RetrogeneDB ID: retro_lafr_684

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_3:95377345..95377688(-)
• Located in intron of: ENSLAFG00000008025

Retrocopy information

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

Parental gene information

• Parental gene symbol: TSEN15
• Ensembl ID: ENSLAFG00000014109
• Aliases: None
• Description: None

Sequence

>retro_lafr_684
ATGGAGGAGCGTGGGGGTTCTGAGCCCACCCTAGCAGCAGCGGCCTGGTCCAGGGTGGCGTAGGCAGTGGAGGTGGCAGC
TGTGATCTGTGGTTCTCCAAGGATGCCTGGATGGGCACCACCCTAAGCACTTAGAGATAATGCAATTAGATATCGGAGAC
ACTCTCCAAGTTTATACAGCATTCTTGGTTTACCTGGATCTCACAGAGATGAAAAATTGGCATAAGGTAAACTGTATGGG
GTTACCAGAACTGCAGCACCTCTGCCTGGTTGGTGGTGAGACAGGAGAAAGATTACAGACTATAGGGCCTACTGCCTTTG
GCGCATCCCTTGGGCATGACAGA

Alignment

ORF - retro_lafr_684 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 68.07 %
• Parental protein coverage: 68.82 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MEERGSSEPT-PGCSGLGRGGARSGGGDGCDLWAPEDAWMGT-HPKYLEMMELDIGDATQVYIAFLVYLD
          MEERG.SEPT.P..SGL..GG..SGGG..CDLW...DAWMGT.HPK.LE.M.LDIGD..QVY.AFLVYLD
Retrocopy MEERGGSEPT<PSSSGLVQGGVGSGGGS-CDLWFSKDAWMGT<HPKHLEIMQLDIGDTLQVYTAFLVYLD

Parental  LMESKSWHEVNCVGLPELQLICLVGTEIEGEGLQTVVPTPVSASLSHNR
          L.E.K.WH.VNC.GLPELQ..CLVG.E..GE.LQT..PT...ASL.H.R
Retrocopy LTEMKNWHKVNCMGLPELQHLCLVGGE-TGERLQTIGPTAFGASLGHDR

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_684 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 16 parental genes, and 24 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000016369	1 retrocopy	retro_btau_971,
Callithrix jacchus	ENSCJAG00000005356	1 retrocopy	retro_cjac_3055,
Dasypus novemcinctus	ENSDNOG00000017611	2 retrocopies	retro_dnov_1176, retro_dnov_2529,
Homo sapiens	ENSG00000198860	1 retrocopy	retro_hsap_1721,
Gorilla gorilla	ENSGGOG00000015804	2 retrocopies	retro_ggor_2267, retro_ggor_240,
Loxodonta africana	ENSLAFG00000014109	1 retrocopy	retro_lafr_684 ,
Macaca mulatta	ENSMMUG00000016409	1 retrocopy	retro_mmul_1214,
Mustela putorius furo	ENSMPUG00000011790	1 retrocopy	retro_mputfur_1261,
Mus musculus	ENSMUSG00000014980	1 retrocopy	retro_mmus_2721,
Nomascus leucogenys	ENSNLEG00000018024	1 retrocopy	retro_nleu_98,
Otolemur garnettii	ENSOGAG00000003128	1 retrocopy	retro_ogar_3264,
Pongo abelii	ENSPPYG00000000421	4 retrocopies	retro_pabe_1436, retro_pabe_3065, retro_pabe_3196, retro_pabe_469,
Pan troglodytes	ENSPTRG00000023202	2 retrocopies	retro_ptro_1229, retro_ptro_147,
Pteropus vampyrus	ENSPVAG00000001103	1 retrocopy	retro_pvam_1458,
Ictidomys tridecemlineatus	ENSSTOG00000013230	2 retrocopies	retro_itri_1538, retro_itri_1849,
Vicugna pacos	ENSVPAG00000002941	2 retrocopies	retro_vpac_381, retro_vpac_565,