RetrogeneDB ID: retro_lafr_704

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_31:10729026..10729432(-)
• 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_704
TGGGAAGTGATGGAGACTGCAGTGGCACTAGAAGTAATTAAATATGAGTATCCTGTCTTGTATTCCTGTAGCTACCAAGT
ACCTGTGCTTTACTTCAGGGCAATCTTTTAAGATGGAAGAACTTTAACTCTGAAGACATATGGAAAACAGTCCATGAGTG
CTACCAGATGCAGCTTCTGCATGGACCATGGGACACCATTACCCAATAGGAACACCCAATACTTGAGCAACACTTTTTTG
TACTTCATCCATGCAAGATGAATGAATTGATGATTCCCGTATTAAAGAATTCTCAAAAAATCAATAGAAACATTGGCTAC
ATCACATCATGGCTGAGTAAGAATCTAGGACTTACTTTTGGGCTGAATCTACCTCTGAGCTAGCTAACGTTACCTCTCAG
GATGAC

Alignment

ORF - retro_lafr_704 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.19 %
• Parental protein coverage: 63.08 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  FEVLETAAASEVIKYEYHVLYSCSYQVPVLYFRASFLDGRPLTLK-DIWERVHECYKTRLLQGPWDTITQ
          .EV.ETA.A.EVIKYEY.VLYSCSYQVPVLYFRA.F.DGR.LTLK.DIW..VHECY...LL.GPWDTITQ
Retrocopy WEVMETAVALEVIKYEYPVLYSCSYQVPVLYFRAIF*DGRTLTLK<DIWKTVHECYQMQLLHGPWDTITQ

Parental  QEHPILGQPFFVLHPCKTNEFMTPVLQNSQKIKRNVNYITSWLS-IVGPVVGLNLPLS-YANTTFQGE
          .EHPIL.Q.FFVLHPCK.NE.M.PVL.NSQKI.RN..YITSWLS...G...GLNLPLS..AN.T.Q..
Retrocopy *EHPILEQHFFVLHPCKMNELMIPVLKNSQKINRNIGYITSWLSKNLGLTFGLNLPLS<LANVTSQDD

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_704 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,