RetrogeneDB ID: retro_dmel_56

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 3R:6962973..6965325(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: FBgn0037862
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Acon
• Ensembl ID: FBgn0010100
• Aliases: None
• Description: Aconitase [Source:FlyBase gene name;Acc:FBgn0010100]

Sequence

>retro_dmel_56
ATGGCTCAACGAACACATAGATATATATGTTTGGCGGGTTCCATGGTGCGAAACTTTCACACGGCGCGTTTTCCACGATG
TGATAAAGTGGCAATGTCAAATTTTGATACCGGAATTCCCTTGCCCTATAAGAAGTTGAGGGAAAACCTGGATTGCATCA
AGGGTCGACTGGGTGGACCGCTAACCTTGTCGGAGAAGGTGTTATATTCCCATTTGGATCAACCGGATTCACAGGAAATC
GAACGAGGCAAGTCCTATTTGCGATTGCGACCAGATCGCGTTGCCCTGCAGGATGCGACTGCCCAGATGACGCTACTGCA
GTTCATTTCGTCGGGCCTGAAGAAGGTAGCAGTTCCATCCACCGTCCACTGTGATCACTTAATTGAGGCCCAGATCAGTG
GCGATAAGGACTTGGCCAGGGCTAAGGATCTGAACAAGGAGGTGTACGATTTTCTGTCCTCGGCGTGTGCCAAGTATAAC
TTGGGTTTCTGGAAGCCTGGCAGCGGCATAATTCATCAGATCATTTTAGAGAACTATGCATTTCCCGGACTACTGATGAT
CGGAACTGATTCCCATACTCCGAATGGCGGCGGATTGGGTTGCCTATGCGTTGGAGTTGGTGGTGCTGATGCCGTCGATG
TGATGGCGAATATACCGTGGGAACTCAAGTGCCCGACCGTGATTGGATGCCATCTCACGGGTAAGATCAGTGGGTGGACT
TCGCCCAAGGATGTCATCCTTAAAGTGGCCGAGATTCTGACCGTTAAAGGAGGTACGGGTGCCATTGTGGAGTACCATGG
TCCTGGCGTCGAATCTATTTCCTGCACAGGCATGGCTACTATTACCAACATGGGTGCTGAAATCGGTGCCACAACTTCAA
TATTTCCATTCAACGAACGCATGGTCACATATTTGCGTGCAACCGGTAGAGGTGCCATCGCTGATGAGGCCACAAAGAAT
AAAGATCTTTTGGTTCCGGATGAGGGTTGCAAATACGATAAGGTGATCGAGATCAATTTGGACACCTTGGAACCGCTGGT
GAATGGCCCCTTCACTCCCGATTTGGCCCATCCCATTAGTAAACTGGGTCAGAACTCCGAGAAGAATGGCTATCCGATGG
AAATCAAAGTGAGTCTAATTGGTTCCTGCACGAACTCCTCCTACGAGGACATGGGACGATGTGCCAGCATAGCCAATGAC
GCACTGGGTCATGGCCTAAAATCGTGCGTTCCATTTAATGTTACCCCGGGATCGGAGCAAGTTCGAGCTACAATCGCACG
GGACGGCATTATAGATGTGCTTGAGAAGTTTGGAGGCACCGTGCTGGCGAATGCCTGTGGTCCCTGCATTGGACAGTGGG
ATCGCAAGGATGTAAAGATGGGAGAGAAGAACACCATTGTCACGTCGTATAATCGCAACTTCACCGGTCGAAATGATGCC
AATCCAGCAACACATTGTTTTGTTACGAGTCCAGAAATGGCAACTGCATTGGCTATCGCCGGACGTTTGGATTTCAATCC
GATGACGGATGAGCTTACGGGTACCGATGGCAAAACGTTCAAGCTCAAGGAACCGCACGGCGAAGAGCTGCCATCCAAGG
GTTTTGATCCCGGAGAGGATACCTATCAGGCTCCCCCAGCGAAAGCAGATGATATCAAGGTCAATGTCGATCCCAAGTCG
GATCGCCTGCAACTGCTCGAACCTTTTGAGAAATGGGACGGCAAGGACTACATTGATTTGATGGTGCTTATCAAAATCAA
AGGCAAATGCACCACCGATCACATCAGTGCCGCTGGACCCTGGCTTAAGTATCGCGGTCATTTGGATAATATATCAAATA
ACATGTTCATTGGGGCAACAAATGCCGAAAACAATGAAATGAACAAGGTCAAAAACCAGAAGACAGGCAGTTTTGACGCC
GTACCAGCGGTGGCACGCGATTACAAGGCCAACAAGATCAAGTGGTGTGCTGTGGGTGAGGAGAACTACGGCGAGGGATC
ATCCAGGGAGCACGCTGCCCTGGAACCTCGACACTTGGGCGGAGTGGCCATTATCGTCAAGTCGTTCGCCCGCATCCACG
AGACGAACCTAAAGAAACAGGGTATGCTCGCCCTGACATTCGCCAATCCCGGTGACTACGACAAAGTTCAGCCGTCGAGC
AAGATTTCGATACTGAACCTCAAGGACTTGGCACCTGGCAAGCCTGTGGATGCTGAGATCAAGAATAATGGTAGCTCCGA
CAAAATCCAGTTGAACCACACCCTTAATGAGCTGCAGATCCAGTGGTTCCAGGCTGGAAGTGCCTTGAATCTAATGAAGG
AGCTTGCCGCCAAGGGTGGCGATAAGAAATAG

