RetrogeneDB ID: retro_lafr_529

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:41499399..41499769(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: AZI2
• Ensembl ID: ENSLAFG00000008538
• Aliases: None
• Description: None

Sequence

>retro_lafr_529
ATGGATACACTGGTAGAAGATGATTTTTGCTTTCTGAATCATGAAAAAGCTGAAGGAGAGATACAGTGACTCTAGCCTCA
GTATATTCAGGAATTAAAGCTGTTGTTTCCTTCTTGCCCTTGTCACTGCATATGAAGACATCAAAAAACAGCTTAAGGAT
TCAGAGAAAGAGAACTCTTTCTTAAAGACAACAACAAGATTTTTGGATGAAAAGCTCATGGAGGGCTTGATTAGATGAAG
AATCAAGTTCTGTGGGCAAAAACAAGTAAATAATGTCTATCGTGCATATCAAGAGGTCTGCATTGATAGAGATCATTTGA
AGAGGAAGTTTGATAAAATGAATGAAGAAAACTCTGACTCTTTGAAGATT

Alignment

ORF - retro_lafr_529 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.75 %
• Parental protein coverage: 57.21 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MDTLVEDDICILNHEKAH-RRDLVTPASVYSGDESVASHF-ALVTAYEDIKKRLKDSEKENSLLKKRVRL
          MDTLVEDD.C.LNHEKA..RRD.VT.ASVYSG...V.S...ALVTAYEDIKK.LKDSEKENS.LK...R.
Retrocopy MDTLVEDDFCFLNHEKAE<RRDTVTLASVYSGIKAVVSFL<ALVTAYEDIKKQLKDSEKENSFLKTTTRF

Parental  LEEKLIG-ARLDDES-SVGR-EQVNKAYHAYREVCIDRDNLKSKLDKMNKDNSESLKV
          L.EKL...A.LD.ES.SVG...QVN..Y.AY.EVCIDRD.LK.K.DKMN..NS.SLK.
Retrocopy LDEKLME>A*LDEESSSVGK<KQVNNVYRAYQEVCIDRDHLKRKFDKMNEENSDSLKI

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_529 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 14 parental genes, and 22 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000010432	2 retrocopies	retro_chof_1794, retro_chof_234,
Dasypus novemcinctus	ENSDNOG00000011053	2 retrocopies	retro_dnov_1377, retro_dnov_542,
Homo sapiens	ENSG00000163512	2 retrocopies	retro_hsap_1491, retro_hsap_1564,
Gorilla gorilla	ENSGGOG00000022881	2 retrocopies	retro_ggor_1145, retro_ggor_1189,
Loxodonta africana	ENSLAFG00000008538	2 retrocopies	retro_lafr_529 , retro_lafr_925,
Myotis lucifugus	ENSMLUG00000000043	3 retrocopies	retro_mluc_1707, retro_mluc_435, retro_mluc_611,
Macaca mulatta	ENSMMUG00000000056	1 retrocopy	retro_mmul_2135,
Monodelphis domestica	ENSMODG00000015075	1 retrocopy	retro_mdom_1786,
Nomascus leucogenys	ENSNLEG00000004069	1 retrocopy	retro_nleu_1714,
Oryctolagus cuniculus	ENSOCUG00000014956	1 retrocopy	retro_ocun_1778,
Otolemur garnettii	ENSOGAG00000005896	1 retrocopy	retro_ogar_3078,
Pongo abelii	ENSPPYG00000014053	2 retrocopies	retro_pabe_1241, retro_pabe_3784,
Pan troglodytes	ENSPTRG00000014707	1 retrocopy	retro_ptro_1052,
Tursiops truncatus	ENSTTRG00000016434	1 retrocopy	retro_ttru_1093,