RetrogeneDB ID: retro_dmel_58

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 3L:22543420..22544971(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: FBgn0037170
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Trxr-1
• Ensembl ID: FBgn0020653
• Aliases: None
• Description: Thioredoxin reductase-1 [Source:FlyBase gene name;Acc:FBgn0020653]

Sequence

>retro_dmel_58
ATGTCGACGATAAAGTTTCTGCGATCCTCCACACACAACGCACTTCGGTCCAGCCTCGGATGGTGCCGCCTTGCTGCCTC
AAGACCACGCTATGATTACGACCTTGTGGTGCTCGGCGGGGGCTCGGCGGGATTGGCGTGTGCCAAGGAGGCTGCTGGCT
GTGGAGCCCGCGTGCTCTGCTTCGACTACGTCAAGCCCACTCCAGTGGGCACCAAGTGGGGCATCGGCGGCACCTGCGTG
AATGTGGGCTGCATCCCCAAGAAGCTAATGCACCAGGCCTCGCTGCTGGGCGAGGCTGTTCACGAGGCGGTGGCCTACGG
CTGGAATGTAGACGACACGAACATACGGCCCGATTGGCGCAAGTTGGTGCGCTCCGTCCAGAACCACATCAAGTCCGTCA
ACTGGGTGACCCGCGTGGACCTGCGCGACAAAAAGGTGGAGTACGTAAATTCGATGGCCACCTTTCGCGACAGCCACACC
ATCGAGTATGTGGCGATGCCAGGTGCCGAGCACCGTCAAGTGACCTCAGAGTACGTGGTGGTAGCCGTCGGCGGGAGGCC
ACGCTACCCGGACATTCCCGGAGCCGTTGAACTGGGCATCACCAGCGACGATATATTCAGCTACGAGCGAGAGCCGGGTC
GTACCCTTGTGGTGGGCGCCGGATACGTGGGTCTCGAGTGCGCCTGTTTCCTTAAGGGTCTCGGCTACGAGCCCACTGTC
ATGGTGCGCTCCATTGTGCTGCGCGGCTTCGATCGCCAGATGTCCGAGCTGCTGGCCGCCATGATGACTGAGCGCGGCAT
TCCCTTCCTGGGCACCACAATCCCCAAGGCCGTGGAGAGGCAGGCGGACGGACGGCTGCTAGTTCGGTACCGCAACACAA
CCACCCAAATGGACGGCAGCGACGTTTTCGACACCGTGCTGTGGGCCATTGGGCGCAAAGGTCTCATCGAGGACCTCAAC
CTGGACGCCGCCGGAGTGAAGACTCATGACGACAAGATTGTGGTAGACGCCGCGGAGGCCACCAGCGTGCCTCATATATT
TGCAGTTGGGGACATCATATATGGTCGACCAGAGCTAACGCCGGTGGCCATCCTGTCGGGCCGCCTGCTTGCCAGGCGTC
TGTTCGCCGGCTCCACGCAGCTGATGGACTATGCCGACGTGGCAACCACAGTTTTTACTCCGCTAGAATACAGTTGCGTC
GGCATGTCGGAGGAAACGGCCATCGAACTGCGTGGTGCTGACAACATCGAGGTCTTCCACGGCTACTACAAGCCCACAGA
GTTCTTTATTCCCCAGAAGAGCGTGCGTCACTGCTACCTCAAGGCCGTAGCCGAAGTGTCCGGGGACCAGAAGATCCTTG
GCCTGCACTACATCGGCCCAGTCGCCGGCGAGGTCATCCAGGGCTTCGCCGCAGCCCTCAAGACCGGCTTGACCGTAAAG
ACGCTTCTGAACACGGTGGGAATCCACCCCACCACCGCCGAAGAGTTCACCCGGCTGTCAATCACCAAGCGATCTGGTCG
GGATCCTACACCAGCCTCCTGTTGCAGTTAG

Alignment

ORF - retro_dmel_58 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.91 %
• Parental protein coverage: 100. %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MAPVQGSYDYDLIVIGGGSAGLACAKEAVLNGARVACLDFVKPTPTLGTKWGVGGTCVNVGCIPKKLMHQ
          .A.....YDYDL.V.GGGSAGLACAKEA...GARV.C.D.VKPTP..GTKWG.GGTCVNVGCIPKKLMHQ
Retrocopy LAASRPRYDYDLVVLGGGSAGLACAKEAAGCGARVLCFDYVKPTP-VGTKWGIGGTCVNVGCIPKKLMHQ

