RetrogeneDB ID: retro_lafr_1159

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_8:36673314..36673710(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: NAA50
• Ensembl ID: ENSLAFG00000004023
• Aliases: None
• Description: None

Sequence

>retro_lafr_1159
ACCCGGATCGAGCTAGGAGATGTGACATCATCCAATTTTAAACAGTTGAAGAGATTAAACCAGGTCACCTTTCCACTCTG
CTACAATGACAAGTTCTACAAGAATGTCCTGGAGGCTGGTGAGCTAGCAAAACTTGCGTATTTCAAGATATTGCACTAGG
TGCCGTACGCTGTAGGGTGGATCGTTCACAGAAACCGAAGAGACTTTTACATCATGACCTAGGATGCCTGGCACCTTACC
GAAGGCTAAAAATAGGAACTAAAATGTTAAATCATTGTCATAAACATATGTGGAAATGATGGTACTTTTGACAACACCTA
TCTACACGTCCAGGTCAGCACTGAGTCAGCAATGGAATTCTACAGGAAGTCTGGCTTTCAGATTATTGAGACAAAA

Alignment

ORF - retro_lafr_1159 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.12 %
• Parental protein coverage: 78.11 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SRIELGDVTPHNIKQLKRLNQVIFPVSYNDKFYKDVLEVGELAKLAY-FNDIAVGAVCCRVDHSQNQKRL
          .RIELGDVT..N.KQLKRLNQV.FP..YNDKFYK.VLE.GELAKLAY.F.DIA.GAV.CRVD.SQ..KRL
Retrocopy TRIELGDVTSSNFKQLKRLNQVTFPLCYNDKFYKNVLEAGELAKLAY<FQDIALGAVRCRVDRSQKPKRL

Parental  YIMTLGCLAPYRRLGIGTKMLNH-VLNICEKDGTFDNIYLHVQISNESAIDFYRKFGFEIIETK
          ....LGCLAPYRRL.IGTKMLNH.V.NIC..DGTFDN.YLHVQ.S.ESA..FYRK.GF.IIETK
Retrocopy LHHDLGCLAPYRRLKIGTKMLNH>VINICGNDGTFDNTYLHVQVSTESAMEFYRKSGFQIIETK

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_1159 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 7 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000014169	6 retrocopies	retro_cpor_1027, retro_cpor_1028, retro_cpor_1199, retro_cpor_1200, retro_cpor_217, retro_cpor_480,
Gorilla gorilla	ENSGGOG00000006589	2 retrocopies	retro_ggor_432, retro_ggor_710,
Loxodonta africana	ENSLAFG00000004023	1 retrocopy	retro_lafr_1159 ,
Oryctolagus cuniculus	ENSOCUG00000006467	2 retrocopies	retro_ocun_466, retro_ocun_984,
Otolemur garnettii	ENSOGAG00000011197	1 retrocopy	retro_ogar_157,
Procavia capensis	ENSPCAG00000009780	2 retrocopies	retro_pcap_205, retro_pcap_459,
Ictidomys tridecemlineatus	ENSSTOG00000009438	1 retrocopy	retro_itri_1703,