RetrogeneDB ID: retro_dmel_52

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 2R:9395248..9396718(+)
• Located in intron of: FBgn0033846

Retrocopy information

• Ensembl ID: FBgn0024556
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: CG12736
• Ensembl ID: FBgn0033184
• Aliases: None
• Description: None

Sequence

>retro_dmel_52
ATGTCACATGCATTTGCCGCCGCCGTCTGCCGGTCCACCGCATCCATGTCATTGGCCCTGCGCTGCAGCCGGCGCGCCAT
GAGCTCTGCCAGAATGCTGCGTATGGCGGGTGCCACTGCCACCTCCACGGCCTGCAAGGATTGGCAGAGAAACGGACTAC
TTGCTGCGCCCAGAACCGGCAACATGCAGCAGTACCTGCGCGAGTACGCCAACGAGAAGAAGGTGTTCGAGCGAACCAAG
CCCCATTGCAATGTGGGCACCATTGGCCATGTGGATCACGGCAAGACCACGCTCACGGCGGCCATTACCAAGGTCCTGGC
CGACAAGCAGCTGGCCGAGAGCAAGAAGTACAATGAAATCGACAATGCGCCCGAGGAGAAGGCTCGTGGTATTACCATCA
ATGTAGCCCACGTGGAGTACCAGACGGAGACGCGTCACTACGGCCACACAGATTGTCCGGGACATGCCGATTATATTAAG
AACATGATCACCGGCACAGCCCAGATGGATGGCGCCATTCTCGTTGTGGCCGCCACCGATGGCGCCATGCCCCAAACTCG
CGAGCATATGCTGCTAGCCAAGCAGATCGGCATTGATCACATCGTGGTGTTCATCAACAAGGTGGACGCCGCCGATGAGG
AGATGGTCGACCTGGTGGAGATGGAGATCCGAGAGCTGCTTACCGAGATGGGCTATGATGGTGACAAGATCCCTGTGGTA
AAGGGCTCGGCGCTGTGCGCCCTCGAGGACAAGAGTCCCGAGATCGGCAAGGAGGCGATCCTGAAACTGCTCCAGGAGGT
GGATAGCTTCATCCCCACGCCTGTGCGCGAGCTGGACAAGCCCTTCCTGCTGCCTGTTGAGAATGTGTATTCGATTCCCG
GACGCGGCACCGTCGTCACTGGTCGCCTGGAGCGCGGAGTGGTCAAGAAGGGCATGGAGTGCGAGTTCGTGGGCTATAAC
AAGGTGCTGAAGTCGACGGTGACGGGCGTGGAGATGTTCCACCAGATTCTGGAGGAGGCGCAAGCCGGTGATCAGCTGGG
AGCTCTGGTGCGCGGCGTTAAGCGAGATGACATCAAGCGCGGCATGGTCATGTGCAAGCCGGGCAGTGTGAAGGCACTCG
ATCAGCTGGAGGCCCAGGTGTACATCCTGTCCAAGGATGAAGGCGGTCGCACAAAGCCCTTCATGTCCTTCATCCAACTG
CAGATGTTCTCCCGCACCTGGGACTGTGCCGTGCAGGTGCAGATTCCCGATAAGGAGATGGTCATGCCCGGCGAAGACAC
CAAGCTCATTCTGCGCCTCATCCGGCCAATGGTCCTGGAGCAGGGACAACGCTTCACGCTGCGTGACGGAAACCTGACCC
TGGGCACTGGTGTCGTCACCAGCACTCTGCCCCCATTGACTGAATCGCAGCGATCCGAGTTGACGGAGGGCAAGAAGGCG
CGCGAGAAGAAGGTGGCGGCTAAGAAGTAG

Alignment

ORF - retro_dmel_52 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.33 %
• Parental protein coverage: 85.53 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RELPHCNVGTIGHVDHGKTTLTAAITRIQSQKGLAEYLSYDQIDRAPEEKARGITINACHIGYSTTERTY
          R..PHCNVGTIGHVDHGKTTLTAAIT.....K.LAE...Y..ID.APEEKARGITIN..H..Y.T..R.Y
Retrocopy RTKPHCNVGTIGHVDHGKTTLTAAITKVLADKQLAESKKYNEIDNAPEEKARGITINVAHVEYQTETRHY

