RetrogeneDB ID: retro_dmel_47

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 3R:15287657..15288686(-)
• Located in intron of: FBgn0260003

Retrocopy information

• Ensembl ID: FBgn0038708
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Scsalpha
• Ensembl ID: FBgn0004888
• Aliases: None
• Description: Succinyl coenzyme A synthetase alpha subunit [Source:FlyBase gene name;Acc:FBgn0004888]

Sequence

>retro_dmel_47
ATGTCACTAAATCGAGGAAGCAAGATGCTCCTGCGGGCGTTAACGCCCCAAATTTTGAGGCGTGGCAAGGCGGACTATGG
CAAGACGGTGTGCAACCTGAAGATCAACAAGGCAACAAAGGTTCTAGTCCAGGGATTCACCGGCAAGCAGGCCACTTTCC
ACTCGGAGGAGTCCATAAAGTACGGAACCAATATAGTTGGCGGTGTGAATCCCAAAAAGGGAGGTACGGAGCATCTGGGC
AAGCCCGTATTCAAATCGGTGGCAGAAGCTGTGGAGAAGGCGAAGCCAGATGCCACGGTGATCTTTATACCACCTCCATC
CGCCGCCGAGGGTATTTGCGCGGCTATCGAGAGTGAAATTGGCTTGATTGTGGCCATCACCGAGGGTATTCCCCAGGCGG
ATATGGTGCGGATATCGCAAATGCTGAATTGCCAGGAGAAGTCCCGCCTGCTGGGACCCAACTGTCCGGGAATCATCTCG
CCGGATCAGTGCAAAATCGGAATAATGCCGGGAGATATCCACAAGCGAGGAGTGGTGGGCATAGTCTCGCGGTCGGGAAC
CCTGACCTACGAGTCCGTCCATCAGACCACCAACGTGGGATTGGGTCAGGCTCTTTGCGTTGGCCTCGGCGGGGATCCCT
TTAACGGAACTAGCTTCATAGACGCCCTCAAAGTGTTTCTGTCCGACAAGGAGATCAAGGGCATTGTCATGATTGGAGAG
ATTGGCGGATCCGCCGAGGAAGAGGCTGCCGATTTCCTTAAGGAGAAGAACACTGGCTGCGAGGCCAAGCCAGTAGTTGG
CTTCATTGCTGGACAGACTGCTCCACCGGGTCGTCGAATGGGTCACGCCGGCGCCATCATTTCCGGTGGCAAGGGAGCGG
CCAAGGACAAGGTGGCCGCCCTGGAGAAAGCGGGAGTCCGTATGACCGCCAATCCCTGCCACCTGGGCTCCACGCTCCTC
GAGGAAATGATCCGCCTGAAACTGGTGCCCAAGCCGAACAAAAAGAAGGCTCAGGCCGGGAAGAAGTAG

Alignment

ORF - retro_dmel_47 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 67.64 %
• Parental protein coverage: 94.21 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  RCNSQYNKTRGNLKLNGDSRVICQGFTGKQGTFHSQQALEYGTKLVGGISPKKGGTQHLGLPVFASVAEA
          R....Y.KT..NLK.N....V..QGFTGKQ.TFHS.....YGT..VGG..PKKGGT.HLG.PVF.SVAEA
Retrocopy RGKADYGKTVCNLKINKATKVLVQGFTGKQATFHSEESIKYGTNIVGGVNPKKGGTEHLGKPVFKSVAEA

Parental  KKATDPHATVIYVPPPGAAAAIIEALEAEIPLIVCITEGVPQHDMVKVKHALISQSKSRLVGPNCPGIIA
          .....P.ATVI..PPP.AA..I..A.E.EI.LIV.ITEG.PQ.DMV.....L..Q.KSRL.GPNCPGII.
Retrocopy VEKAKPDATVIFIPPPSAAEGICAAIESEIGLIVAITEGIPQADMVRISQMLNCQEKSRLLGPNCPGIIS

Parental  PEQCKIGIMPGHIHKRGKIGVVSRSGTLTYEAVHQTTEVGLGQTLCVGIGGDPFNGTDFIDCLEVFLKDP
          P.QCKIGIMPG.IHKRG..G.VSRSGTLTYE.VHQTT.VGLGQ.LCVG.GGDPFNGT.FID.L.VFL.D.
Retrocopy PDQCKIGIMPGDIHKRGVVGIVSRSGTLTYESVHQTTNVGLGQALCVGLGGDPFNGTSFIDALKVFLSDK

Parental  ETKGIILIGEIGGVAEEKAADYLTEYNSGIKAKPVVSFIAGVSAPPGRRMGHAGAIISGGKGGANDKIAA
          E.KGI..IGEIGG.AEE.AAD.L.E.N.G..AKPVV.FIAG..APPGRRMGHAGAIISGGKG.A.DK.AA
Retrocopy EIKGIVMIGEIGGSAEEEAADFLKEKNTGCEAKPVVGFIAGQTAPPGRRMGHAGAIISGGKGAAKDKVAA

Parental  LEKAGVIVTRSPAKMGHELFKEMKRLELV
          LEKAGV..T..P...G..L..EM.RL.LV
Retrocopy LEKAGVRMTANPCHLGSTLLEEMIRLKLV

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_47 retrocopy.

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_47 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 5 parental genes, and 6 retrocopies.

Species	Parental gene accession	Retrocopies number
Cavia porcellus	ENSCPOG00000003017	1 retrocopy	retro_cpor_1170,
Myotis lucifugus	ENSMLUG00000012370	1 retrocopy	retro_mluc_1231,
Procavia capensis	ENSPCAG00000013405	1 retrocopy	retro_pcap_356,
Pteropus vampyrus	ENSPVAG00000003656	2 retrocopies	retro_pvam_1160, retro_pvam_670,
Drosophila melanogaster	FBgn0004888	1 retrocopy	retro_dmel_47 ,