RetrogeneDB ID: retro_dmel_59

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 2R:13482788..13484897(+)
• Located in intron of: FBgn0029006

Retrocopy information

• Ensembl ID: FBgn0034251
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CG9140
• Ensembl ID: FBgn0031771
• Aliases: None
• Description: None

Sequence

>retro_dmel_59
ATGATATCGTTTCTGTTAAAACGCCGAGCTTGTGATGCTTACAAGATTTCATTAGGACTAACTCGTGCATATAGAGCCTT
AACAGAAGTAAAAAGCCTTCAAAATGCCTTACGACCTGGTAATAAAACTGGAAATATCAAGCTGGTAAACATATACCGAA
CTTCTAGCATACAAAATGTGAAGAAGAACCAACTAAGTGACGCTGAAAGCGTTATTCCACTCTTATTGCGGCCAGCCAAA
CCTGTGCTGATTATGAGAGAAGGATCTCAAACCGATTGTAACGACGATTTGCTGTCCTCTGAGCAAAGAGCCAAAAAAAG
GGAAAGCATAAAAAAATCCGAAGTAGATTGCCCAAAATTTCCAGCTGAGAAACTTCCGCCCACAACGAAATTTCCTATTA
ATGAAAATGCCAAGAAGGTTTTAGATCCAGCCGACCAAAGAGAACTCGAGGCCAATTTGTTAAAAAGGCTTAAAGATATG
GCTAAAAGAAAGAAATCTCGACTAGATGAGAAAGTTGACGAGCTGAGGGATAATTTTATAGGCTGGAATTATGCTGCTCT
ACAAGGAAGAACTATTGTGACTGTGGATGCCAAGGAATCAACTCCACCGAAAGGATCTGGGCCGGCCACCCCGGCAGGCT
CTCCTCCACCTAAAAATGTTTCTGCACCGCCGACGGGCGGTTCTCCGCCTGCCAAAAGCGGCGCTCCACCACCCCCAAAG
GGGCCACCGCCCGGAACTCCACCACCGCAGACGAAAACTACTTTTGGACCACTTGCTGATGCTGATCGAATCTTTACCAA
TTTATACGGACGGCACGATTGGCGATTGAAGGCAGCAATGAAGCGCGGTGACTGGTACAAGACGAAGGAGATCATAGCCA
AGGGTGACAAGTGGATAGTCAACGAGATTAAGACATCTGGACTGCGAGGACGCGGTGGCGCCGGATTTCCCAGTGGACTT
AAGTGGTCATTTATGCATAAACCGCCTGATGGAAGACCCAAGTTTCTGGTGGTCAATGCGGATGAAGGAGAGCCCGGTAC
TTGCAAGGATCGTGAGATAATGCGCCATGATCCACACAAACTGGTAGAGGGATGTCTCATTGCTGGACGGGCTATGGGTG
CCAACACTGGTTTTATTTACATTCGCGGAGAGTTTTACAACGAAGCTTGCAATCTTCAGTATGCCATTATTGAGGCCTAT
AAGGCTGGCTACCTGGGAAAGAATGCCTGCGGTTCTGGGTTCGATTTCGATCTTTATGTGCAACGTGGAGCAGGAGCCTA
TATTTGCGGTGAGGAAACCTCTCTGATTGAATCCCTGGAGGGCAAGGCGGGTAAGCCAAGGAACAAGCCTCCCTTTCCGG
CTGATATCGGCGTCTTTGGCTGTCCGTCTACGGTGACCAATGTGGAAACGGTGGCCGTGTCTCCCACTATTTGCCGGCGT
GGTGGCAATTGGTTTGCCAGCTTTGGACGTACCCGAAACTCTGGCACCAAGCTGTTTAATATCTCTGGTCATGTTTGCAA
CCCTTGTACCGTCGAGGAGGAGATGTCCATGCCAACCAGAGAGCTTATCGAACGCCATGCTGGCGGAGTGATCGGGGGCT
GGGACAATCTACTGGCCATCATTCCGGGTGGCTCCTCCACTCCCTGCATTACCAAGGAGCACGCCTCGAGTGCGATTCAC
GACTACGATGGGCTGATGGCAGTGCGTTCGTCCATGGGAACGGGTGCCTTAATTGTTATGAATAAGGATACGGACATTAT
CAAGGCCATTGCCCGATTATCGGCTTTCTATAAGCACGAGAGCTGCGGCCAGTGCACTCCTTGCCGCGAGGGTCTCCACT
GGGTGAACATGATCATGCATAGATTTGTGACAGGACAGGCGCAAATTGCAGAGATCGATATGCTGTTCGAACTGACGAAG
CAGATCGAGGGACATACCATTTGTGCCCTGGCCGATGGTGCTGCTTGGCCGCCCCAAGGACTCATCCGGAACTTCCGACC
GGTCATCGAGGAGAGGATCAAGAAGCGGGCGGCCGAGGACCAAGCTAAAGCTGAAGCACTCGAAGCCGAACGTTTCCCTT
GTCAAACGGTGACTCCTTGTCCAGAATAA