Alignment

ORF - retro_dmel_56 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.33 %
• Parental protein coverage: 98.22 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RLGKHVASEATVVRQFHASCYT-ASKVALSKFDSDVYLPYEKLNKRLEVVRGRLNRPLTLSEKVLYSHLD
          R...........VR.FH........KVA.S.FD....LPY.KL...L....GRL..PLTLSEKVLYSHLD
Retrocopy RTHRYICLAGSMVRNFHTARFPRCDKVAMSNFDTGIPLPYKKLRENLDCIKGRLGGPLTLSEKVLYSHLD

Parental  DPANQDIVRGTSYLRLRPDRVAMQDATAQMALLQFISSGLKKVAVPSTVHCDHLIEAQIGGPKDLARAKD
          .P..Q.I.RG.SYLRLRPDRVA.QDATAQM.LLQFISSGLKKVAVPSTVHCDHLIEAQI.G.KDLARAKD
Retrocopy QPDSQEIERGKSYLRLRPDRVALQDATAQMTLLQFISSGLKKVAVPSTVHCDHLIEAQISGDKDLARAKD

Parental  LNKEVYDFLASTCAKYGLGFWKPGSGIIHQIILENYAFPGLLMIGTDSHTPNGGGLGGLCIGVGGADAVD
          LNKEVYDFL.S.CAKY.LGFWKPGSGIIHQIILENYAFPGLLMIGTDSHTPNGGGLG.LC.GVGGADAVD
Retrocopy LNKEVYDFLSSACAKYNLGFWKPGSGIIHQIILENYAFPGLLMIGTDSHTPNGGGLGCLCVGVGGADAVD

Parental  VMADIPWELKCPKVIGVNLTGKISGWTSPKDVILKVADILTVKGGTGAIIEYHGKGVDSISCTGMATICN
          VMA.IPWELKCP.VIG..LTGKISGWTSPKDVILKVA.ILTVKGGTGAI.EYHG.GV.SISCTGMATI.N
Retrocopy VMANIPWELKCPTVIGCHLTGKISGWTSPKDVILKVAEILTVKGGTGAIVEYHGPGVESISCTGMATITN

Parental  MGAEIGATTSLFPFNQRMADYLKSTGRAGIASEAQKYQAKILSADKNCEYDELIEINLDTLEPHVNGPFT
          MGAEIGATTS.FPFN.RM..YL..TGR..IA.EA.K.....L..D..C.YD..IEINLDTLEP.VNGPFT
Retrocopy MGAEIGATTSIFPFNERMVTYLRATGRGAIADEATKNK-DLLVPDEGCKYDKVIEINLDTLEPLVNGPFT

Parental  PDLGHPISKLGENSKKNGYPMDIRVGLIGSCTNSSYEDMGRCASIAKDAMSHGLKSKIPFNVTPGSEQIR
          PDL.HPISKLG.NS.KNGYPM.I.V.LIGSCTNSSYEDMGRCASIA.DA..HGLKS..PFNVTPGSEQ.R
Retrocopy PDLAHPISKLGQNSEKNGYPMEIKVSLIGSCTNSSYEDMGRCASIANDALGHGLKSCVPFNVTPGSEQVR

