RetrogeneDB ID: retro_lafr_492

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_19:33597024..33597592(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NRAS
• Ensembl ID: ENSLAFG00000020706
• Aliases: None
• Description: None

Sequence

>retro_lafr_492
ATGACTGAGTACAAACTGGTGGTGGTTGGAGCAGGTGGTGTTGGGAAAAGTGCACTGACAATCCAGCTAATCCAGAACCA
TTTTGTAGATGAGTATGATCCCACCGTAAAGGATTCATACCGAAAACAAGTGGTTATAGATGGTGAAACCTGTCTGTTGG
ACATACTGGATACAGCTGGACAAGAGGAGTACAGTGCCATGAGAGACCAATACATGAGGACAGGTGAAGGCTTCCTCTGT
GTGTTTGCCATCAATAATAGCAAATCATTTGCAGATATTAACCTCTACAGGGAGCAGATTAAATGAGTAAAAGACTCAGA
TGATGTACCTATGGTGCTGGTGGGAAACAAGTGTGATTTGCCAATAAGGACAGTTGACACAAAACAAGCACATGAACTGG
CTAAGAGTTATGGGATTCCGTTCATTGAAACCTCAGCCAAGACCAGACAGGGTGTCGAAGATGTCTTTTACACACTGGTA
AGAGAAATACGTCAGTACCGAATGAAAAAAATTCAACAGCAGCGATGATGGAACTCAAGGTTGTATGGGGCTGCCTTGTG
TGATGATG

Alignment

ORF - retro_lafr_492 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 95.79 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 1
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTIEDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQ
          MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPT..DSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQ
Retrocopy MTEYKLVVVGAGGVGKSALTIQLIQNHFVDEYDPTVKDSYRKQVVIDGETCLLDILDTAGQEEYSAMRDQ

Parental  YMRTGEGFLCVFAINNSKSFADINLYREQIKRVKDSDDVPMVLVGNKCDLPTRTVDTKQAHELAKSYGIP
          YMRTGEGFLCVFAINNSKSFADINLYREQIK.VKDSDDVPMVLVGNKCDLP.RTVDTKQAHELAKSYGIP
Retrocopy YMRTGEGFLCVFAINNSKSFADINLYREQIK*VKDSDDVPMVLVGNKCDLPIRTVDTKQAHELAKSYGIP

Parental  FIETSAKTRQGVEDAFYTLVREIRQYRMKKL-NSSDDGTQGCMGLPCVVM
          FIETSAKTRQGVED.FYTLVREIRQYRMKK..NSSDDGTQGCMGLPCV.M
Retrocopy FIETSAKTRQGVEDVFYTLVREIRQYRMKKI>NSSDDGTQGCMGLPCVMM

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_492 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 12 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000017134	1 retrocopy	retro_amel_885,
Callithrix jacchus	ENSCJAG00000036517	1 retrocopy	retro_cjac_2400,
Felis catus	ENSFCAG00000019026	1 retrocopy	retro_fcat_1191,
Loxodonta africana	ENSLAFG00000016460	1 retrocopy	retro_lafr_482,
Loxodonta africana	ENSLAFG00000020706	1 retrocopy	retro_lafr_492 ,
Macropus eugenii	ENSMEUG00000002675	1 retrocopy	retro_meug_2136,
Myotis lucifugus	ENSMLUG00000022354	1 retrocopy	retro_mluc_741,
Monodelphis domestica	ENSMODG00000004590	1 retrocopy	retro_mdom_51,
Oryctolagus cuniculus	ENSOCUG00000022455	1 retrocopy	retro_ocun_850,
Rattus norvegicus	ENSRNOG00000023079	2 retrocopies	retro_rnor_2867, retro_rnor_619,
Sus scrofa	ENSSSCG00000006753	1 retrocopy	retro_sscr_520,