RetrogeneDB ID: retro_lafr_764

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_36:4621242..4621583(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000003359
• Aliases: None
• Description: None

Sequence

>retro_lafr_764
AAGATGTACTGGCCTGCTGTAATTCATTGGTCTCCTACTTGCAGCCAATTCTGGAATCATTAGTGGGGAAAGCACGTGGC
TTGGGCCACCCACATGGACGATCTCAGCTGCAGAAAAAATACTTCGGTAAATGCCTGGATCTGAATAGACAACTGGACCT
TAACAGCATGCTCCACAAGTTGGAGATAAAGCCATTTATCAATGACTACCAGATTGCAGATATTCAAGTTGCTCTTGCCA
GTGTATCTTAGGTGATGCCGTAAGCCCAGCATCTTCCACCAGAACAGAATGGGGAAGTACAGACCATTGGTCAGATAGAA
TCGTGTCTCACCAAGGACCTG

Alignment

ORF - retro_lafr_764 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.48 %
• Parental protein coverage: 51.58 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  KMYWPDVIHRSPNCSHFWKHEWEKHGTCVAQLATLSS-EKKYFSKILDLYKQLDLNSVLQKLGIKPSLNY
          KMYWP.VIH.SP.CS.FW.H.W.KH.........LS...KKYF.K.LDL..QLDLNS.L.KL.IKP..N.
Retrocopy KMYWPAVIHWSPTCSQFWNH*WGKHVAWATHMDDLSC<QKKYFGKCLDLNRQLDLNSMLHKLEIKPFIND

Parental  YQIADIKDALASIYGVMPKVQCLPPEKNEDVQTIGQIELCFTKDL
          YQIADI..ALAS...VMP..Q.LPPE.N..VQTIGQIE.C.TKDL
Retrocopy YQIADIQVALASVS*VMP*AQHLPPEQNGEVQTIGQIESCLTKDL

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_764 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 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Loxodonta africana	ENSLAFG00000003359	1 retrocopy	retro_lafr_764 ,
Microcebus murinus	ENSMICG00000014184	1 retrocopy	retro_mmur_1544,
Macaca mulatta	ENSMMUG00000005673	1 retrocopy	retro_mmul_1684,
Monodelphis domestica	ENSMODG00000006193	1 retrocopy	retro_mdom_1994,
Nomascus leucogenys	ENSNLEG00000011573	1 retrocopy	retro_nleu_3005,
Pongo abelii	ENSPPYG00000017277	1 retrocopy	retro_pabe_3128,
Pan troglodytes	ENSPTRG00000018796	1 retrocopy	retro_ptro_2529,