RetrogeneDB ID: retro_lafr_586

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_24:13288725..13289554(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: CHPT1
• Ensembl ID: ENSLAFG00000004678
• Aliases: None
• Description: None

Sequence

>retro_lafr_586
TCTTGTTCTCTTTAGGGAAACTCTTTGACCATGGTTTTGACTTTCTTTCCATAGTATTTATGGCAGCTGGAGTTTCAGTT
GCTGTTTGCTTAGGAACTCATCCTAACTGGTTGTTTTTCTGCTCATTTATTGGAATGTTCATGTTTTATTGTGTTCATTG
GCAGACTTATGCTTCAGGCATGCTGAGGTTTGGAAAAGTGGATGTAACTGAAATTTAGGTAGCTTTGATAATCATCTTTG
TGTTGTCCACATTTGGAGCAGCAACAATAGGGGACTATATGATACTCATTCTAGAAATAAAATGGAAGATCTTTTCAGTT
TTTGGAGTAGTGGGTGGAACAATATTTTCCTGTTCAAATTATTTCCATGTTATCCTCCACGATGACGTTGGCAAGAGTGG
ATCCATGATAGCAAGCACTAGTGTCTTGTCACCTTGACTCGACATAGGACTAATTATTCGTACTGGCAATAATGATCTAT
AAAAAGTCTGTAATTAATGTGTTTGAAAAACATCCTTGTCTTTATACCCTAATGTTTGGATGTGTCTTTCCTAAAGTTGC
ACAAAAATTGGTGGTGGATCACATGACCAGAAGTGAACTGTGTCTTCAAGACACAATGTTTGTTGGGCTAGGTTTTTTTT
TTTTTAGACCAGCACTTCAGGAATTTTGTAGATGAATATGTTGTCCTGTGAATAGCAATGGTCATTGCTACATTTGATAT
GATGACATACTTTAGTGCTTTGTGCCTGCAAATTTCAAGACACCTTCATTTCAACAGCTTCAAGTCTTACTTTTATCAAG
CACCTGAACAGGTTCGTATGCATATTGAC

Alignment

ORF - retro_lafr_586 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.21 %
• Parental protein coverage: 68.66 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  SCS-PLGELFDHGCDSLSTVFMALGASIAVRLGTHPDWLFFCSFIGMFMFYCAHWQTYVSGVLRFGKVDV
          SCS..LG.LFDHG.D.LS.VFMA.G.S.AV.LGTHP.WLFFCSFIGMFMFYC.HWQTY.SG.LRFGKVDV
Retrocopy SCS<SLGKLFDHGFDFLSIVFMAAGVSVAVCLGTHPNWLFFCSFIGMFMFYCVHWQTYASGMLRFGKVDV

Parental  TEIQVALIIVFVLSTFGGATMWDYTIPILEIKWKIFPVLGVVGGAIFSCSNYFHVILHGGVGKNGSTIAG
          TEI.VALII.FVLSTFG.AT..DY.I.ILEIKWKIF.V.GVVGG.IFSCSNYFHVILH..VGK.GS.IA.
Retrocopy TEI*VALIIIFVLSTFGAATIGDYMILILEIKWKIFSVFGVVGGTIFSCSNYFHVILHDDVGKSGSMIAS

Parental  TSVLSPGLHIGLII-ILAIMIYKKSATNVFEKHPCLYTLMFGCVFAKVAQKLVVAHMTKSELYLQDTVFI
          TSVLSP.L.IGLII..LAIMIYKKS..NVFEKHPCLYTLMFGCVF.KVAQKLVV.HMT.SEL.LQDT.F.
Retrocopy TSVLSP*LDIGLII>VLAIMIYKKSVINVFEKHPCLYTLMFGCVFPKVAQKLVVDHMTRSELCLQDTMFV

Parental  GPG-LLFLDQYFSNFVDEYVVLWIAMVIASFDMMTYFSALCLQISRHLHLSIFKTSCHQAPEQVHKHID
          G.G...FLDQ.F.NFVDEYVVL.IAMVIA.FDMMTYFSALCLQISRHLH...FK....QAPEQV..HID
Retrocopy GLG>FFFLDQHFRNFVDEYVVL*IAMVIATFDMMTYFSALCLQISRHLHFNSFKSYFYQAPEQVRMHID

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_586 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Choloepus hoffmanni	ENSCHOG00000013377	1 retrocopy	retro_chof_712,
Loxodonta africana	ENSLAFG00000004678	1 retrocopy	retro_lafr_586 ,
Monodelphis domestica	ENSMODG00000002564	1 retrocopy	retro_mdom_1135,