Parental  ASLLGEAVHEAAAYGWNVDE-KIKPDWHKLVQSVQNHIKSVNWVTRVDLRDKKVEYINGLGSFVDSHTL-
          ASLLGEAVHEA.AYGWNVD...I.PDW.KLV.SVQNHIKSVNWVTRVDLRDKKVEY.N....F.DSHT..
Retrocopy ASLLGEAVHEAVAYGWNVDDTNIRPDWRKLVRSVQNHIKSVNWVTRVDLRDKKVEYVNSMATFRDSHTIE

Parental  -LAKLKSGERTITAQTFVIAVGGRPRYPDIPGAVEYGITSDDLFSLDREPGKTLVVGAGYIGLECAGFLK
          ..A......R..T....V.AVGGRPRYPDIPGAVE.GITSDD.FS..REPG.TLVVGAGY.GLECA.FLK
Retrocopy YVAMPGAEHRQVTSEYVVVAVGGRPRYPDIPGAVELGITSDDIFSYEREPGRTLVVGAGYVGLECACFLK

Parental  GLGYEPTVMVRSIVLRGFDQQMAELVAASMEERGIPFLRKTVPLSVEKQDDGKLLVKYKNVETGEEAEDV
          GLGYEPTVMVRSIVLRGFD.QM.EL.AA.M.ERGIPFL..T.P..VE.Q.DG.LLV.Y.N..T.....DV
Retrocopy GLGYEPTVMVRSIVLRGFDRQMSELLAAMMTERGIPFLGTTIPKAVERQADGRLLVRYRNTTTQMDGSDV

Parental  YDTVLWAIGRKGLVDDLNLPNAGVTVQKDKIPVDSQEATNVANIYAVGDIIYGKPELTPVAVLAGRLLAR
          .DTVLWAIGRKGL..DLNL..AGV....DKI.VD..EAT.V..I.AVGDIIYG.PELTPVA.L.GRLLAR
Retrocopy FDTVLWAIGRKGLIEDLNLDAAGVKTHDDKIVVDAAEATSVPHIFAVGDIIYGRPELTPVAILSGRLLAR

Parental  RLYGGSTQRMDYKDVATTVFTPLEYACVGLSEEDAVKQFGADEIEVFHGYYKPTEFFIPQKSVRYCYLKA
          RL..GSTQ.MDY.DVATTVFTPLEY.CVG.SEE.A....GAD.IEVFHGYYKPTEFFIPQKSVR.CYLKA
Retrocopy RLFAGSTQLMDYADVATTVFTPLEYSCVGMSEETAIELRGADNIEVFHGYYKPTEFFIPQKSVRHCYLKA

Parental  VAERHGDQRVYGLHYIGPVAGEVIQGFAAALKSGLTINTLINTVGIHPTTAEEFTRLAITKRSGLDPTPA
          VAE..GDQ...GLHYIGPVAGEVIQGFAAALK.GLT..TL.NTVGIHPTTAEEFTRL.ITKRSG.DPTPA
Retrocopy VAEVSGDQKILGLHYIGPVAGEVIQGFAAALKTGLTVKTLLNTVGIHPTTAEEFTRLSITKRSGRDPTPA

Parental  SCCS
          SCCS
Retrocopy SCCS

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

10 EST(s) were mapped to retro_dmel_58 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BE975157	22543366	22543921	100	555	0	555
BE978309	22544174	22544326	98.1	149	3	146
BF490677	22543346	22543860	99.5	511	3	508
BF491478	22543343	22543954	100	611	0	611
BF491489	22543325	22544010	99.9	684	1	683
BF493128	22543348	22544041	99.9	692	1	691
BF500785	22543350	22544066	99.5	712	4	708
BF503426	22543356	22544064	99.5	704	4	700
BG634118	22543362	22543814	98.7	446	6	440
CK657069	22543349	22544039	100	690	0	690

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_58 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Gorilla gorilla	ENSGGOG00000001980	1 retrocopy	retro_ggor_3081,
Drosophila melanogaster	FBgn0020653	1 retrocopy	retro_dmel_58 ,