RetrogeneDB ID: retro_dmel_66

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 3R:22170052..22171168(-)
• Located in intron of: FBgn0053970

Retrocopy information

• Ensembl ID: FBgn0039421
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: alph
• Ensembl ID: FBgn0086361
• Aliases: None
• Description: alphabet [Source:FlyBase gene name;Acc:FBgn0086361]

Sequence

>retro_dmel_66
ATGGGTCATAAAATGGGTGGCTTCTTGGAAAAACCAGAAACTGAAAAGCAGGCTCAAGAGGGTCATGGGAATGGGCTGCG
ATACTGCGTAAGTTCTATGCAAGGTTGGCGATTGGAAATGGAGGATAGCCACTCGGCTGCTTGCCGGCTGAAGGATCCCT
TCGCAACGTGGTCATATTTTGCGGTGTTCGATGGTCACGCTGGCAGTCAAATATCACTGCATTGCGCTGAACATCTAATG
AGTACTATATTGGAATCCGAATCTTTTTCGAAGCACAAATACGAGGCTGGCATACGAGAGGGCTTCCTGCAGTTGGATGA
GGATATGAGGAAGCTGTATCACGACCAGCAAGGCGGCTCGACGGCCATTTGTGTTTTTGTATCACCGGACAAAATATATC
TGGTCAATTGTGGTGACTCGCGTGCAGTGATATCGCGAAATGGAGCAGCTGTCATCAGTACAATTGATCACAAGCCGTTT
TCTCCCAAAGAACAAGAACGCATTCAAAATGCCGGAGGCAGTGTAATGATTAAAAGGATAAATGGCACTCTGGCAGTTTC
CCGGGCCTTCGGTGACTATGATTTCAAGAATGATGGCTCAAAGTCTCCTGTCGATCAGATGGTGTCTCCGGAACCTGATA
TAATAGTTTGCAATCGGTCCGAACACGATGAATTCATAGTTGTAGCCTGCGATGGCATTTGGGATGTGATGACTAGCAGC
GAGGTTTGTGAATTTATTAGGTCACGGCTTTTGGTGACCTATGACCTGCCGATGATTGTTAACAGCGTATTGGATATTTG
CCTGCATAAAGGCAGCAGGGACAATATGACACTGCTCCTCCTACTTTTGCCTGGAGCACCAAAGGTCGATATGGATGCAG
TTAAGGCCGAAAGGAGTCTTGATCAAACTATTGTGCAAATAACCAAGGAAGTGATTGAGAAGCACGAAATACACGACTTT
GAAACACTTATACGACTGATGAAAAGAATGGCCATTAACATTCCAAATCTACCACCTGGCGGTGGTCTTTATGCAAAATA
TTACATTATAGAGCAAGCTTTCCACGAGAAATTTCCAGATACTCCGGCTGAAATATATGATTATTTTTCCATGTAG

Alignment

ORF - retro_dmel_66 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 54.58 %
• Parental protein coverage: 67.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  GGTTAVCAFVGLTQVYIANCGDSRAVLCRQGVPVFATQDHKPILPEEKERIYNAGGSVMIKRVNGTLAVS
          GG.TA.C.FV.....Y..NCGDSRAV..R.G..V..T.DHKP..P.E.ERI.NAGGSVMIKR.NGTLAVS
Retrocopy GGSTAICVFVSPDKIYLVNCGDSRAVISRNGAAVISTIDHKPFSPKEQERIQNAGGSVMIKRINGTLAVS

Parental  RALGDYDFKNVKEKGQCEQLVSPEPEIFCQSRQDSDEFLVLACDGIWDVMSNEDVCSFIHSRMRVTSNLV
          RA.GDYDFKN...K....Q.VSPEP.I....R...DEF.V.ACDGIWDVM....VC.FI.SR..VT..L.
Retrocopy RAFGDYDFKNDGSKSPVDQMVSPEPDIIVCNRSEHDEFIVVACDGIWDVMTSSEVCEFIRSRLLVTYDLP

Parental  SIANQVVDTCLHKGSRDNMSIIIIAFPGAPKPTEEAIEAEHRLEKQIEKITRDEIESSKITDYVDLLKCL
          .I.N.V.D.CLHKGSRDNM.......PGAPK....A..AE..L...I..IT...IE...I.D...L....
Retrocopy MIVNSVLDICLHKGSRDNMTLLLLLLPGAPKVDMDAVKAERSLDQTIVQITKEVIEKHEIHDFETLIRLM

Parental  QNRD-DIEGLPPGGGLQSKYHVIERTFKQEFPDRPCELYAY
          ......I..LPPGGGL..KY..IE..F...FPD.P.E.Y.Y
Retrocopy KRMAINIPNLPPGGGLYAKYYIIEQAFHEKFPDTPAEIYDY

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

No EST(s) were mapped for retro_dmel_66 retrocopy.

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_66 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 6 parental genes, and 7 retrocopies.

Species	Parental gene accession	Retrocopies number
Mus musculus	ENSMUSG00000021096	2 retrocopies	retro_mmus_2925, retro_mmus_2926,
Mus musculus	ENSMUSG00000061130	1 retrocopy	retro_mmus_468,
Oryctolagus cuniculus	ENSOCUG00000005461	1 retrocopy	retro_ocun_1094,
Otolemur garnettii	ENSOGAG00000003689	1 retrocopy	retro_ogar_1834,
Drosophila melanogaster	FBgn0035425	1 retrocopy	retro_dmel_64,
Drosophila melanogaster	FBgn0086361	1 retrocopy	retro_dmel_66 ,