echinops telfairi	ENSETEG00000018837	1 retrocopy	retro_etel_1721,
Homo sapiens	ENSG00000145782	1 retrocopy	retro_hsap_1860,
Gorilla gorilla	ENSGGOG00000016888	2 retrocopies	retro_ggor_1814, retro_ggor_2150,
Loxodonta africana	ENSLAFG00000015307	1 retrocopy	retro_lafr_450 ,
Myotis lucifugus	ENSMLUG00000002759	1 retrocopy	retro_mluc_2259,
Pongo abelii	ENSPPYG00000015699	3 retrocopies	retro_pabe_1518, retro_pabe_1519, retro_pabe_2158,
Pan troglodytes	ENSPTRG00000017154	2 retrocopies	retro_ptro_1240, retro_ptro_1748,
Rattus norvegicus	ENSRNOG00000000157	1 retrocopy	retro_rnor_2811,
Ictidomys tridecemlineatus	ENSSTOG00000011755	1 retrocopy	retro_itri_156,