RetrogeneDB ID: retro_lafr_32

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_2:104919137..104920430(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000031855
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: STK11
• Ensembl ID: ENSLAFG00000011567
• Aliases: None
• Description: None

Sequence

>retro_lafr_32
ATGCATGTGGTGCACCCCCAGCAGCTGGGCATGGTCACTGAGGCCAAGCTGATGTCTGTGGGAATGGACACCTTCATCCA
CTGCAACGACTCTTTTGAGGTCATTGACCAGCAGCGCCCTCAAAAGCCTGCCAAGCTCCTTGGCAAGTACCTGCTGGGGG
ACCTGCTGGGGGAGGGCTCCTATGGCAAGGTGAAAGAGGTGCTGGACTTGGACACGCTGTGCCGGCGCGCCCTCAAGATC
GTCAAGAAGAATAAGCTGCGGCGGATTCCCGACGGGGTCGCCAACGTGGAGAAGGAGATCCAGCTCTTGCGGCGGCTGCG
GCACCGGAACGTCATCCAGCTAGTGGATGTGCTGCACAATGAGAAGCAGAAGACGTATATGGTGATGGAGTACTGCGCGT
GCGACCTGCAGGAGATGCTGGACAGTGTGCCAGAGAAGAGGTTCCCTGTGTGCCAGGCTCACGGGTACTTCTGCCAGCTC
ATCGACGGGCTGGAGTACCTGCACAGCCAGGGCATCGTGCACAAGGACATCAAGCCCAGCAACTTGCTGCTCACCACAGG
CGGCACGCTCAAGATCTCCGACCTGGGCATGGCAGAGGCTCTGCACCGGTTTGCCGAGGATGACACGTGCCAGACCAGAC
AGGGCTCGCCAGCCTTCCAGCCGCCGGAGATCTTGAACGGCCTGGACACCTTCTCCGGCTTCAAGGTGGACATCTGGTCG
GCAGGGGTCACGCTTTACATCATCACCACGGGCCTGTACCCTTTTGATGGGGACAACATCTACCAGCTGTTCCAGAACAT
CAGGAAGTGGGACTACACGATTCCAGGCGACTGTGGCCCGCTGCTGTCCCACCTGCTGAGAAGGATGCTTGAGTACGATC
CTGCCCGGAGGCTCTCCATCCAGCAGATCCGGCAGCACGTCTGGTTTCAGAAGAGGCACCCACCGGCTGAGGGGCTGGTG
CCCATCCCTCCCCGCCCGGACACCGAGGACAGGTGGCGCAGCATGACAGTAGTGCCCTACCTGGAAGATCTGCATGGCTG
TGCCAGCGATGCTGACAAGGAGGGCCTCTTTAACACTGAGGATGCCATCATCTATACTCAGGACTTCACTATGCCTGGAC
AGGTCCTGGAGGTGGAGGCCGGTCAGAACCAGGGCTTGCCCAAGGCCCTGTGCATGAATGGCACCGAGGCAGCCCAGCGG
AGCCCCAAGTCAAAGGCCAAGCGCCGCGCCAGCTTCTCCTCCAACCCTATCAGCAGCAAGATCCGCCGCCTGTCGCCCTA
CAAGCAGCAGTGA

Alignment

ORF - retro_lafr_32 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 83.1 %
• Parental protein coverage: 95.44 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDVVDPQELGVFTEGELMSVGMDTFIHRIDSTEVIYQPR-RKRAKLIGKYLMGDLLGEGSYGKVKEVLDS
          M.VV.PQ.LG..TE..LMSVGMDTFIH..DS.EVI.Q.R..K.AKL.GKYL.GDLLGEGSYGKVKEVLD.
Retrocopy MHVVHPQQLGMVTEAKLMSVGMDTFIHCNDSFEVIDQQRPQKPAKLLGKYLLGDLLGEGSYGKVKEVLDL

Parental  ETLCRRAVKILKKKKLRRIPNGEANVKKEIQLLRRLRHRNVIQLVDVLCNEEKQKTYMVMEYCVCGMQEM
          .TLCRRA.KI.KK.KLRRIP.G.ANV.KEIQLLRRLRHRNVIQLVDVL.NE.KQKTYMVMEYC.C..QEM
Retrocopy DTLCRRALKIVKKNKLRRIPDGVANVEKEIQLLRRLRHRNVIQLVDVLHNE-KQKTYMVMEYCACDLQEM

Parental  LDSVPEKRFPVCQAHGYFCQLIDGLEYLHSQGIVHKDIKPGNLLLTTGGTLKISDLGVAEALHPFAEDDT
          LDSVPEKRFPVCQAHGYFCQLIDGLEYLHSQGIVHKDIKP.NLLLTTGGTLKISDLG.AEALH.FAEDDT
Retrocopy LDSVPEKRFPVCQAHGYFCQLIDGLEYLHSQGIVHKDIKPSNLLLTTGGTLKISDLGMAEALHRFAEDDT

Parental  CRTSQGSPAFQPPEIANGLDTFSGFKVDIWSAGVTLYNITTGLYPFEGDNIYKLFENIGKGDYTIPGDCG
          C.T.QGSPAFQPPEI.NGLDTFSGFKVDIWSAGVTLY.ITTGLYPF.GDNIY.LF.NI.K.DYTIPGDCG
Retrocopy CQTRQGSPAFQPPEILNGLDTFSGFKVDIWSAGVTLYIITTGLYPFDGDNIYQLFQNIRKWDYTIPGDCG

Parental  PPLSDLLRGMLEYEPARRLSIQQIRQRSWFRKKHPPAEALVPIPPSPDTKDRWRSMTVVPYLEDLHGCAG
          P.LS.LLR.MLEY.PARRLSIQQIRQ..WF.K.HPPAE.LVPIPP.PDT.DRWRSMTVVPYLEDLHGCA.
Retrocopy PLLSHLLRRMLEYDPARRLSIQQIRQHVWFQKRHPPAEGLVPIPPRPDTEDRWRSMTVVPYLEDLHGCAS

Parental  DADDEGLFDIEDDIIYTQDFTVPGQVLEEEASQNGQSRGLPKALCMNGTEVAQPGPKSKAERRSSASSNP
          DAD.EGLF..ED.IIYTQDFT.PGQVLE.EA...GQ..GLPKALCMNGTE.AQ..PKSKA.RR.S.SSNP
Retrocopy DADKEGLFNTEDAIIYTQDFTMPGQVLEVEA---GQNQGLPKALCMNGTEAAQRSPKSKAKRRASFSSNP

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_32 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
Loxodonta africana	ENSLAFG00000011567	1 retrocopy	retro_lafr_32 ,
Procavia capensis	ENSPCAG00000008434	1 retrocopy	retro_pcap_190,
Sarcophilus harrisii	ENSSHAG00000007173	1 retrocopy	retro_shar_612,