Parental  AHTDCPGHADYIKNMISGASQMDGAILVVAATDGQMPQTREHLLLAKQVGIQRIIVFINKADLVDQEVLE
          .HTDCPGHADYIKNMI.G..QMDGAILVVAATDG.MPQTREH.LLAKQ.GI..I.VFINK.D..D.E...
Retrocopy GHTDCPGHADYIKNMITGTAQMDGAILVVAATDGAMPQTREHMLLAKQIGIDHIVVFINKVDAADEEMVD

Parental  LVEIEMREMLSDFGFDGVNSPVICGSALLALREDKSEFGVPSIEKLLEQCDSYIPTPQRDISSPFILPID
          LVE.E.RE.L...G.DG...PV..GSAL.AL.....E.G...I.KLL...DS.IPTP.R....PF.LP..
Retrocopy LVEMEIRELLTEMGYDGDKIPVVKGSALCALEDKSPEIGKEAILKLLQEVDSFIPTPVRELDKPFLLPVE

Parental  NAFTVPGRGTVVVGTIKRGTIPRNADADLLGFNQNLKTSISDIQIFRKSVPQAQAGENVGALLRGIKISA
          N....PGRGTVV.G...RG...........G.N..LK........F......AQAG...GAL.RG.K...
Retrocopy NVYSIPGRGTVVTGRLERGVVKKGMECEFVGYNKVLKSTVTGVEMFHQILEEAQAGDQLGALVRGVKRDD

Parental  VERGMLLCATGSEDISNHFEGSMYLLSRAEGGRVKPMLSKYIQQLFSQTWNVPARIDIVPSEAMLMPGEH
          ..RGM..C..GS.......E...Y.LS..EGGR.KP..S....Q.FS.TW.......I.P...M.MPGE.
Retrocopy IKRGMVMCKPGSVKALDQLEAQVYILSKDEGGRTKPFMSFIQLQMFSRTWDCAVQVQI-PDKEMVMPGED

Parental  GQVRVTLLRKMVMTPGQAFTIRENGATVATGMVTQRLPSL
          ......L.R.MV...GQ.FT.R....T..TG.VT..LP.L
Retrocopy TKLILRLIRPMVLEQGQRFTLRDGNLTLGTGVVTSTLPPL

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

8 EST(s) were mapped to retro_dmel_52 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AI237915	9395309	9395923	99.7	611	2	608
AI387825	9395142	9395759	100	561	0	560
BF502509	9395128	9395851	99.3	662	5	656
BF506484	9395126	9395899	100	717	0	716
BG635995	9395248	9395675	100	427	0	427
EL883577	9395903	9396226	100	323	0	323
EL883895	9395104	9395917	99.9	756	1	754
EV590738	9396172	9396350	100	104	0	103

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_52 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 11 retrocopies.

Species	Parental gene accession	Retrocopies number
Dipodomys ordii	ENSDORG00000016474	1 retrocopy	retro_dord_278,
Homo sapiens	ENSG00000178952	1 retrocopy	retro_hsap_1816,
Macropus eugenii	ENSMEUG00000011131	1 retrocopy	retro_meug_1783,
Monodelphis domestica	ENSMODG00000015564	1 retrocopy	retro_mdom_384,
Mus musculus	ENSMUSG00000073838	1 retrocopy	retro_mmus_10,
Ornithorhynchus anatinus	ENSOANG00000013114	1 retrocopy	retro_oana_36,
Oryctolagus cuniculus	ENSOCUG00000002683	1 retrocopy	retro_ocun_333,
Pan troglodytes	ENSPTRG00000007939	1 retrocopy	retro_ptro_1174,
Rattus norvegicus	ENSRNOG00000018604	1 retrocopy	retro_rnor_1134,
Vicugna pacos	ENSVPAG00000009541	1 retrocopy	retro_vpac_346,
Drosophila melanogaster	FBgn0033184	1 retrocopy	retro_dmel_52 ,