RetrogeneDB ID: retro_lafr_110

Retrocopy location

• Organism: Elephant (Loxodonta africana)
• Coordinates: scaffold_71:2992373..2994680(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: ENSLAFG00000027486
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: ENSLAFG00000016653
• Aliases: None
• Description: None

Sequence

>retro_lafr_110
ATGAGTGCAACTGGGGCAGCAGAGAGCCTTCTGACTTTGAGCCATCAGGAAGAATTAGCAGATTTGCCAAAGGACTGCCC
CTGGAGCACCAGTGAAGACGAAGGGGACAGTGATAGAGAGAGGAAGCATCAAAAGCTTCTGGAAGCAATCAGTTCCCTTG
ATGGAAAGAATAGGCGGAAACTGGCTGAGAGATCAGAGGCCAGTTGGGATGTGTCGGAGTTCAGTGTCGGTTGTGAAGGA
ACAGGAGAACAGCTGGTCCTCTCAGATCTGCTTCAGCCCATTAAAACTTCATCCTCCTTGGCCACGGTGAAAAAGCAGCT
GAAGGGGGTCCAAGCAAAGAAGACTGTGGAGTTGCCCCTTGACCAAGAAGAGGCTGCACAGGTCCACAGAGAAGTGGCAT
TCAGTACAACCTCCCAAGCTCTTTCCAAATGGGATCCTGTAGTTCTAAAGAACCGGAACGCAGAGCAGCTGGTTTTTCCC
CTGAAGCAGCAGCAGCTGGACTTTGCTCCCATCGAACATGTGCTCGGTGGCTGGAAGGCAAGAAGTCCCCTGGAGCAGGA
AATTTTTAACGTCCTCCACAAGAACAAGCAGCCAGTGATAGACCCTTTACTGACTCCAGTGGAGAAGGCCTCTCTCAAAG
CCACGAGCCTGGAAGAGGCTCAGATGCGCCAAGCAGAGCTTCAGAAAGCCCGGGCCCTGCAGTCCTACTATGAGGCCAAG
GCTCGGAGAGAGAAGAAAATCAAAAGCAAAAAGTATCACAAAGTTGTGAAGAAAGGAAAGGCCAAGATAGCCCTAAAAGA
CTTTGAGACCCTTCAGAAGGCCAGTCCTACCACAGCATTAGAAGAACTGGAGAAAATCGAAAAGGCCAGGATGGTGGAGC
GGATGAGCCTGAAGCACCAGAACAAGGGGAAGTGGGCCAAGTCCAAGGCAATTATGGCCAAATATGACCCAGAGGCTCGC
CAGGCCATGCACGAACAGTTGGCCAAGAACAAAGAACTGACACAGAAACTCCAGGCACCTTCTGAGAGTGAGGAAGAGGA
GGGGGCTGTAGAGGAGGATGGACTCTTTGTCCCTGATGTCGTGAACGAAGTCCAGATGGACACACATGGGCCCAACCCCT
GGATGCACACAAGTTGCACCAGTGATGTGAAAGAGGCTGAAGTCCTGAAGGACCCTGAACAGCTTCCTGAGCACCTGGCC
TTCGAGGATTCAGAAGGTGAGGGGGAAGAAGGTCCAGTAGCAGAAGAAGCAATGTTGCTGAAAGAATCTGAGGAAAGGCG
ATGCCTTAGGAAAAGGCCTGAGCTCAACCAGGACACCAAGCCCGTAGGTCGTCAAGAAACACAAGACCCTAGCAGCCAGG
AGGTGCTGTCCGAATTGAGGGCGCTGTCTCAGAAACTCAGCAAGGAAGACCGTCAGCCCAGGAAGCAAAAAGCGAACTCA
GCGGGGGCCATTCTCCCAGTCCAGAGAGAGGAACCGGCCCGGGAGGAGGAGGAGCCCTTGTTGCCGCAGAGGCCAGAGAG
AGTGCAGACTCCAAAAGAGCTGGGCAAAGGAGGCTGTTCGCAAAATACGGAACTTCGCAGACCTGTGTTACAAGGGCAGC
AGATGGAGAAGAACGCAAATAATCAGCCTGATGCCCCGAAGAAGAAGAAAAGGAAGGAGCAAATGATTGATTTACAGAAC
CTCCTGACCACAAAATCTCCTTCCAGGGAGTCTTTGGCAGTTCCTACGACGATAGACAAGTTGGAAGGTGAAGAAGAGAG
AGACCAAAAGCAGATGATAAAGGAAGCTTTTGCTGGGGATGATGTCATCAGAGACTTCTTGAAAGAGAAGAGGGAAGCTG
TGGAGGCGAGTAAGCCAAAGGACGTGGACCTGACGCTGCCTGGCTGGGGCGAGTGGGGCGGTGTGGGCCTACAGCCCCGT
GCCAAAAAAAGACGCTGTTTTTTAATGAAAGCCCCTGAGGGTCCTCCAAGAAAAGACGAGAATTTGCCGAATGTGATTAT
CAGTGAGGAGCGCAACATCCACGCCGCAGCTCACCAGGTGCACGTGCTTCCATACCCATTCAGCCACCATCAGCAATTTG
AAAGGACCATTCGGACCCCTATAGGGTCTATGTGGAACACCCAGAGGGCCTTCCACAAGCTGACTACCCCCAAGGTTGTC
ACTAAGCCAGGCCATATCATTAAGCCCATAGAAGCTGAGGACGTGGGCTACCGGTCTTCCTCAAGGTTGGACCTCTCCGT
GGTACAGAGGAACCCAAAGCGACTCTCCATCCATCACAAAAGACCCCTGAAGAAAAACTCCGTAGGC

