RetrogeneDB ID: retro_dmel_7

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 3L:11915835..11917791(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: FBgn0036222
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: SdhA
• Ensembl ID: FBgn0261439
• Aliases: None
• Description: Succinate dehydrogenase A [Source:FlyBase gene name;Acc:FBgn0261439]

Sequence

>retro_dmel_7
ATGAATCGCCTGTTTCTCAAAAGGGCGGGACAGCATGTAACCAGGAGCCTTCTTGGTCCAAATGGGAGTCGTCTGCTTCA
AGTGTCCTGCGTTCGAGATGCCAGTTGCAAAGATGAGTACTCCTTGATAGACCACAAGTTCGATGCGATTGTCATTGGTG
CCGGTGGAGCTGGAATGCGGGCTGGATTTGGGCTGGCGGAGAAGGGTTTCCAAACGGCCATTATATCAAAGCTATTTCCC
ACCCGATCTCACACGGTGGCTGCCCAGGGTGGTGTTAATGCCGCCCTCTCAAATATGGACAAGGACGACTGGAAGTACCA
CTTCTACGACACGGTGAAGGGCTCCGATTGGCTGGGTGATCAGAACGCGATCCATTACATGTGTCGGGAGGCGGAGAGGG
CGGTCTGCGAACTGGACATGTACGGGATGCCCTTCTCGCGAAAGCCCGATGGCAAGATCTACCAGCGACCTTTTGGAGGT
CAGACCTTGGACTACGGAAAGGGCGGGGTGGCCAGAAGGGCGTGTGCATGTGCAGATCGCACGGGTCACGCCCTTATCCA
CACACTGTACGGACAAACGCTGAAGCACTCCGATTCTTGCCACTATTTTGTGGACTACTTCGTTCTGGATCTGATCATGT
CGCAGGGTGCATGTGTGGGATGTTTGGCTTGGAAACTGGATGATGGCACCTTCCATCGGTTTTTGGCCAAAAATACGGTT
GTTGCCGCCGGCGGTTGTGGTCGGGTGTACTTCTCCACGACCGCCGGACACACATGTACCGGCGATGGCAATGCGTGGGT
GTCTAGACAGGAGCTGCCGCTCATGGATATGGAATTTGTGCAGTTTCATCCCACTGGCATCTACGGAGCCGGATGCCTTA
TCACCGAGGGAGTTAGGGGCGAAGGCGGTTTCTTCTTGAACTGCAAGGGAGAACGTTTCATGGAACGCTATGCTCCAAAG
GCCAAGGATCTGGCGTCCAGAGATGTGGTGGCGCGGGCCATGACCATGGAGGTTCTTGCTGGCAATGGTTGTGGTCCGCT
CAAGGATCATGTGCACCTTCAGCTCCACCATATCGACGCCAAGATCATCAAGCAACGATTGCCGGGCATTATGGTCACCG
CCCGGATTTTTGCCAAAGTGGATGTGACCAAGGAACCAGTACCAGTGCTGCCAACTGTGCACTACAACATGGGCGGCATA
CCAACGGATTACAAGGGTCGTGTGGTCACCATCGATGAGAATGGCAAGGAACAGGTTGTCAAGGGACTGTACTCCTGCGG
GGAAACTTCCTGCGCCTCAGTACACGGAGCAAATCGATTGGGTGCCAACTCCCTGCTGGATCTGATCATCTTTGGCCGCG
TCTGTGCTCTGGACATTGCCGCAAACAACTGTCCGGGGGATAAGCCGCCCCAGGTGGAGGACAAAGCCACGGAGAAGTCG
CTGGATAATTTTAAGCGCCTGCGCTGCGCCGACGGATGCATTCCCACTGCGGTGTTGAGAATGGAACTTCAGCGGACCAT
GACCAAACATGCGGCTGTTTTCCGGGAGGGAAAACTGCTCAAGGAGGGTCTGCTCAAAGTGGCCGAGTTATGTGAACAGT
TCAAGGACATCAAGACAACCGATCGTACGATGGTGTGGAACTCCAACCTAGTTGAGACGCTAGAGCTGCAGAATATGCTA
GCCAATGCGGTGCACATCATTACAGCCATGGAAAATCGCAAGGAGTCGAGGGGCTCCCATGCTCGCGAGGATTTCAAGAC
GCGCGTGGATGAGCTGGACTATGGAGCACCACTGGCCGGACAGAAAAAGAAACCATTCGAGGAGCATTGGCGCAAGCACA
CCATGACCTTTGCACTGGGTAACAAAGGATGTGCATCGATCAAATATCGCCCGGTTGTGGACACCACCTTGGACAGCTCC
GTTGCACCCATTCCACCTGCTCCGCGCACCTACTGA

