RetrogeneDB ID: retro_lafr_223

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_10:8567025..8567467(+)
• Located in intron of: ENSLAFG00000014862

Retrocopy information

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

Parental gene information

• Parental gene symbol: MOB1A
• Ensembl ID: ENSLAFG00000014338
• Aliases: None
• Description: None

Sequence

>retro_lafr_223
ACACTGGATTTCTTCAACTAGATCAACATGTTATATGGAACGATTACAGAATTCTGCACTAAAGCAAGCTGTCCAGTCAT
GTCTGTAAGTCCACGATATGAGTATCAATGGACAGATATTACTAATACTAAAAAACCAATCAAATGTTCTGCACCAAAAT
ACAGTGACTATTTGATGACTTGGGTTCAGGGTCAGCTTGACAATGAAACTCCTTCTCCTTCTAAGACTGGTGTCCCATTT
GCCAAAGACTTTTATGTCTGTCGCAAAGACTATTCTAAAGCGTCTGTTCAGGGTTTATGCCCATATTTATCATCAGCACT
TTGATTCTGTGATGCAGCTGCATGAGGAGGTCCACCTCAACACCTCTTTTAAGTACTTTACTTTCTTTGTACAGGAGTTT
AATCTGATTGCTAGGAGTGAGCTGACACCTCTTCAGGAATTG

Alignment

ORF - retro_lafr_223 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.11 %
• Parental protein coverage: 69.67 %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TVDFFNQINMLYGTITEFCTEASCSVMSAGPRYEYHWADGTNIKKPIKCSAPKYIDYLMTWVQDQLDDET
          T.DFFN.INMLYGTITEFCT.ASC.VMS..PRYEY.W.D.TN.KKPIKCSAPKY.DYLMTWVQ.QLD.ET
Retrocopy TLDFFN*INMLYGTITEFCTKASCPVMSVSPRYEYQWTDITNTKKPIKCSAPKYSDYLMTWVQGQLDNET

Parental  LFPSKIGVPF-PKNFMSVAKTILKRLFRVYAHIYHQHFDSVMQLQEEAHLNTSFKHFIFFVQEFNLIDRR
          ..PSK.GVPF.PK.FMSVAKTILKRLFRVYAHIYHQHFDSVMQL.EE.HLNTSFK.F.FFVQEFNLI.R.
Retrocopy PSPSKTGVPF>PKTFMSVAKTILKRLFRVYAHIYHQHFDSVMQLHEEVHLNTSFKYFTFFVQEFNLIARS

Parental  ELAPLQEL
          EL.PLQEL
Retrocopy ELTPLQEL

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_223 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 11 parental genes, and 18 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000007277	1 retrocopy	retro_chof_502,
Echinops telfairi	ENSETEG00000018245	1 retrocopy	retro_etel_425,
Homo sapiens	ENSG00000114978	2 retrocopies	retro_hsap_1223, retro_hsap_4670,
Gorilla gorilla	ENSGGOG00000010015	1 retrocopy	retro_ggor_954,
Loxodonta africana	ENSLAFG00000014338	2 retrocopies	retro_lafr_223 , retro_lafr_285,
Macaca mulatta	ENSMMUG00000015208	2 retrocopies	retro_mmul_1299, retro_mmul_297,
Nomascus leucogenys	ENSNLEG00000000321	2 retrocopies	retro_nleu_2161, retro_nleu_694,
Otolemur garnettii	ENSOGAG00000003504	1 retrocopy	retro_ogar_2688,
Pongo abelii	ENSPPYG00000012284	2 retrocopies	retro_pabe_1017, retro_pabe_3629,
Pan troglodytes	ENSPTRG00000012079	2 retrocopies	retro_ptro_3103, retro_ptro_837,
Rattus norvegicus	ENSRNOG00000042657	2 retrocopies	retro_rnor_2544, retro_rnor_2545,