RetrogeneDB ID: retro_lafr_289

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_11:35611191..35611569(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000028352
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: NPC2
• Ensembl ID: ENSLAFG00000002876
• Aliases: None
• Description: None

Sequence

>retro_lafr_289
TTCAAAGACTGTGGGTCGGTGGTCAGAGTTGTAATGGAAGTGAATGAGAGCCCATGCTCCGCCCAGCCATGTCGCCTGCT
CAAAGGACAGTCTTACAGTGTCAATGTCCCCTTCACCAGCAATACTTATTCCAAAAATAGCACAGCTTTGGTGCATGGCA
TTGTGATGGGCCTCCCAGTTCCCTTTCCTATCCCTGAACCTGATGGTTTTAAGAGTAGAATCGACTGCCCCATCCAAAAA
GACGGGACCTATTACTACCTGAATAAACTACCAGTGAAGAATGAATACCCCACTCTAAAACTGGTGGTGGAATGGGAACT
CCTGGATGACAAAGGGCAGCATCTCTTCTGCTGGAAAAACCCATTAGAGATCATATCC

Alignment

ORF - retro_lafr_289 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 89.68 %
• Parental protein coverage: 84.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FKDCGSVVGVIKEVNVSPCPTQPCRLLKGQSYSVNVTFTSNTYSKNSTALVHGIVMGLPVPFHIPEPDGC
          FKDCGSVV.V..EVN.SPC..QPCRLLKGQSYSVNV.FTSNTYSKNSTALVHGIVMGLPVPF.IPEPDG.
Retrocopy FKDCGSVVRVVMEVNESPCSAQPCRLLKGQSYSVNVPFTSNTYSKNSTALVHGIVMGLPVPFPIPEPDGF

Parental  KSGIDCPIQKDKTYYYLNKLPVKNEYPTIKLVVEWELLDDKGQHLFCWKIPLEIIS
          KS.IDCPIQKD.TYYYLNKLPVKNEYPT.KLVVEWELLDDKGQHLFCWK.PLEIIS
Retrocopy KSRIDCPIQKDGTYYYLNKLPVKNEYPTLKLVVEWELLDDKGQHLFCWKNPLEIIS

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_289 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Canis familiaris	ENSCAFG00000016932	1 retrocopy	retro_cfam_2050,
Choloepus hoffmanni	ENSCHOG00000009488	1 retrocopy	retro_chof_2335,
Echinops telfairi	ENSETEG00000003719	2 retrocopies	retro_etel_1610, retro_etel_1866,
Loxodonta africana	ENSLAFG00000002876	1 retrocopy	retro_lafr_289 ,
Tursiops truncatus	ENSTTRG00000013025	1 retrocopy	retro_ttru_85,