Alignment

ORF - retro_lafr_110 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.39 %
• Parental protein coverage: 98.57 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  SLLAL-RQQELVDLPKDYLLSTSDDEGDSDGERKHQKLLEAISSLDGKNRRKLAERSEPSLKVSEFNISS
          SLL.L..Q.EL.DLPKD...STS.DEGDSD.ERKHQKLLEAISSLDGKNRRKLAERSE.S..VSEF....
Retrocopy SLLTLSHQEELADLPKDCPWSTSEDEGDSDRERKHQKLLEAISSLDGKNRRKLAERSEASWDVSEFSVGC

Parental  EGTREKLVLSDLLQPTKTSSSLATVKKQLSRVKSKKTVELPLNKEEVARIHREVAFSKTSQVLSKWDPIV
          EGT.E.LVLSDLLQP.KTSSSLATVKKQL..V..KKTVELPL..EE.A..HREVAFS.TSQ.LSKWDP.V
Retrocopy EGTGEQLVLSDLLQPIKTSSSLATVKKQLKGVQAKKTVELPLDQEEAAQVHREVAFSTTSQALSKWDPVV

Parental  LKNRKAEQLVFPLEKEQAAFAPIEHVLSGWKARTPLEQEIFDVLHKNKQPVTDPLLTPVEKASLKAMSLE
          LKNR.AEQLVFPL...Q..FAPIEHVL.GWKAR.PLEQEIF.VLHKNKQPV.DPLLTPVEKASLKA.SLE
Retrocopy LKNRNAEQLVFPLKQQQLDFAPIEHVLGGWKARSPLEQEIFNVLHKNKQPVIDPLLTPVEKASLKATSLE

Parental  EAKMRRAELQRARALQSYYEAKARREKKIKSKKYHKVVKKGKAKKAVKDFETLQKVDPSAALEELEKIEK
          EA.MR.AELQ.ARALQSYYEAKARREKKIKSKKYHKVVKKGKAK.A.KDFETLQK..P..ALEELEKIEK
Retrocopy EAQMRQAELQKARALQSYYEAKARREKKIKSKKYHKVVKKGKAKIALKDFETLQKASPTTALEELEKIEK

Parental  ARMMERMSLKHQNSGKWAKSKAIMAKYDLEARQAIQEQLAKNKELTQKLQAASESEEEEGDVEENGLLVP
          ARM.ERMSLKHQN.GKWAKSKAIMAKYD.EARQA..EQLAKNKELTQKLQA.SESEEEEG.VEE.GL.VP
Retrocopy ARMVERMSLKHQNKGKWAKSKAIMAKYDPEARQAMHEQLAKNKELTQKLQAPSESEEEEGAVEEDGLFVP