Alignment

ORF - retro_dmel_59 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 79.68 %
• Parental protein coverage: 92.41 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QAPPPGTPPPQTKTKFGPLADEDRIFTNLYGRHDWRLKGALKRGDWYKTKEIVLKGADWIVNEIKTSGLR
          ..PPPGTPPPQTKT.FGPLAD.DRIFTNLYGRHDWRLK.A.KRGDWYKTKEI..KG..WIVNEIKTSGLR
Retrocopy KGPPPGTPPPQTKTTFGPLADADRIFTNLYGRHDWRLKAAMKRGDWYKTKEIIAKGDKWIVNEIKTSGLR

Parental  GRGGAGFPSGMKWSFMNKPGDGRPKYLVVNADEGEPGTCKDREIMRHDPHKLVEGCLIAGRAMGAQAAYI
          GRGGAGFPSG.KWSFM.KP.DGRPK.LVVNADEGEPGTCKDREIMRHDPHKLVEGCLIAGRAMGA....I
Retrocopy GRGGAGFPSGLKWSFMHKPPDGRPKFLVVNADEGEPGTCKDREIMRHDPHKLVEGCLIAGRAMGANTGFI

Parental  YIRGEFYNEASNMQLAIAEAYQAGLIGKNACGTGYDFDVFMHRGAGAYICGEETALIESLEGKQGKPRLK
          YIRGEFYNEA.N.Q.AI.EAY.AG..GKNACG.G.DFD....RGAGAYICGEET.LIESLEGK.GKPR.K
Retrocopy YIRGEFYNEACNLQYAIIEAYKAGYLGKNACGSGFDFDLYVQRGAGAYICGEETSLIESLEGKAGKPRNK

Parental  PPFPADVGVFGCPTTVTNVETVAVAPTICRRGGVWFASFGRTRNSGTKLFNISGHVNRPCTVEEEMSIPL
          PPFPAD.GVFGCP.TVTNVETVAV.PTICRRGG.WFASFGRTRNSGTKLFNISGHV..PCTVEEEMS.P.
Retrocopy PPFPADIGVFGCPSTVTNVETVAVSPTICRRGGNWFASFGRTRNSGTKLFNISGHVCNPCTVEEEMSMPT

Parental  KELIERHCGGVTGGWDNLLGVIPGGSSTPIIPKNVCDDVIMDFDGLIAAQTSLGTAAIIVMDKSTDVIKA
          .ELIERH.GGV.GGWDNLL..IPGGSSTP.I.K......I.D.DGL.A...S.GT.A.IVM.K.TD.IKA
Retrocopy RELIERHAGGVIGGWDNLLAIIPGGSSTPCITKEHASSAIHDYDGLMAVRSSMGTGALIVMNKDTDIIKA

Parental  IARLISFYKHESCGQCTPCREGIGWMNKIMTRFVKGDAQPAEIDMLWEISKQIEGHTICALGDGAAWPVQ
          IARL..FYKHESCGQCTPCREG..W.N.IM.RFV.G.AQ.AEIDML.E..KQIEGHTICAL.DGAAWP.Q
Retrocopy IARLSAFYKHESCGQCTPCREGLHWVNMIMHRFVTGQAQIAEIDMLFELTKQIEGHTICALADGAAWPPQ

Parental  GLIRHFRPEIEKRMQLHA
          GLIR.FRP.IE.R....A
Retrocopy GLIRNFRPVIEERIKKRA

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

4 EST(s) were mapped to retro_dmel_59 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI946900	13483773	13484196	99.3	420	3	417
BF498010	13482781	13483378	99.5	592	3	589
BF498897	13483785	13484190	99.3	402	3	399
BF505939	13482771	13483431	99.1	654	6	648

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_59 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Macropus eugenii	ENSMEUG00000005135	1 retrocopy	retro_meug_728,
Xenopus tropicalis	ENSXETG00000003396	1 retrocopy	retro_xtro_49,
Drosophila melanogaster	FBgn0031771	1 retrocopy	retro_dmel_59 ,