RetrogeneDB ID: retro_dmel_35

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 2R:4125561..4127181(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: FBgn0013726
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Sep1
• Ensembl ID: FBgn0011710
• Aliases: None
• Description: Septin-1 [Source:FlyBase gene name;Acc:FBgn0011710]

Sequence

>retro_dmel_35
ATGAATAGTCCTCGCTCGAACGCGGTTAATGGCGGCAGCGGCGGCGCCATCTCCGCTCTGCCCAGCACTCTGGCCCAACT
GGCTCTGCGCGACAAGCAGCAGGCTGCGTCGGCATCGGCGTCCTCTGCCACGAACGGCAGCAGCGGCAGCGAGTCCTTGG
TGGGCGTCGGTGGACGACCGCCCAATCAGCCGCCCAGTGTGCCAGTGGCCGCCAGTGGCAAGCTGGACACCAGCGGCGGA
GGCGCCTCCAACGGCGACTCGAACAAACTGACCCACGATCTGCAGGAGAAGGAGCACCAGCAGGCGCAGAAGCCACAGAA
GCCACCGCTCCCGGTGCGCCAGAAGCCCATGGAGATCGCCGGCTATGTGGGCTTCGCCAACCTGCCCAATCAGGTCTATC
GCAAGGCCGTCAAGCGGGGATTCGAGTTCACTCTGATGGTGGTGGGCGCCAGTGGGCTGGGCAAGTCGACGCTGATCAAC
TCCATGTTCCTGTCGGACATCTACAACGCGGAACAGTATCCGGGCCCCTCGCTGCGCAAAAAGAAGACCGTGGCCGTGGA
GGCCACCAAAGTAATGCTCAAGGAGAACGGCGTCAATCTGACACTCACGGTGGTGGACACACCCGGATTCGGTGATGCCG
TTGACAACAGCAACTGCTGGGTGCCCATACTGGAGTACGTGGATAGCAAGTACGAGGAGTACCTGACAGCCGAGTCGCGG
GTGTACCGAAAAACCATTTCGGACAGCCGGGTGCACTGCTGCCTCTACTTCATAGCGCCATCGGGACACGGACTCCTGCC
GCTGGACATTGCCTGCATGCAGAGCCTGTCGGACAAGGTAAATCTGGTGCCGGTGATCGCCAAGGCGGACACCATGACGC
CCGACGAGGTGCATCTATTTAAGAAGCAGATCCTTAACGAGATCGCCCAGCACAAGATCAAGATCTACGACTTCCCCGCC
ACGCTGGAGGATGCGGCCGAGGAGGCCAAAACCACGCAGAATTTGCGCAGCCGAGTGCCATTCGCGGTGGTGGGTGCCAA
CACCATCATCGAGCAGGACGGAAAGAAGGTCCGGGGTAGGCGTTATCCCTGGGGCCTGGTGGAGGTGGAGAACCTGACGC
ATTGCGACTTTATAGCGCTGCGCAACATGGTCATACGCACGCACCTTCAGGACCTCAAGGACGTGACGAACAACGTCCAC
TACGAGAACTACCGCTGCCGGAAGCTATCCGAGCTGGGATTGGTGGACGGCAAGGCCAGGCTGTCCAACAAGAACCCACT
CACCCAGATGGAGGAGGAAAAGCGGGAGCACGAGCAGAAGATGAAGAAGATGGAGGCCGAGATGGAGCAGGTGTTTGACA
TGAAGGTCAAGGAGAAGATGCAGAAGCTCAGGGACTCGGAGCTGGAGCTGGCGCGGCGCCACGAGGAGCGCAAGAAGGCG
CTGGAGCTGCAGATCCGGGAGCTGGAGGAGAAGAGACGCGAGTTCGAGCGCGAGAAGAAGGAGTGGGAGGATGTCAACCA
CGTGACGCTCGAGGAGCTCAAGCGACGCAGCCTGGGGGCCAACAGCAGCACGGACAATGTGGATGGCAAGAAGGAGAAGA
AAAAGAAGGGTCTGTTCTAA

Alignment

ORF - retro_dmel_35 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.12 %
• Parental protein coverage: 81.72 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  IETPGYVGFANLPNQVHRKSVKKGFEFTLMVVGESGLGKSTLVNSLFLTDLYPERIIPDAIEKQKQTVKL
          .E..GYVGFANLPNQV.RK.VK.GFEFTLMVVG.SGLGKSTL.NS.FL.D.Y.....P......K.TV..
Retrocopy MEIAGYVGFANLPNQVYRKAVKRGFEFTLMVVGASGLGKSTLINSMFLSDIYNAEQYPGPSLRKKKTVAV

