RetrogeneDB ID: retro_dmel_76

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 3L:12965625..12966669(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: FBgn0036328
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Mdh2
• Ensembl ID: FBgn0262559
• Aliases: None
• Description: Malate dehydrogenase 2 [Source:FlyBase gene name;Acc:FBgn0262559]

Sequence

>retro_dmel_76
ATGTTTTTGGCCTCTAGATTGTTAAGCCATGTTGGCAACTTGCCTCCCAAGGTCCAGCAGCTTGGATATATCAACCGAGG
TCTCAAGGTCGCCGTTGTGGGATCGGTGGGTGGAATCGGTCAGCCGCTGTCCCTTCTTCTCAAGCATAATCCGCAAATCT
CGACCCTGTCTCTGTACGACATTAAGAATACAACCGGTGTAGGAGTAGACTTATCTCATATCAACACCCGTGCTTCAGTG
TGCCCATTCGAGGGTAAGAATGGTTTAAAAAAAGCTATGGATAAGGCTGATATAGTGGTGATACCGGCGGGTTTGCCACG
TAAGCCCGGAATGAAGCGCGAAGATTTGGTGGACGTGAATGCCAGCGTTGCCTGCGAAGTGGCTTTTGCGGCTAGCGAAG
TTTGTCCCGGTGCCATGCTTGCCTTCATCACGAACCCCATCAACGTGATAGTACCCATCGTGGCCACGATCCTTAAAGCA
AAGGGTACATACGATCCGAATCGACTATTTGGTGTCACCACTCTGGATGTGGTACGAGCCCAGACCTTTGTAGCGGACAT
TCTCAACGTTGATCCCCAGAAAGTGAATATACCCGTAATCGGTGGCCATACAGGTCGGACCATCCTGCCCATACTGTCGC
AGTGTGATCCCCCCTTTAAGGGTACCGATAAGGAGCGCGAAGCGTTGATCCAACGCATCCAAAATGCGGGCACAGAAGTG
GTTAATGCCAAGGATGGCCTGGGCTCGGCCACCCTATCGATGGCCTTTGCAGCCACTCAGTTTGTAAGCTCGTTGATAAA
GGGTATCAAGGGTTCAAAGGACGAGTGCATTGTGGAATGTGCCTATGTGGAGTCTGATGTCACGGAGGCCCAGTTCTTCG
CCACCCCACTGATACTGGGACCCCAGGGTGTCAAGGAAAACACAGGATTGCCCGATTTGGACGATGAGGAAAGGAAGGCT
CTAAATGGTATGCTACCCATTTTGAAGGAGAGTATCGCAAAGGGCATCAAATTGGGCGAGGGTATGATATGCAGTTGTGC
ATAA

Alignment

ORF - retro_dmel_76 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 57.47 %
• Parental protein coverage: 91.07 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVTVCGAAGGIGQPLSLLLKQNPLVTDLALYDIVHTPGVAADLSHIDTKSKTAGFIGADQLGDSLKGSDV
          KV.V.G..GGIGQPLSLLLK.NP....L.LYDI..T.GV..DLSHI.T......F.G...L.......D.
Retrocopy KVAVVGSVGGIGQPLSLLLKHNPQISTLSLYDIKNTTGVGVDLSHINTRASVCPFEGKNGLKKAMDKADI

Parental  VVIPAGVPRKPGMTRDDLFNVNAGIIKDISNSIAKNCPKALVAIITNPVNTCVPIAAEILKKAGVYDPKR
          VVIPAG.PRKPGM.R.DL..VNA.............CP.A..A.ITNP.N..VPI.A.ILK..G.YDP.R
Retrocopy VVIPAGLPRKPGMKREDLVDVNASVACEVAFAASEVCPGAMLAFITNPINVIVPIVATILKAKGTYDPNR

Parental  LFGVSTLDVVRARAFIGHALGVDPQTVQIPVIGGHSGVTILPVLSQSQPLFKGNQDTIEKLTVRIQEAGT
          LFGV.TLDVVRA..F....L.VDPQ.V.IPVIGGH.G.TILP.LSQ..P.FKG.....E.L..RIQ.AGT
Retrocopy LFGVTTLDVVRAQTFVADILNVDPQKVNIPVIGGHTGRTILPILSQCDPPFKGTDKEREALIQRIQNAGT

Parental  EVVKAKAGAGSATLSMAYAGARFAGSLLKGLNGEKN--VIECSYVQSTVTEATFFSTPLVLGKNGVQENL
          EVV.AK.G.GSATLSMA.A...F..SL.KG..G.K.....EC.YV.S.VTEA.FF.TPL.LG..GV.EN.
Retrocopy EVVNAKDGLGSATLSMAFAATQFVSSLIKGIKGSKDECIVECAYVESDVTEAQFFATPLILGPQGVKENT

Parental  GLPKLNDYEKKLLEAAIPELKKNIQKGI
          GLP.L.D.E.K.L....P.LK..I.KGI
Retrocopy GLPDLDDEERKALNGMLPILKESIAKGI

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

3 EST(s) were mapped to retro_dmel_76 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI946351	12965600	12966013	99.6	411	2	409
AI946619	12965683	12966154	99.4	468	3	465
BF487766	12965573	12966005	96.6	423	8	411

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_76 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 11 parental genes, and 14 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000010846	1 retrocopy	retro_amel_361,
Canis familiaris	ENSCAFG00000013515	2 retrocopies	retro_cfam_182, retro_cfam_41,
Myotis lucifugus	ENSMLUG00000017795	1 retrocopy	retro_mluc_1948,
Monodelphis domestica	ENSMODG00000013680	1 retrocopy	retro_mdom_1711,
Mustela putorius furo	ENSMPUG00000016000	2 retrocopies	retro_mputfur_1607, retro_mputfur_478,
Mus musculus	ENSMUSG00000019179	1 retrocopy	retro_mmus_2451,
Otolemur garnettii	ENSOGAG00000009705	1 retrocopy	retro_ogar_3068,
Pteropus vampyrus	ENSPVAG00000003397	1 retrocopy	retro_pvam_981,
Tupaia belangeri	ENSTBEG00000003190	1 retrocopy	retro_tbel_440,
Tursiops truncatus	ENSTTRG00000014834	1 retrocopy	retro_ttru_1550,
Drosophila melanogaster	FBgn0262559	2 retrocopies	retro_dmel_54, retro_dmel_76 ,