Alignment

ORF - retro_dmel_7 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 63.68 %
• Parental protein coverage: 94.25 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QASAANPDKISKQYPVVDHAYDAIVVGAGGAGLRAAFGLVAEGFRTAVITKLFPTRSHTIAAQGGINAAL
          Q.S..........Y...DH..DAIV.GAGGAG.RA.FGL...GF.TA.I.KLFPTRSHT.AAQGG.NAAL
Retrocopy QVSCVRDASCKDEYSLIDHKFDAIVIGAGGAGMRAGFGLAEKGFQTAIISKLFPTRSHTVAAQGGVNAAL

Parental  GNMEEDDWKWHMYDTVKGSDWLGDQDAIHYMTREAPKAVIELENYGMPFSRTQDGKIYQRAFGGQSLKFG
          .NM..DDWK.H.YDTVKGSDWLGDQ.AIHYM.REA..AV.EL..YGMPFSR..DGKIYQR.FGGQ.L..G
Retrocopy SNMDKDDWKYHFYDTVKGSDWLGDQNAIHYMCREAERAVCELDMYGMPFSRKPDGKIYQRPFGGQTLDYG

Parental  KGGQAHRCCAVADRTGHSLLHTLYGQSLSYD--CNYFVEYFALDLIFEDGECRGVLALNLEDGTLHRFRA
          KGG.A.R.CA.ADRTGH.L.HTLYGQ.L.....C.YFV.YF.LDLI...G.C.G.LA..L.DGT.HRF.A
Retrocopy KGGVARRACACADRTGHALIHTLYGQTLKHSDSCHYFVDYFVLDLIMSQGACVGCLAWKLDDGTFHRFLA

Parental  KNTVIATGGYGRAFFSCTSAHTCTGDGTAMVARQGLPSQDLEFVQFHPTGIYGAGCLITEGCRGEGGYLI
          KNTV.A.GG.GR..FS.T..HTCTGDG.A.V.RQ.LP..D.EFVQFHPTGIYGAGCLITEG.RGEGG...
Retrocopy KNTVVAAGGCGRVYFSTTAGHTCTGDGNAWVSRQELPLMDMEFVQFHPTGIYGAGCLITEGVRGEGGFFL

Parental  NGNGERFMERYAPVAKDLASRDVVSRSMTIEIMEGRGAGPEKDHVYLQLHHLPPKQLAERLPGISETAMI
          N..GERFMERYAP.AKDLASRDVV.R.MT.E...G.G.GP.KDHV.LQLHH...K....RLPGI..TA.I
Retrocopy NCKGERFMERYAPKAKDLASRDVVARAMTMEVLAGNGCGPLKDHVHLQLHHIDAKIIKQRLPGIMVTARI

Parental  FAGVDVTREPIPVLPTVHYNMGGVPTNYRGQVITIDKDGKDVIVPGLYAAGEAASSSVHGANRLGANSLL
          FA.VDVT.EP.PVLPTVHYNMGG.PT.Y.G.V.TID..GK...V.GLY..GE....SVHGANRLGANSLL
Retrocopy FAKVDVTKEPVPVLPTVHYNMGGIPTDYKGRVVTIDENGKEQVVKGLYSCGETSCASVHGANRLGANSLL

Parental  DLVVFGRACAKTIAELNKPGAPAPTLKENAGEASVANLDKLRHANGQITTADLRLKMQKTMQHHAAVFRD
          DL..FGR.CA..IA..N.PG...P.....A.E.S..N...LR.A.G.I.TA.LR...Q.TM..HAAVFR.
Retrocopy DLIIFGRVCALDIAANNCPGDKPPQVEDKATEKSLDNFKRLRCADGCIPTAVLRMELQRTMTKHAAVFRE

Parental  GPILQDGVNKMKEIYKQFKDIKVVDRSLIWNSDLVETLELQNLLANAQMTIVSAEARKESRGAHAREDFK
          G..L..G..K..E...QFKDIK..DR...WNS.LVETLELQN.LANA...I...E.RKESRG.HAREDFK
Retrocopy GKLLKEGLLKVAELCEQFKDIKTTDRTMVWNSNLVETLELQNMLANAVHIITAMENRKESRGSHAREDFK

Parental  VREDEYDFSKPLDGQQKKPMDQHWRKHTLSWVCNDNGDITLDYRNVIDTTLDNEVSTVPPAIRSY
          .R.DE.D...PL.GQ.KKP...HWRKHT........G.....YR.V.DTTLD..V...PPA.R.Y
Retrocopy TRVDELDYGAPLAGQKKKPFEEHWRKHTMTFALGNKGCASIKYRPVVDTTLDSSVAPIPPAPRTY

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_7 retrocopy.

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_7 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Nomascus leucogenys	ENSNLEG00000001292	1 retrocopy	retro_nleu_2643,
Ornithorhynchus anatinus	ENSOANG00000010157	1 retrocopy	retro_oana_90,
Xenopus tropicalis	ENSXETG00000023408	1 retrocopy	retro_xtro_61,
Drosophila melanogaster	FBgn0261439	1 retrocopy	retro_dmel_7 ,