Parental  ATIERDGISEVFDKFGGTVLANACGPCIGQWDRKDVKKGDKNTIVTSYNRNFTGRNDANPATHCFVTSPE
          ATI.RDGI..V..KFGGTVLANACGPCIGQWDRKDVK.G.KNTIVTSYNRNFTGRNDANPATHCFVTSPE
Retrocopy ATIARDGIIDVLEKFGGTVLANACGPCIGQWDRKDVKMGEKNTIVTSYNRNFTGRNDANPATHCFVTSPE

Parental  LVTALSIAGRLDFNPLTDELTGADGKKFKLKAPFGDELPAKGFDPGQDTYTAPPPSGENVKVAVDPKSTR
          ..TAL.IAGRLDFNP.TDELTG.DGK.FKLK.P.G.ELP.KGFDPG.DTY.APP......KV.VDPKS.R
Retrocopy MATALAIAGRLDFNPMTDELTGTDGKTFKLKEPHGEELPSKGFDPGEDTYQAPPAKADDIKVNVDPKSDR

Parental  LQLLEPFDKWNGQDLTDLTVLIKVKGKCTTDHISAAGPWLKYRGHLDNISNNMFIGATNYENNEMNNIKN
          LQLLEPF.KW.G.D..DL.VLIK.KGKCTTDHISAAGPWLKYRGHLDNISNNMFIGATN.ENNEMN..KN
Retrocopy LQLLEPFEKWDGKDYIDLMVLIKIKGKCTTDHISAAGPWLKYRGHLDNISNNMFIGATNAENNEMNKVKN

Parental  QRNGSWGGVPDVARDYKANGIKWVAVGDENYGEGSSREHAALEPRHLGGRAIIVKSFARIHETNLKKQGL
          Q..GS...VP.VARDYKAN.IKW.AVG.ENYGEGSSREHAALEPRHLGG.AIIVKSFARIHETNLKKQG.
Retrocopy QKTGSFDAVPAVARDYKANKIKWCAVGEENYGEGSSREHAALEPRHLGGVAIIVKSFARIHETNLKKQGM

Parental  LPLTFANPADYDKIQPTSKISLLNLKSLAPGKPVDAEIKNGDKVERIKLNHTLNDLQIGWFKAGSALNRM
          L.LTFANP.DYDK.QP.SKIS.LNLK.LAPGKPVDAEIKN......I.LNHTLN.LQI.WF.AGSALN.M
Retrocopy LALTFANPGDYDKVQPSSKISILNLKDLAPGKPVDAEIKNNGSSDKIQLNHTLNELQIQWFQAGSALNLM

Parental  KELA
          KELA
Retrocopy KELA

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Drosophila melanogaster was not studied using RNA-Seq expression data.

ChIP-Seq

Drosophila melanogaster was not studied using ChIP-Seq data.

EST

8 EST(s) were mapped to retro_dmel_56 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI944654	6963817	6964164	100	347	0	347
BF485923	6962916	6963292	98.7	371	5	366
BF491564	6963001	6963395	98.8	392	2	389
BF493049	6963181	6963788	99.4	603	4	599
BF493078	6963181	6963782	98.6	597	4	591
BF494409	6962898	6963627	99.2	725	3	720
BF497308	6962913	6963453	100	540	0	540
BF504011	6962941	6963591	98.8	642	8	634

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_56 was not experimentally validated.

Homology

Retrocopy orthology:

Drosophila melanogaster 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 8 parental genes, and 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Homo sapiens	ENSG00000100412	2 retrocopies	retro_hsap_2583, retro_hsap_324,
Myotis lucifugus	ENSMLUG00000002472	1 retrocopy	retro_mluc_2566,
Macaca mulatta	ENSMMUG00000001454	2 retrocopies	retro_mmul_647, retro_mmul_694,
Mus musculus	ENSMUSG00000022477	1 retrocopy	retro_mmus_535,
Nomascus leucogenys	ENSNLEG00000015482	2 retrocopies	retro_nleu_1519, retro_nleu_1767,
Pongo abelii	ENSPPYG00000011871	1 retrocopy	retro_pabe_1903,
Pan troglodytes	ENSPTRG00000014428	1 retrocopy	retro_ptro_260,
Drosophila melanogaster	FBgn0010100	1 retrocopy	retro_dmel_56 ,