RetrogeneDB ID: retro_dmel_54

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 3L:12964381..12965431(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: FBgn0036327
• 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_54
ATGTTGTTACTGACAAGTCTTAAAAGCCTGGCAAAACCAGCTACATGGGGAGTTGTGGTCCGCACTTTAAAGGTCGCCGT
TGTCGGTGCCGGAGGAGGAATTGGACAACCGCTATCGCTTCTGCTCCGTCGCTGTCCTGGAATCGATGAGCTGGCTCTAC
ATGATCTCAGCGAAATGAAGGGAATTGCTACGGATCTATCCCATATAAGCCAAACGGGAAAGGTGATAGGTTTTACCGGT
GAAAAGGAACTGGAGTCGGCGGTGAGTGGAGCTGATGTGGTGGTTGTGGCGGCAGGGATGCCACGTCTGCCAGGAATGCA
AAGGGATCACCTGATGGCCGCCAATGGAAATGTTGCAGTGAAAGTTGCCACTGCCATTAGCAATGCCTCTCCACGAGCTC
ATCTTGCCTTTATTACCAATCCGGTCAATATGATTGTGCCCGCCGCAGCTGAGGTTCTTATGGCCCATGGAACTTTTGAT
TCTCGTCGGCTCTTCGGTATTACGACTTTGGATGTGGTGCGATCGAAAAAGTTCATTGGTGATTCTATGAACATATCACC
GGATGACGTAAACATTCCAGTTATTGGTGGCCATGCGGGGATTACAATTCTACCGCTCATTTCGCAGTGTCAGCCGATAT
ATAGATGTGATCTCCAGGAGATCCAGAATCTAACTCATCGCATTCAGGAGGCGGGCACAGAGGTGGTGAATGCCAAAGCT
GGAAAAGGATCTGCCACCCTATCGATGGCTTATGCTGGCGCAACTTTCGTGAACTCCCTGCTGCGTGGAATTGCTGGACA
GGATGGTCTAATCGAGTGCGCTTTTGTCGCCTCCAAACTAACCGACGCCCCATTCTTTGCTAGTCCATTGGAATTGGGAA
AGGATGGTATCAAGCGCTATATACCACTTCCCCAGATGAGTGACTACGAAAAGGAGGCTTTGGAAAAGCTACTACCTATT
CTACGACAGAATGCTGATGAGGGTGTCAATTTTGCAAAAATGATTTTGAGTGGACAATCACATTCTCCCATTCCAGCGGC
CTTGCCGTAA

Alignment

ORF - retro_dmel_54 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 52.43 %
• Parental protein coverage: 91.96 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  KVTVCGAAGGIGQPLSLLLKQNPLVTDLALYDIVHTPGVAADLSHIDTKSKTAGFIGADQLGDSLKGSDV
          KV.V.GA.GGIGQPLSLLL...P....LAL.D.....G.A.DLSHI....K..GF.G...L.....G.DV
Retrocopy KVAVVGAGGGIGQPLSLLLRRCPGIDELALHDLSEMKGIATDLSHISQTGKVIGFTGEKELESAVSGADV

Parental  VVIPAGVPRKPGMTRDDLFNVNAGIIKDISNSIAKNCPKALVAIITNPVNTCVPIAAEILKKAGVYDPKR
          VV..AG.PR.PGM.RD.L...N..........I....P.A..A.ITNPVN..VP.AAE.L...G..D..R
Retrocopy VVVAAGMPRLPGMQRDHLMAANGNVAVKVATAISNASPRAHLAFITNPVNMIVPAAAEVLMAHGTFDSRR

Parental  LFGVSTLDVVRARAFIGHALGVDPQTVQIPVIGGHSGVTILPVLSQSQPLFKGNQDTIEKLTVRIQEAGT
          LFG..TLDVVR...FIG......P..V.IPVIGGH.G.TILP..SQ.QP........I..LT.RIQEAGT
Retrocopy LFGITTLDVVRSKKFIGDSMNISPDDVNIPVIGGHAGITILPLISQCQPIYRCDLQEIQNLTHRIQEAGT

Parental  EVVKAKAGAGSATLSMAYAGARFAGSLLKGLNGEKNVIECSYVQSTVTEATFFSTPLVLGKNGVQENLGL
          EVV.AKAG.GSATLSMAYAGA.F..SLL.G..G....IEC..V.S..T.A.FF..PL.LGK.G......L
Retrocopy EVVNAKAGKGSATLSMAYAGATFVNSLLRGIAGQDGLIECAFVASKLTDAPFFASPLELGKDGIKRYIPL

Parental  PKLNDYEKKLLEAAIPELKKNIQKGIDFA
          P...DYEK..LE...P.L..N...G..FA
Retrocopy PQMSDYEKEALEKLLPILRQNADEGVNFA

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

No EST(s) were mapped for retro_dmel_54 retrocopy.

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_54 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,