RetrogeneDB ID: retro_lafr_563

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_21:40343469..40343978(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000006271
• Aliases: None
• Description: None

Sequence

>retro_lafr_563
TCACAGTCTGTGGAGGAACTTGGAGTCCGGAGTGATCTGGTCTCAGTAAAGAAATCTGTGGGCGGTAATCAGCTCCTTCC
TCAGGGACTGGCTGTGTATGCATCCGTGAAAACAAGAAGCTGTTTGAAGAGGAGAACTTGCTGAGACAAGAAGGAAAATT
AGAGAAGATCCAGACAAAGGCAGGTGTGGTGACAGTGAAATTTCTGAGAAGCTGTCACCTGGAAGGGAGGATGAAGAACA
ATGTCAAATAGGAGCTAAACCCTGAAATAGTTGCCCACCACTTCTTCAAGAACCTTGATGTTATGGTAGCTCCCCATACG
ATAAAGTGACCAGAAGAGCCCATCACACAGTGGGGCGAGCACTGGTTTGAGGTGACGGTAAATAGGCTTGACATTGTGAG
GGTGCCTATGGCTGTGCCGAACTTTGAGAAGCCCAAGACCAAAAGATGTAAGTACTGGTCAGTTCAGCAGGCTGCTGAGG
AAATGGCCTCCAAAAGCTCCCAGAGACTC

Alignment

ORF - retro_lafr_563 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.12 %
• Parental protein coverage: 63.43 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  TQSVEELGIRGDLVSVKKSVGRNRLLSQGLAVYASP-ENKKLFEEEKLLRQQGKLEKIQTKAGEATVKFL
          .QSVEELG.R.DLVSVKKSVG.N.LL.QGLAVYAS..ENKKLFEEE.LLRQ.GKLEKIQTKAG..TVKFL
Retrocopy SQSVEELGVRSDLVSVKKSVGGNQLLPQGLAVYASV<ENKKLFEEENLLRQEGKLEKIQTKAGVVTVKFL

Parental  RSCHLEVGMKNNVKWELNPEIVARHFFKNLGVVVAPHAIKLPEEPITRWGEYWCEVTVNGLDTVRVPMSV
          RSCHLE..MKNNVK.ELNPEIVA.HFFKNL.V.VAPH.IK.PEEPIT.WGE.W.EVTVN.LD.VRVPM.V
Retrocopy RSCHLEGRMKNNVK*ELNPEIVAHHFFKNLDVMVAPHTIK*PEEPITQWGEHWFEVTVNRLDIVRVPMAV

Parental  VNFERPKTKRYKYWLAQQAAKEMASKSAQML
          .NFE.PKTKR.KYW..QQAA.EMASKS.Q.L
Retrocopy PNFEKPKTKRCKYWSVQQAAEEMASKSSQRL

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_563 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 11 parental genes, and 13 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000000258	1 retrocopy	retro_chof_10,
Dasypus novemcinctus	ENSDNOG00000011403	1 retrocopy	retro_dnov_1989,
Homo sapiens	ENSG00000143436	1 retrocopy	retro_hsap_4078,
Gorilla gorilla	ENSGGOG00000001902	1 retrocopy	retro_ggor_2735,
Loxodonta africana	ENSLAFG00000006271	2 retrocopies	retro_lafr_498, retro_lafr_563 ,
Nomascus leucogenys	ENSNLEG00000010275	1 retrocopy	retro_nleu_2045,
Oryctolagus cuniculus	ENSOCUG00000001383	1 retrocopy	retro_ocun_725,
Otolemur garnettii	ENSOGAG00000030456	1 retrocopy	retro_ogar_159,
Pongo abelii	ENSPPYG00000000857	1 retrocopy	retro_pabe_3347,
Pan troglodytes	ENSPTRG00000001295	2 retrocopies	retro_ptro_2765, retro_ptro_2996,
Vicugna pacos	ENSVPAG00000000664	1 retrocopy	retro_vpac_123,