RetrogeneDB ID: retro_dmel_16

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 3R:12964828..12966760(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: FBgn0038486
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CG1041
• Ensembl ID: FBgn0037440
• Aliases: None
• Description: None

Sequence

>retro_dmel_16
ATGAAGTTCCGTGACAATGGAAAGGTCCTTTGGAATTTCGCAAGGATATCGGCTCTGCAACAGACTCGATATACGTTCGG
CAAAAAAATGCCAATTGCCAGCTATAGCACTGCCAAGGATAAGCCTAAATCCGATCAGCCAAACCTTCTAAAGTATCATG
TCTTACCTCTTGAAGAAATCCTCAACCGCTTCATGATTACCGTACAACCATTGCTGACACCCGAGGAGTTCAAAAAGCAA
GAGAAGATTACTAACGAATTCCAGAGGAAGGAGGGCGCTAAGCTACAAAAGCTCCTCGAAGAAACTGGTGAACAGGAGAA
GAACTGGTTAGCCCATCGCTGGCTGAAGGTTGCCTACTTACAGTTTCGGTCGCCAGTGACTTGCTTCTCCAGTCCCGGCA
TGACCTTTCCCAAACAGAAATTTGAAAGTGTCCACGAATTTGTGGACTACACGTCTAGGGTTATCTTCGGTTTGGGTGAG
TTCAATGACTTGGTGCACGCCAAAAAGATTCCGATTGTGAAAATGGGCAAGAACGAGCTGGACAACAGTCAGTTTGGAAA
GGTTTTCGGCACATGCCGGATACCGAGAAGGTTTACCGACGATATCGTCTACAATCCGTGCTCTGATTATGTGGTGGTTA
TCTACCGGAATCACTTTTATCAACTGAAAATATACGACAAGGAAGGAAAGCTTATAATTGCACCATGTCTGGCTGTTCAA
CTGGAGGAAATAATGGCAAAGGAAAAGGAACCGGGAGTTCCTTATGGAATCTTGACCACCGATTCGCGGGACAACTGGGC
CGAGGCATACGAACACTTGTCAAATACGCCCCGTAATAGAGTTGCCCTGAAAACCATTCAGAATGCTATGTTCACAGTGT
CCCTCGACGAGTGTACCAGTCCAAAAGAAGGTCGAGATGCCGAAGAATTGATCCTTACGCTGATCCATGGAAAGGGCAGC
AAGTGCAACAGTGCCAACCGCTGGATGGATAAGACAATTCAATTGGTGGTAAACCCAAATGGACACGTTGGATTCACCTA
TGAGCACTCACCAGCCGAGGGCCAACCGATCGCAATGATGATGGACTATGTAGTGAAGAAGATGAAGGATGACCCTAGTT
ATGGGGAATGCGGATCGGAAAACTTTATTCCAGCGAAGAAAATAAAGTTCTGTGATGTAAGCAAATGCGTGGAGCAATGG
TTGATAATCGCGCAAAAAAACGTGGACAAACTTGTCCAGGACCTGCAAATGAAGGTTCTTAAGTTCGATTGCTACGGCAA
GGATTTCATCAAGAAACAGCGACTTGGTCCAGATAGCTTTGTTCAGATGGCATTGCAGTTGGCATTCTTTAAATTGCACT
ATGAGCCAGCTGCTCAATATGAATCGGCGCATTTGCGCATCTTCGATGGCGGCCGAACCGAAACCATCCGTTCGTGCTCC
AATGAATCCCTGGCTTTTTGCCACGCCATGGATGATGTGAGTGCATCAGCTCAGGAGCGGGCTAGTAAGATTCGCGAGGC
AGTGATGTGCCATCAGATGTATGCGAAGCTGGCGCTTCTGGGAAAGGGTGTCGATCGTCACCTCTTTGGACTTAAACTAA
TGGCGGTGGAGAACTGCCTACCTGTTCCGGAGTTCTTCTCTTCGCCAGGATATGTAAAGTCCACGCACTTTCGAATGTCC
ACTTCGCAGGTGGCCACCAAATATGATGCCTTCATGGGATATGGACCTTCTGTAGAAGATGGATATGCCTGTTGCTACAA
TCCCCGTGAACATGACATCATTTTGGCCATATCCGCATGGCGACATTGTCAGGCAACTGATCACCAAAAGATCGCCAAGG
CGCTTGCGCAGTCCTTTGCTGAAATGAAGGATGTACTTGAAACATGTCCAGCTTCAAAAGACAAGCCGCCAGAGCTTAAG
TGCAAGTATTGA

Alignment

ORF - retro_dmel_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.64 %
• Parental protein coverage: 95.32 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MKFRGNGKLLWNLTKNSLAQQSPNGIAKKVLPASSYSTVQKTIPLEQPNLLKYHVLPLEETLNRFMTTVE
          MKFR.NGK.LWN....S..QQ......KK..P..SYST........QPNLLKYHVLPLEE.LNRFM.TV.
Retrocopy MKFRDNGKVLWNFARISALQQTRYTFGKK-MPIASYSTAKDKPKSDQPNLLKYHVLPLEEILNRFMITVQ

