RetrogeneDB ID: retro_lafr_136

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_0:34128233..34129128(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000031954
• Aliases: None
• Status: KNOWN_PSEUDOGENE

Parental gene information

• Parental gene symbol: ZDHHC3
• Ensembl ID: ENSLAFG00000012733
• Aliases: None
• Description: None

Sequence

>retro_lafr_136
ATGATGCTTATCCCCAGCCACCACTTCCAAAACACTGAGCAAAAACCAGAATACTTCCAGCAGCAGAGGTGCATGACACC
TCCCCACCCTGGACCTGTGGGAACCCTGTGGTTTATCCATGATGGCTGTGGCATCTCCTGTGCCACTGTCACCTGGTTTC
TGGTCCTCTGCTCAGAGTTTGTGGTCCTCTTTGTCACACTGATTCCATCCCAAGACTATGCCTACTGCATCATCAACGGA
ATTGTGTTCAACTTGGTGGCCTTCTTGGCCCCAGCCTCCCACTGCCAGGCCATGCTGACGGACCCTGGAGCAGTGCCAAA
GGAAGTGCCACTAAAGAATTCATCTAGAGCTTACAGCTGAAGCCCTGACAGGTGGTATACAAGTGTCCCAAGTGCTGCCA
CATCGAGCCCGACTGGGTCCACTACTGAAGTGTATGTAAGTGGTGCATTTGGGAGATGGCCCACCACTGTCCCTCGGTCA
AAAAATGTGTCAGTGAGAACAACCAGAACTATTTCATCCTATTTACAATGTACACAGCTCTCATCTCCTTGCACGCCCTC
ACCCTGGTGGAATTTTGCTTCCTGCCCTTGCTTTGAAGAAAATTGGACAAAGTGTAACTCCTTCTCTCCACCCAGATGGT
GATCCTCCTCATCCTGCTGTGCTTTGAGGGGCTCCTCTTTCTCATATTCACATCAGTGATGTTTGGGACCCAGGTATGCT
CCATCTGCACGAATGAGAAGGGAATAGAAAATTGAAAACGGAAGAGCGAAGATGGGCTTAAAAAACAAAATGGGTGAACA
TGAAAACCGATTTTGGCCACCCCTTCTCCCTAGGCTGAGCCAATCCCTTTGCCACTCCAGACCAAGCAAAGGCAGACCCG
AACCAGTATGTGGTC

Alignment

ORF - retro_lafr_136 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76.9 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 5
• Number of frameshifts detected: 4

Retrocopy - Parental Gene Alignment:

Parental  MMLIPTHHFRDIERKPEYLQPEKCVPPPHPGPVGTMWFIRDGCGIACAIVTWFLVLYAEFVVLFVMLIPS
          MMLIP.HHF...E.KPEY.Q...C..PPHPGPVGT.WFI.DGCGI.CA.VTWFLVL..EFVVLFV.LIPS
Retrocopy MMLIPSHHFQNTEQKPEYFQQQRCMTPPHPGPVGTLWFIHDGCGISCATVTWFLVLCSEFVVLFVTLIPS

Parental  RDYVYSIINGIVFNLLAFLALASHCRAMLTDPGAVPK-GNATKEFIESLQLKPGQVVYKCPKCCSIKPDR
          .DY.Y.IINGIVFNL.AFLA.ASHC.AMLTDPGAVPK.G.ATKEFI.SLQLKP.QVVYKCPKCC.I.PD.
Retrocopy QDYAYCIINGIVFNLVAFLAPASHCQAMLTDPGAVPK<GSATKEFI*SLQLKP*QVVYKCPKCCHIEPDW

Parental  AHHCSVCKRCIRKMDHHCPWVNNCVGENNQKYFVLFTMYIALISLHALIMVGFHFLH-CFEEDWTKCSSF
          .H..SVCK.CI..M.HHCP.V..CV.ENNQ.YF.LFTMY.ALISLHAL..V.F.FL..CFEE.WTKC.SF
Retrocopy VHY*SVCKWCIWEMAHHCPSVKKCVSENNQNYFILFTMYTALISLHALTLVEFCFLP>CFEENWTKCNSF

Parental  SPPT-TVILLILLCFEGLLFLIFTSVMFGTQVHSICTDETGIE-QLKKEERRWAKKTKWMNMKAVFGHPF
          SPP...VILLILLCFEGLLFLIFTSVMFGTQV.SICT.E.GIE..LK.EERRWA.KTKW.NMK..FGHPF
Retrocopy SPPR<MVILLILLCFEGLLFLIFTSVMFGTQVCSICTNEKGIE<KLKTEERRWA*KTKWVNMKTDFGHPF

Parental  SLGWASPFATPDQGKADPYQYVV
          SLG.A.PFATPDQ.KADP.QYVV
Retrocopy SLG*ANPFATPDQAKADPNQYVV

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_136 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000013490	1 retrocopy	retro_ggor_2187,
Loxodonta africana	ENSLAFG00000012733	1 retrocopy	retro_lafr_136 ,
Nomascus leucogenys	ENSNLEG00000006024	1 retrocopy	retro_nleu_2725,
Rattus norvegicus	ENSRNOG00000004344	1 retrocopy	retro_rnor_1688,