Parental  EASTVEIEERGVKLRLTVVDTPGFGDAIDNSNSFGAILEYIDEQYERFLRDESGLNRRNIVDNRIHCCFY
          EA..V...E.GV.L.LTVVDTPGFGDA.DNSN....ILEY.D..YE..L..ES...R..I.D.R.HCC.Y
Retrocopy EATKVMLKENGVNLTLTVVDTPGFGDAVDNSNCWVPILEYVDSKYEEYLTAESRVYRKTISDSRVHCCLY

Parental  FISPFGHGLKPLDVEFMKKLHSKVNIVPVIAKADCLTKKEILRLKCRIMQEIESHGIKIYPLPDCDSDED
          FI.P.GHGL.PLD...M..L..KVN.VPVIAKAD..T..E....K..I..EI..H.IKIY..P....D..
Retrocopy FIAPSGHGLLPLDIACMQSLSDKVNLVPVIAKADTMTPDEVHLFKKQILNEIAQHKIKIYDFPATLEDAA

Parental  EDYKEQVKQLKEAVPFAVCGANTLLEVKGKKVRGRLYPWGVVEVENPDHCDFIKLRTMLI-THMQDLQEV
          E..K.....L...VPFAV.GANT..E..GKKVRGR.YPWG.VEVEN..HCDFI.LR.M.I.TH.QDL..V
Retrocopy EEAK-TTQNLRSRVPFAVVGANTIIEQDGKKVRGRRYPWGLVEVENLTHCDFIALRNMVIRTHLQDLKDV

Parental  TQEVHYENYRSDRLAK
          T..VHYENYR...L..
Retrocopy TNNVHYENYRCRKLSE

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

30 EST(s) were mapped to retro_dmel_35 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
AA246222	4125564	4126121	98.6	543	5	528
AA263475	4125458	4126120	99	655	4	645
AA390672	4125495	4126096	99	593	5	585
AA694740	4125906	4126121	100	214	0	213
AA816884	4125458	4125997	99.3	531	4	523
AA940717	4125421	4126163	99.4	728	4	717
AA948821	4125449	4126169	99.6	709	3	699
AA951299	4125458	4126009	98.6	548	2	542
AA951769	4125492	4126063	96.5	557	2	542
AI511835	4125441	4126051	99.9	608	1	607
AI513033	4125463	4126103	100	640	0	640
AI513885	4125586	4126091	99.7	503	2	501
AI519873	4125458	4125999	100	541	0	541
AI520603	4125441	4126061	99.9	619	1	618
AI531443	4125585	4125943	99.8	357	1	356
AI114086	4125786	4126210	99.8	423	1	422
BI169443	4125627	4126277	100	645	0	641
BI239637	4125567	4125726	100	159	0	159
BI351994	4125585	4126287	99.8	700	2	698
BI353316	4125942	4126558	99.7	614	2	612
BI374925	4125442	4126048	99.7	603	2	601
BI374951	4125442	4126101	99.7	656	2	654
CO179295	4126552	4126823	99.3	269	2	267
CO306310	4126427	4126633	99.6	205	1	204
CO311156	4125796	4125993	99.5	196	1	195
EC195907	4126550	4126823	99.3	271	2	269
EC200844	4126445	4126839	96.8	384	10	373
EC213530	4125512	4125993	99	476	5	471
EC214626	4126206	4126633	99.6	425	2	423
EL873773	4125449	4126111	100	662	0	662

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_35 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 16 parental genes, and 20 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000002608	1 retrocopy	retro_btau_1185,
Canis familiaris	ENSCAFG00000012960	1 retrocopy	retro_cfam_1477,
Choloepus hoffmanni	ENSCHOG00000008715	5 retrocopies	retro_chof_1371, retro_chof_1579, retro_chof_2198, retro_chof_275, retro_chof_614,
Callithrix jacchus	ENSCJAG00000006122	1 retrocopy	retro_cjac_1501,
Cavia porcellus	ENSCPOG00000013687	1 retrocopy	retro_cpor_845,
Loxodonta africana	ENSLAFG00000011964	1 retrocopy	retro_lafr_4,
Macropus eugenii	ENSMEUG00000016519	1 retrocopy	retro_meug_39,
Myotis lucifugus	ENSMLUG00000007108	1 retrocopy	retro_mluc_1594,
Monodelphis domestica	ENSMODG00000016041	1 retrocopy	retro_mdom_888,
Mustela putorius furo	ENSMPUG00000000166	1 retrocopy	retro_mputfur_436,
Nomascus leucogenys	ENSNLEG00000013873	1 retrocopy	retro_nleu_1848,
Otolemur garnettii	ENSOGAG00000004457	1 retrocopy	retro_ogar_2239,
Pteropus vampyrus	ENSPVAG00000000558	1 retrocopy	retro_pvam_448,
Rattus norvegicus	ENSRNOG00000017952	1 retrocopy	retro_rnor_1110,
Ictidomys tridecemlineatus	ENSSTOG00000013357	1 retrocopy	retro_itri_1227,
Drosophila melanogaster	FBgn0011710	1 retrocopy	retro_dmel_35 ,