RetrogeneDB ID: retro_lafr_1199

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_88:2787790..2788194(+)
• Located in intron of: ENSLAFG00000017341

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000027507
• Aliases: None
• Description: None

Sequence

>retro_lafr_1199
CAAGTCCTGGGAAACTCTGCTGGACTTGGCCTGTCACTGTAGCGGGCTCTGTTTGTGGAGCCCAGGCTTTGATCAACGGT
TCTAGACTCCATGCTGGACTGTAACACTGATGCTGTAACCCTGAGGAAATCCATCTTGGTGGCCTTCTGCCCTCAGGAGG
TCTGTTACCAGATGCACTGCGAGGTGCACTGCCAGCTTCTCGAGCAGGTGCTCCATTTGGTTTCAATAACACTTCAAGCC
TCAGGCCCGTAAATCTAGCTCAGTGTCCCGGTGGCTCGCTCATTTTTAACACTTGGCAACAGCAGCTTTCTCAGTTTACT
TCAGGACAACCACCTCAGCAACCCACAACTTGTAGTCCTCAACAGCCAGGAGGCAGGGTTCTGGACCAGGCTCGGGCAGT
TCAG

Alignment

ORF - retro_lafr_1199 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.52 %
• Parental protein coverage: 50.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  QVMANSAGVNF-INVLGSVCGAQALMSGS-NPMLGYNTGAVT-PAGIQLSGLLPSGGLLPNALPAALPAS
          QV..NSAG......V.GSVCGAQAL..GS...ML..NT.AVT.P..I.L.GLLPSGGLLP.AL..ALPAS
Retrocopy QVLGNSAGLGL<VTVAGSVCGAQALINGS>DSMLDCNTDAVT<PEEIHLGGLLPSGGLLPDALRGALPAS

Parental  QAAGVPFGLKNTSSLRPLNLLQQQQLSQFTPQPQPQQPTASSPQQPGE--QCSEQ--GSASQEQALSAQ
          ..AG.PFG..NTSSLRP.NL.Q....S......Q.Q.....S.Q.P.....CS.Q..G.....QA...Q
Retrocopy R-AGAPFGFNNTSSLRPVNLAQCPGGSLIFNTWQQQLSQFTSGQPPQQPTTCSPQQPGGRVLDQARAVQ

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_1199 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.

---

Parental genes homology:

Parental genes homology involve 9 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Equus caballus	ENSECAG00000000116	2 retrocopies	retro_ecab_1052, retro_ecab_1101,
Homo sapiens	ENSG00000102710	2 retrocopies	retro_hsap_4659, retro_hsap_4794,
Loxodonta africana	ENSLAFG00000027507	1 retrocopy	retro_lafr_1199 ,
Macaca mulatta	ENSMMUG00000003590	2 retrocopies	retro_mmul_2479, retro_mmul_2555,
Pongo abelii	ENSPPYG00000005288	2 retrocopies	retro_pabe_3619, retro_pabe_3729,
Pan troglodytes	ENSPTRG00000005791	2 retrocopies	retro_ptro_3095, retro_ptro_3189,
Pteropus vampyrus	ENSPVAG00000014609	1 retrocopy	retro_pvam_401,
Tarsius syrichta	ENSTSYG00000013227	1 retrocopy	retro_tsyr_2160,
Vicugna pacos	ENSVPAG00000007288	1 retrocopy	retro_vpac_193,