RetrogeneDB ID: retro_dmel_72

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 2L:22079687..22080719(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: FBgn0032971
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: ttm50
• Ensembl ID: FBgn0250874
• Aliases: None
• Description: tiny tim 50 [Source:FlyBase gene name;Acc:FBgn0250874]

Sequence

>retro_dmel_72
ATGCATAAAATTGTTTGGTTTGGAACTTTAAATAAGTCGATTGGCTACATCGGTAAAAAGAAGACCTGTCTTCTGAGTCC
ATGCGAGAAAATATGCCTGAATTCAGCTAGAAAAACAGTACAGAGATGCGACAAAAACTATTCACCACCAAAGTTAAGAA
GAATCAAGAATTTCTATACCTACAGTGTTGTGTTGGGGAGTCTCTTCAGTATAGTCATGTGGGCCATCTATAAGCTGGGC
AAGCCCGAGGAAGACCATCGGGGTCCCATAGAAGATGAGTTCAGTCAGCTTCCCTGGTTCCGCCAGTACATAATGAGGAT
GTGGCACACACTTCAGTATTATGAAAAAATGATGGAAGAGCCCCAGATGGCAAGGCTGCTGCCAAATGTTGTCCCACCGC
CGTATATACAACCTCCCTATTCACTGGTGCTGGAAATCAAAGACGTACTGGTGCATCCAGATTGGACTTATCAGACGGGG
TGGCGGTTTAAAAAGCGGCCTGGTGTGGATTACTTTCTTCAGCAGTGCAGTCGAAATTTTGAAATTGTGATATATACTTC
TGAACAAGGTATGACCGCATTCCCCCTTCTGGATGCTTTAGATCCCTATGGCTACATAAAATATCGGCTAGTAAGAGGTG
CCACGGACTTGGTAGAGGGTCAGCATACCAAGAACCTCGATTATCTTAACAGGGATCTGAGCCGTGTGATAGTGGTGGAC
TGTGATCCGTATACCACTCCCCTGCATCCCGATAATAGCTTGGTGCTCACAAAGTGGCTGGGTAACGATGATGATGTCCA
GCTCTTTGATCTCACGGCTTTCCTGCAGTTGATTGCCGAACACCAAGTAAATGATGTAAGGGAGGTGCTGCGATACTATC
GCCAATTCGAGGACCCCATGGAACAGTTTAAGGACAACCAACGTCGACTGCAGGAGCAGAGTCAGGAAAGCATTCAGAAT
TTACCAACTAGTGAACGTCAGTGGAACTTAACTTTATTGGGACGCTCCCTTCGAGGGTCTTCAATCAAATAA

Alignment

ORF - retro_dmel_72 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.63 %
• Parental protein coverage: 60.28 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  FAIFGGSAVAAGFWAVYEFGKPEVDPNGQPIEDEFTHKPLVQQYLQRMWKSIHYYQRMIQEPSRAKLLPD
          .....GS......WA.Y..GKPE.D..G.PIEDEF...P...QY..RMW....YY..M..EP..A.LLP.
Retrocopy YSVVLGSLFSIVMWAIYKLGKPEEDHRG-PIEDEFSQLPWFRQYIMRMWHTLQYYEKMMEEPQMARLLPN

Parental  PLKPPYVQPRYTLVLEMKDVLVHPDWTYQTGWRFKKRPGVDHFLAECAKDFEIVVFTAEQGMTVFPILDA
          ...PPY.QP.Y.LVLE.KDVLVHPDWTYQTGWRFKKRPGVD.FL..C...FEIV..T.EQGMT.FP.LDA
Retrocopy VVPPPYIQPPYSLVLEIKDVLVHPDWTYQTGWRFKKRPGVDYFLQQCSRNFEIVIYTSEQGMTAFPLLDA

Parental  LDPNGYIMYRLVRDATHFVDGHHVKNLDNLNRDLKKVIVVDWDANATKMHPDNTFGLARWHGNDDDGQLL
          LDP.GYI.YRLVR.AT..V.G.H.KNLD.LNRDL..VIVVD.D...T..HPDN...L..W.GNDDD.QL.
Retrocopy LDPYGYIKYRLVRGATDLVEGQHTKNLDYLNRDLSRVIVVDCDPYTTPLHPDNSLVLTKWLGNDDDVQLF

Parental  DLIAFLKIIAQNNVDDVREVLHYYRQFDDPINQFRENQRKLAEQMLEA
          DL.AFL..IA...V.DVREVL.YYRQF.DP..QF..NQR.L.EQ..E.
Retrocopy DLTAFLQLIAEHQVNDVREVLRYYRQFEDPMEQFKDNQRRLQEQSQES

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_72 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
EC052616	22079918	22080206	99.7	287	1	286
EC054088	22079918	22080213	99.7	294	1	293
EC056154	22079918	22080347	99.8	428	1	427

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_72 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 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Macaca mulatta	ENSMMUG00000019376	1 retrocopy	retro_mmul_143,
Oryctolagus cuniculus	ENSOCUG00000002166	1 retrocopy	retro_ocun_1046,
Drosophila melanogaster	FBgn0250874	2 retrocopies	retro_dmel_72 , retro_dmel_8,