RetrogeneDB ID: retro_lafr_61

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_17:12827310..12827664(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000022545
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: GABARAP
• Ensembl ID: ENSLAFG00000000744
• Aliases: None
• Description: None

Sequence

>retro_lafr_61
ATGAAGTTCGTGTATAAAGAGGAGCATCCGTTCGAAAAGCGCCGCTCTGAGGGCGAGAAGATCCGAAAGAAATACCCGGA
CCGGGGCCCGGTGATAGTAGAGAAGGCCCCCAAAGCTCGGATAGGAGATCTGGACAAAAAGAAATACTTGGTGCCTTCTG
ACCTCACAGTTGGTCAGTTCTACTTCTTGATCCGGAAGCGAATTCATCTCCGAACTGAAGATGCCTTGTTTTTCTTTGTC
AACAATGTCATTCCACCCACCAGTGCCACAATGGGTCAGCTATACCAGGAACAGCACAAAGAAAACTTCTTTCTATACAT
TGCCTGCAGTAATGAAAGTGTCTACCATCTGTGA

Alignment

ORF - retro_lafr_61 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 93.16 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFVYKEEHPFEKRRSEGEKIRKKYPDRVPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHL
          MKFVYKEEHPFEKRRSEGEKIRKKYPDR.PVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHL
Retrocopy MKFVYKEEHPFEKRRSEGEKIRKKYPDRGPVIVEKAPKARIGDLDKKKYLVPSDLTVGQFYFLIRKRIHL

Parental  RAEDALFFFVNNVIPPTSATMGQLYQEHHEEDFFLYIAYSDESVYGL
          R.EDALFFFVNNVIPPTSATMGQLYQE.H.E.FFLYIA.S.ESVY.L
Retrocopy RTEDALFFFVNNVIPPTSATMGQLYQEQHKENFFLYIACSNESVYHL

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_61 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 20 parental genes, and 34 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000014883	1 retrocopy	retro_btau_905,
Ciona intestinalis	ENSCING00000012473	1 retrocopy	retro_cint_25,
Callithrix jacchus	ENSCJAG00000016655	2 retrocopies	retro_cjac_2851, retro_cjac_3820,
Dipodomys ordii	ENSDORG00000005229	1 retrocopy	retro_dord_308,
Echinops telfairi	ENSETEG00000004652	7 retrocopies	retro_etel_1020, retro_etel_1078, retro_etel_1562, retro_etel_2068, retro_etel_493, retro_etel_666, retro_etel_976,
Gorilla gorilla	ENSGGOG00000013770	1 retrocopy	retro_ggor_821,
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,
Macaca mulatta	ENSMMUG00000010545	1 retrocopy	retro_mmul_155,
Mustela putorius furo	ENSMPUG00000010473	2 retrocopies	retro_mputfur_1290, retro_mputfur_258,
Mus musculus	ENSMUSG00000018567	1 retrocopy	retro_mmus_3107,
Nomascus leucogenys	ENSNLEG00000008049	2 retrocopies	retro_nleu_1670, retro_nleu_4,
Oryctolagus cuniculus	ENSOCUG00000006997	1 retrocopy	retro_ocun_311,
Otolemur garnettii	ENSOGAG00000004388	2 retrocopies	retro_ogar_1212, retro_ogar_1224,
Pongo abelii	ENSPPYG00000007901	1 retrocopy	retro_pabe_122,
Pan troglodytes	ENSPTRG00000034115	1 retrocopy	retro_ptro_60,
Rattus norvegicus	ENSRNOG00000017417	2 retrocopies	retro_rnor_1818, retro_rnor_2093,
Sus scrofa	ENSSSCG00000017936	1 retrocopy	retro_sscr_163,
Drosophila melanogaster	FBgn0052672	1 retrocopy	retro_dmel_23,