RetrogeneDB ID: retro_lafr_705

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_31:10748729..10749194(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: ATG10
• Ensembl ID: ENSLAFG00000013183
• Aliases: None
• Description: None

Sequence

>retro_lafr_705
AGTAACATCTGTCAGCATACAGACATGCCTCCCTACTGAGGTTTCAGAACTATTCCCAATGATTTTGAAGTAATGGAGAC
TACCCAGCATCAGAAGTGATTAAATATGAGTATTATGTCTTGTATTCCTGTAGCTACCAAGTGCTTTACCTCAAGGCAAT
CTCTTTAGATGGAAGATCTTTAACTCTGAAGGACATATGTAAAGGAGTCAATGAGTGCTACCAGACGTGGCTTCTTCAGT
GACCATGGGACACCATTACCCAACAGGAACATCCAATACTTGGGCAACCATTTTTTTGTACTTCCTCCCTGCAAGATGAA
TGAATTGATGATTTCTGTATTAAAGAATTCTCAAAAAATCAACAGGAATGTCAACTACATCATGTCATGTCTAAGTATGA
ATCCAAGGCCAGTTATTGGGTTGAATCTACCTCTGAGCTATTCTAACACCACCTTTCAGGATGAA

Alignment

ORF - retro_lafr_705 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 66.67 %
• Parental protein coverage: 72.9 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  TSACIQTCLPTEEALELPLDDFEVLETAA-ASEVIKYEYHVLYSCSYQVPVLYFRASFLDGRPLTLKDIW
          ...C..T..P..........DFEV.ET...ASEVIKYEY.VLYSCSYQV..LY..A..LDGR.LTLKDI.
Retrocopy SNICQHTDMPPY*GFRTIPNDFEVMETTQ<ASEVIKYEYYVLYSCSYQV--LYLKAISLDGRSLTLKDIC

Parental  ERVHECYKTRLLQGPWDTITQQEHPILGQPFF-VLHPCKTNEFMTPVLQNSQKIKRNVNYITSWLSI-VG
          ..V.ECY.T.LLQ.PWDTITQQEHPILGQPFF.VL.PCK.NE.M..VL.NSQKI.RNVNYI.S.LS....
Retrocopy KGVNECYQTWLLQ*PWDTITQQEHPILGQPFF>VLPPCKMNELMISVLKNSQKINRNVNYIMSCLSMNPR

Parental  PVVGLNLPLSYANTTFQGE
          PV.GLNLPLSY.NTTFQ.E
Retrocopy PVIGLNLPLSYSNTTFQDE

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_705 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 3 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000013183	2 retrocopies	retro_lafr_704, retro_lafr_705 ,
Oryctolagus cuniculus	ENSOCUG00000008736	1 retrocopy	retro_ocun_1349,
Vicugna pacos	ENSVPAG00000009426	1 retrocopy	retro_vpac_320,