RetrogeneDB ID: retro_lafr_575

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_22:23487255..23487557(-)
• Located in intron of: ENSLAFG00000004709

Retrocopy information

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

Parental gene information

• Parental gene symbol: SPCS1
• Ensembl ID: ENSLAFG00000016073
• Aliases: None
• Description: None

Sequence

>retro_lafr_575
TTGGAGCATCTGGGCTCGCCGCCCATATAAATGGATTACGAGGCCAGAAGCTAGCTGAACAGATGTTTCAGAGAATTATT
CTTTTTTCTGCAGTAGTTGGCCTTATCTATGGGTATGTGGCTGAACAGTTTGGATGAACTGTCCGTATAGTTGTGGCTGG
ATTTGCTTTTTTGCATTTGCTGATACTTCTTCCTTGGCCCATTTATTGCTGGCACCCCCTGAACTGGTCACCTGTTCAAG
ATTCGGGAACAAAAGACAAGAATCTAGGGGATAGAAAAATTAGTAGTTGTGCTAAGAAGAAT

Alignment

ORF - retro_lafr_575 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.59 %
• Parental protein coverage: 99.02 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  IETLGSLPTQMDY-KGQKLAEQMFQGIILSSAIVGFVYGYVAEQFGWTVYIVMAGFAFSCLLTLPPWPIY
          .E.LGS.P..MDY..GQKLAEQMFQ.IIL.SA.VG..YGYVAEQFG.TV.IV.AGFAF..LL.L.PWPIY
Retrocopy LEHLGSPPI*MDY<RGQKLAEQMFQRIILFSAVVGLIYGYVAEQFG*TVRIVVAGFAFLHLLILLPWPIY

Parental  RRHPLKWLPVQDSGTEDKKPGDRKIKRHAKNN
          ..HPL.W.PVQDSGT.DK..GDRKI...AK.N
Retrocopy CWHPLNWSPVQDSGTKDKNLGDRKISSCAKKN

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_575 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 8 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Dasypus novemcinctus	ENSDNOG00000012421	3 retrocopies	retro_dnov_2086, retro_dnov_2245, retro_dnov_698,
Dipodomys ordii	ENSDORG00000000678	4 retrocopies	retro_dord_273, retro_dord_274, retro_dord_686, retro_dord_734,
Equus caballus	ENSECAG00000023559	1 retrocopy	retro_ecab_86,
Erinaceus europaeus	ENSEEUG00000007914	1 retrocopy	retro_eeur_25,
Echinops telfairi	ENSETEG00000004020	1 retrocopy	retro_etel_1056,
Loxodonta africana	ENSLAFG00000016073	2 retrocopies	retro_lafr_575 , retro_lafr_625,
Mus musculus	ENSMUSG00000021917	2 retrocopies	retro_mmus_2758, retro_mmus_2928,
Vicugna pacos	ENSVPAG00000007380	1 retrocopy	retro_vpac_269,