RetrogeneDB ID: retro_lafr_146

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:96436461..96436710(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: FAM136A
• Ensembl ID: ENSLAFG00000002304
• Aliases: None
• Description: None

Sequence

>retro_lafr_146
ATGGTGGAACTGCACCAGCTCCGAGTGCACAAGGCAGTCGACTCCATGGTGAAGGGTTTGGAGACAGAGACCATCCGGAA
GATGTGGGGCATCGTGTTCCAGGGCAACCAGCTGCTGTGGGCATAGCCAGGCATCCATGCTGCGGTTGTACCAGTGCACT
GAGCGCTGCCATCACCGCTGGCTCAAGCCCAGGCCCTGGTGACCAGCCAGTTGGAGAAGATCCAGCACCAAATACAGACT
GTATACTGT

Alignment

ORF - retro_lafr_146 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.36 %
• Parental protein coverage: 62.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MAELQQLRVQEAVDSMVKSLERENIRKMQGIMF-RCSASCCEDSQASMQQVHQCIERCH-APLAQAQALV
          M.EL.QLRV..AVDSMVK.LE.E.IRKM.GI.F.R....C...SQASM....QC.ERCH..PLAQAQALV
Retrocopy MVELHQLRVHKAVDSMVKGLETETIRKMWGIVF>RATSCC-GHSQASMLRLYQCTERCH<SPLAQAQALV

Parental  TSELEKFQDRLARCTMHC
          TS.LEK.Q......T..C
Retrocopy TSQLEKIQHQIQ--TVYC

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_146 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 13 parental genes, and 45 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000008674	2 retrocopies	retro_btau_37, retro_btau_88,
Canis familiaris	ENSCAFG00000003353	2 retrocopies	retro_cfam_1042, retro_cfam_148,
Cavia porcellus	ENSCPOG00000009117	1 retrocopy	retro_cpor_221,
Dasypus novemcinctus	ENSDNOG00000019447	7 retrocopies	retro_dnov_2036, retro_dnov_2465, retro_dnov_2612, retro_dnov_324, retro_dnov_620, retro_dnov_873, retro_dnov_901,
Felis catus	ENSFCAG00000008119	1 retrocopy	retro_fcat_1459,
Gorilla gorilla	ENSGGOG00000023247	6 retrocopies	retro_ggor_1361, retro_ggor_1625, retro_ggor_2155, retro_ggor_2356, retro_ggor_53, retro_ggor_8,
Loxodonta africana	ENSLAFG00000002304	1 retrocopy	retro_lafr_146 ,
Macropus eugenii	ENSMEUG00000015791	8 retrocopies	retro_meug_1126, retro_meug_1351, retro_meug_1545, retro_meug_167, retro_meug_2131, retro_meug_219, retro_meug_457, retro_meug_719,
Macaca mulatta	ENSMMUG00000007962	5 retrocopies	retro_mmul_1421, retro_mmul_1772, retro_mmul_220, retro_mmul_327, retro_mmul_656,
Monodelphis domestica	ENSMODG00000011533	1 retrocopy	retro_mdom_65,
Mus musculus	ENSMUSG00000057497	2 retrocopies	retro_mmus_240, retro_mmus_3101,
Rattus norvegicus	ENSRNOG00000016273	1 retrocopy	retro_rnor_1679,
Tupaia belangeri	ENSTBEG00000017418	8 retrocopies	retro_tbel_1377, retro_tbel_1875, retro_tbel_2479, retro_tbel_2516, retro_tbel_3373, retro_tbel_3703, retro_tbel_401, retro_tbel_999,