RetrogeneDB ID: retro_lafr_1217

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_9:39254816..39255005(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ELOF1
• Ensembl ID: ENSLAFG00000001534
• Aliases: None
• Description: None

Sequence

>retro_lafr_1217
GAGACCCAGTTCACCTGCCCCTCCTGCAACCACGAGAAGTCTTGTGACACGAAGATGGGCAGTGCCCACAACACCTGAGT
CATCTCTTGTACCTTGTGCCTAGAGGAATTCCAGACGCCCATCACACAGCTCTCAGAACCAGGGGACGTATAGAGAGATT
AGATAGATGCCTGTGAGGCGGCCAACCAA

Alignment

ORF - retro_lafr_1217 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.95 %
• Parental protein coverage: 75.9 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  ETQFTCPFCNHEKSCDVKMDRARNTGVISCTVCLEEFQTPITYLSEPVDVYSDWIDACEAANQ
          ETQFTCP.CNHEKSCD.KM..A.NT.VISCT.CLEEFQTPIT.LSEP.DV..D.IDACEAANQ
Retrocopy ETQFTCPSCNHEKSCDTKMGSAHNT*VISCTLCLEEFQTPITQLSEPGDV*RD*IDACEAANQ

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_1217 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000000064	1 retrocopy	retro_amel_1495,
Cavia porcellus	ENSCPOG00000020359	1 retrocopy	retro_cpor_1091,
Felis catus	ENSFCAG00000004926	1 retrocopy	retro_fcat_699,
Loxodonta africana	ENSLAFG00000001534	2 retrocopies	retro_lafr_1217 , retro_lafr_771,
Macropus eugenii	ENSMEUG00000012101	1 retrocopy	retro_meug_2078,
Otolemur garnettii	ENSOGAG00000026211	1 retrocopy	retro_ogar_2878,
Ictidomys tridecemlineatus	ENSSTOG00000003687	1 retrocopy	retro_itri_1081,
Tupaia belangeri	ENSTBEG00000004812	1 retrocopy	retro_tbel_2163,
Tursiops truncatus	ENSTTRG00000001807	1 retrocopy	retro_ttru_1611,