RetrogeneDB ID: retro_lafr_234

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_10:62037260..62037601(+)
• Located in intron of: ENSLAFG00000012854

Retrocopy information

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

Parental gene information

• Parental gene symbol: GABARAPL2
• Ensembl ID: ENSLAFG00000017065
• Aliases: None
• Description: None

Sequence

>retro_lafr_234
ATGAAGTGGATGTTCAAGGAGGACCACTTGTTGGAACACAGATGCATAAAATCCAAGAAAATCTGAGTGAAATATCCTGA
CCAGACTGTGGAAAAAATCTCCTGCTCTCAGATTGTTGACACTGACAAGTGGAAGTACCTGGTTCCATCTGACATCACTG
TGGCTCAGTTCATGTGGATCATCAGCAGAAGGACCCAGCTTCCTTTGAAAAGTCGATCTTCCTCTTTGTGGATAAGACAG
TCCCACAGTCCAGCCTAACTATGCGGCAGTTTTGTGAGAAGGAAAAAGATAAAGATGGATTTTCGTATGTGGCCTACAGC
AGAGTGAACACTTTTGGCTTT

Alignment

ORF - retro_lafr_234 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 72.03 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MKWMFKEDHSLEHRCVESAKIRAKYPDRVPVSVPGVRGLGIVDIDKRKYLVPSDITVAQFMWIIRKRIQL
          MKWMFKEDH.LEHRC..S.KI..KYPD.....V.......IVD.DK.KYLVPSDITVAQFMWII..R.QL
Retrocopy MKWMFKEDHLLEHRCIKSKKI*VKYPDQ---TVEKISCSQIVDTDKWKYLVPSDITVAQFMWIISRRTQL

Parental  PS-EKAIFLFVDKTVPQSSLTMGQLYEKEKDEDGFLYVAYSGENTFGF
          P..EK.IFLFVDKTVPQSSLTM.Q..EKEKD.DGF.YVAYS..NTFGF
Retrocopy PL<EKSIFLFVDKTVPQSSLTMRQFCEKEKDKDGFSYVAYSRVNTFGF

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_234 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 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000005453	2 retrocopies	retro_amel_1054, retro_amel_1238,
Callithrix jacchus	ENSCJAG00000014253	1 retrocopy	retro_cjac_146,
Dasypus novemcinctus	ENSDNOG00000002240	2 retrocopies	retro_dnov_1755, retro_dnov_2332,
Homo sapiens	ENSG00000034713	1 retrocopy	retro_hsap_4115,
Gorilla gorilla	ENSGGOG00000012299	2 retrocopies	retro_ggor_2761, retro_ggor_342,
Loxodonta africana	ENSLAFG00000000744	1 retrocopy	retro_lafr_61,
Loxodonta africana	ENSLAFG00000017065	2 retrocopies	retro_lafr_234 , retro_lafr_543,
Loxodonta africana	ENSLAFG00000023364	3 retrocopies	retro_lafr_1077, retro_lafr_915, retro_lafr_974,
Myotis lucifugus	ENSMLUG00000015112	1 retrocopy	retro_mluc_1207,
Macaca mulatta	ENSMMUG00000005759	2 retrocopies	retro_mmul_2369, retro_mmul_540,
Nomascus leucogenys	ENSNLEG00000013048	2 retrocopies	retro_nleu_1560, retro_nleu_580,
Pongo abelii	ENSPPYG00000007565	2 retrocopies	retro_pabe_3368, retro_pabe_372,
Pan troglodytes	ENSPTRG00000008362	2 retrocopies	retro_ptro_250, retro_ptro_2794,
Rattus norvegicus	ENSRNOG00000019425	1 retrocopy	retro_rnor_57,