Parental  DVVHKVHMNANELNPWMQRSCTSDAKEAEIQKDPEQLPEPVAHQDSESEGEESPVEEEETLLKEFEERRS
          DVV..V.M.....NPWM..SCTSD.KEAE..KDPEQLPE..A..DSE.EGEE.PV.EE..LLKE.EERR.
Retrocopy DVVNEVQMDTHGPNPWMHTSCTSDVKEAEVLKDPEQLPEHLAFEDSEGEGEEGPVAEEAMLLKESEERRC

Parental  LRKRPELNQDAEPAGHQEAQDASSQEVLSELRALSWKLNQENHQSRKQKGNSTRAVLPVQREEPAQEEEE
          LRKRPELNQD..P.G.QE.QD.SSQEVLSELRALS.KL..E..Q.RKQK.NS..A.LPVQREEPA.EEEE
Retrocopy LRKRPELNQDTKPVGRQETQDPSSQEVLSELRALSQKLSKEDRQPRKQKANSAGAILPVQREEPAREEEE

Parental  PLLLQRPERVQTLEELEELGKEGCLQNTELPRPVLQGQETERNPDDQPGAPKKRKRKEQMIDLQKLLTTK
          PLL.QRPERVQT..EL...GK.GC.QNTEL.RPVLQGQ..E.N...QP.APKK.KRKEQMIDLQ.LLTTK
Retrocopy PLLPQRPERVQTPKEL---GKGGCSQNTELRRPVLQGQQMEKNANNQPDAPKKKKRKEQMIDLQNLLTTK

Parental  SPSVKSLAAPTTME-MEDEEERDQKQMIKEAFAGDDVIRDFLKEKREAVEASKPKDVDLTLPGWGEWGGV
          SPS..SLA.PTT....E.EEERDQKQMIKEAFAGDDVIRDFLKEKREAVEASKPKDVDLTLPGWGEWGGV
Retrocopy SPSRESLAVPTTIDKLEGEEERDQKQMIKEAFAGDDVIRDFLKEKREAVEASKPKDVDLTLPGWGEWGGV

Parental  GLQPSAKKRRRFLIKAPEGPPRKDKNLPNVIINEKRNIHAAAHQVHVLPYPFTHHHQFERTIQTPIGSTW
          GLQP.AKKRR.FL.KAPEGPPRKD.NLPNVII.E.RNIHAAAHQVHVLPYPF.HH.QFERTI.TPIGS.W
Retrocopy GLQPRAKKRRCFLMKAPEGPPRKDENLPNVIISEERNIHAAAHQVHVLPYPFSHHQQFERTIRTPIGSMW

Parental  NTQRAFQKLTTPKVVTKPGHIIKPIKAEDVGYRSSSRSDLSMVQRNPKQLSVRHRKQLKE
          NTQRAF.KLTTPKVVTKPGHIIKPI.AEDVGYRSSSR.DLS.VQRNPK.LS..H...LK.
Retrocopy NTQRAFHKLTTPKVVTKPGHIIKPIEAEDVGYRSSSRLDLSVVQRNPKRLSIHHKRPLKK

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_110 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 14 parental genes, and 17 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000013671	2 retrocopies	retro_btau_133, retro_btau_1706,
Cavia porcellus	ENSCPOG00000014231	2 retrocopies	retro_cpor_1272, retro_cpor_242,
Dasypus novemcinctus	ENSDNOG00000002180	1 retrocopy	retro_dnov_1479,
Homo sapiens	ENSG00000156697	1 retrocopy	retro_hsap_29,
Gorilla gorilla	ENSGGOG00000014930	1 retrocopy	retro_ggor_163,
Loxodonta africana	ENSLAFG00000016653	1 retrocopy	retro_lafr_110 ,
Myotis lucifugus	ENSMLUG00000001984	2 retrocopies	retro_mluc_1643, retro_mluc_308,
Macaca mulatta	ENSMMUG00000020700	1 retrocopy	retro_mmul_35,
Mus musculus	ENSMUSG00000063785	1 retrocopy	retro_mmus_261,
Nomascus leucogenys	ENSNLEG00000015258	1 retrocopy	retro_nleu_2091,
Procavia capensis	ENSPCAG00000006070	1 retrocopy	retro_pcap_127,
Pan troglodytes	ENSPTRG00000022262	1 retrocopy	retro_ptro_824,
Tarsius syrichta	ENSTSYG00000009415	1 retrocopy	retro_tsyr_2104,
Tursiops truncatus	ENSTTRG00000003794	1 retrocopy	retro_ttru_1687,