Parental  PLLTPEEFQRQKGITSEFLKKQGRELQLLLEETGSKEKNWLAHRWLKAAYLTYRDPVTVFVSPGMTFPKQ
          PLLTPEEF..Q..IT.EF..K.G..LQ.LLEETG..EKNWLAHRWLK.AYL..R.PVT.F.SPGMTFPKQ
Retrocopy PLLTPEEFKKQEKITNEFQRKEGAKLQKLLEETGEQEKNWLAHRWLKVAYLQFRSPVTCFSSPGMTFPKQ

Parental  NFRDSRAFVDYTARVIYGLGEFNDMVHANKIPIVKMGKNELDNSQFGKVFGTCRIPRRGTDEIVYNPDSD
          .F.....FVDYT.RVI.GLGEFND.VHA.KIPIVKMGKNELDNSQFGKVFGTCRIPRR.TD.IVYNP.SD
Retrocopy KFESVHEFVDYTSRVIFGLGEFNDLVHAKKIPIVKMGKNELDNSQFGKVFGTCRIPRRFTDDIVYNPCSD

Parental  YVVVIYKNHFYQLKIYSKEGKLIAAPCLAAQLENIVLKETQVGVPYGILTTDSRDNWAEAYEYLVETPGN
          YVVVIY.NHFYQLKIY.KEGKLI.APCLA.QLE.I..KE...GVPYGILTTDSRDNWAEAYE.L..TP.N
Retrocopy YVVVIYRNHFYQLKIYDKEGKLIIAPCLAVQLEEIMAKEKEPGVPYGILTTDSRDNWAEAYEHLSNTPRN

Parental  RDALKTIQGALFTVSLDEGTILKEGEETDELILSLIHGSGSKINSGNRWMDKTIQLVVNPNGNVGFTYEH
          R.ALKTIQ.A.FTVSLDE.T..KEG....ELIL.LIHG.GSK.NS.NRWMDKTIQLVVNPNG.VGFTYEH
Retrocopy RVALKTIQNAMFTVSLDECTSPKEGRDAEELILTLIHGKGSKCNSANRWMDKTIQLVVNPNGHVGFTYEH

Parental  SPAEGQPIAMMMDYVVQKMKEDPSFGQSGSQDFAPAQKIQFSSSNKSLEKSLNVAQENVDKLADALQMKV
          SPAEGQPIAMMMDYVV.KMK.DPS.G..GS..F.PA.KI.F....K..E..L..AQ.NVDKL...LQMKV
Retrocopy SPAEGQPIAMMMDYVVKKMKDDPSYGECGSENFIPAKKIKFCDVSKCVEQWLIIAQKNVDKLVQDLQMKV

Parental  LKFNGFGKDFIKKQRLGPDSFVQMALQLAFYKMHSEPPAQYESAHLRIFDGGRTETIRSCSNESLAFSRA
          LKF...GKDFIKKQRLGPDSFVQMALQLAF.K.H.EP.AQYESAHLRIFDGGRTETIRSCSNESLAF..A
Retrocopy LKFDCYGKDFIKKQRLGPDSFVQMALQLAFFKLHYEPAAQYESAHLRIFDGGRTETIRSCSNESLAFCHA

Parental  MQDPNVTDQERAAKLREAVVSHQTYAKLALQGKGVDRHLLGLKLMALEHSKPIPEFFKSPGFVKSSHFRM
          M.D.....QERA.K.REAV..HQ.YAKLAL.GKGVDRHL.GLKLMA.E...P.PEFF.SPG.VKS.HFRM
Retrocopy MDDVSASAQERASKIREAVMCHQMYAKLALLGKGVDRHLFGLKLMAVENCLPVPEFFSSPGYVKSTHFRM

Parental  STSQVATKYDAFMGYGPATDDGYACCYNPRDNDIILAISAWRHCPITDHLKFVKTLEQSFFEMKNVLEKN
          STSQVATKYDAFMGYGP...DGYACCYNPR..DIILAISAWRHC..TDH.K..K.L.QSF.EMK.VLE..
Retrocopy STSQVATKYDAFMGYGPSVEDGYACCYNPREHDIILAISAWRHCQATDHQKIAKALAQSFAEMKDVLETC

Parental  P
          P
Retrocopy P

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_16 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI946591	12965117	12965518	100	401	0	401
BF486498	12965100	12965631	100	531	0	531
BF495751	12965100	12965705	100	605	0	605

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_16 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
Myotis lucifugus	ENSMLUG00000011287	1 retrocopy	retro_mluc_143,
Drosophila melanogaster	FBgn0037440	1 retrocopy	retro_dmel_16 ,