RetrogeneDB ID: retro_dmel_21

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 2L:3109719..3110730(+)
• Located in intron of: FBgn0015600

Retrocopy information

• Ensembl ID: FBgn0005779
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Pp1alpha-96A
• Ensembl ID: FBgn0003134
• Aliases: None
• Description: Protein phosphatase 1alpha at 96A [Source:FlyBase gene name;Acc:FBgn0003134]

Sequence

>retro_dmel_21
ATGGCCGTGGATACACTGCACAGTTTACATTTCGCGGGGCAGTTGTCGAATAGCGAAGCGAATGCTGACTACCGTCTGCC
TGGTGCCCTGAATCTGAACGATTTGCTCAATAAACTGATGAGCTTTCGACGCTCAAAGATGCAAAGACTTCCATTGTTGG
AGTCAGAAGTGAACTTACTGTGCACCCTGGCACGTGAACTTTTCCTGGACGAGCCCATGTTGCTCAATGTTCCGGCACCC
ATTCGAGTTGTGGGCGACATACACGGGCAGTTTTATGATCTGCTGAAGATCCTCGATCAATGCGGATATCCGCCGCAGAC
ACGGTATCTATTTCTCGGGGATTACGTGGACAGGGGCAAGAATTCGGTGGAAACGATCACCCTGCTCTTGGCACTGCGCG
TCAAGTTCCCAAAGCATATTTACCTACTGCGCGGAAATCACGAATCGCAGTCGGTGAATCGAGTCTATGGATTCTTTGAC
GAGTGCAAGCGGCGCTACACGGTGAAGCTGTGGAAAACCTTTGTCGATTGCTACAACTGCATGCCCGTGGCAGCCATCAT
TTCCCATCGCATCTTCTGTTGCCACGGCGGACTGAGTCCGCAGCTGAAGGAGCTGAGCAACATCGAATCGATTGCCCGTC
CCACTGAAGTGCCCGAAACGGGTCTGCTATGCGATCTGTTGTGGAGCGATCCGGATCGCTATGGATTCGGCTGGACATCG
AGTGATCGAGGTGTTAGCTATCTCTATGGTCGCGATGTCCTCGAGAAGTTTCTGCAAAAGAACGACTTCGATCTGGTGTG
TCGTGCCCACCAGGTGGTGGAGGATGGATACGAGTTCTTTGCCAAACGCCAATTGGTCACCGTCTTCTCGGCACCCAACT
ATTGTGGATTGTACGACAATGCAGGAGCTTCAATGGGCGTGGACAAGGACCTAGTTATCTCTTTCGATATACAGCGGGGT
GACATTCGAAGAATCGTGGTTAGAAATGAGAGCGTTTCTCCCATAAGTTGA

Alignment

ORF - retro_dmel_21 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 59.93 %
• Parental protein coverage: 92.35 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MNIDSIISRLLEVRGARPGKNVQLSESEIRSLCLKSREIFLSQPILLELEAPLKICGDIHGQYYDLLRLF
          .N.......L...R.........L.ESE...LC...RE.FL..P.LL...AP....GDIHGQ.YDLL...
Retrocopy LNLNDLLNKLMSFRRSKM-QRLPLLESEVNLLCTLARELFLDEPMLLNVPAPIRVVGDIHGQFYDLLKIL

Parental  EYGGFPPESNYLFLGDYVDRGKQSLETICLLLAYKIKYAENFFLLRGNHECASINRIYGFYDECKRRYTI
          ...G.PP...YLFLGDYVDRGK.S.ETI.LLLA...K......LLRGNHE..S.NR.YGF.DECKRRYT.
Retrocopy DQCGYPPQTRYLFLGDYVDRGKNSVETITLLLALRVKFPKHIYLLRGNHESQSVNRVYGFFDECKRRYTV

Parental  KLWKTFTDCFNCLPVAAIVDEKIFCCHGGLSPDLSSMEQIRRIMRPTDVPDQGLLCDLLWSDPDKDTMGW
          KLWKTF.DC.NC.PVAAI....IFCCHGGLSP.L.....I..I.RPT.VP..GLLCDLLWSDPD....GW
Retrocopy KLWKTFVDCYNCMPVAAIISHRIFCCHGGLSPQLKELSNIESIARPTEVPETGLLCDLLWSDPDRYGFGW

Parental  GENDRGVSFTFGAEVVGKFLQKHEFDLICRAHQVVEDGYEFFAKRQLVTLFSAPNYCGEFDNAGAMMSVD
          ...DRGVS...G..V..KFLQK..FDL.CRAHQVVEDGYEFFAKRQLVT.FSAPNYCG..DNAGA.M.VD
Retrocopy TSSDRGVSYLYGRDVLEKFLQKNDFDLVCRAHQVVEDGYEFFAKRQLVTVFSAPNYCGLYDNAGASMGVD

Parental  DTLMCSFQILKPADKRRFVYPN
          ..L..SF.I....D.RR.V..N
Retrocopy KDLVISFDIQR-GDIRRIVVRN

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

1 EST(s) were mapped to retro_dmel_21 retrocopy

EST ID	Start	End	Identity	Match	Mis-match	Score
BG634875	3109671	3110079	98.1	405	3	401

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_21 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 18 parental genes, and 41 retrocopies.

Species	Parental gene accession	Retrocopies number
Ailuropoda melanoleuca	ENSAMEG00000013861	1 retrocopy	retro_amel_1721,
Bos taurus	ENSBTAG00000011198	2 retrocopies	retro_btau_6, retro_btau_960,
Ciona intestinalis	ENSCING00000004542	1 retrocopy	retro_cint_3,
Callithrix jacchus	ENSCJAG00000000983	1 retrocopy	retro_cjac_923,
Callithrix jacchus	ENSCJAG00000009147	7 retrocopies	retro_cjac_1062, retro_cjac_1165, retro_cjac_1408, retro_cjac_2304, retro_cjac_2535, retro_cjac_3288, retro_cjac_822,
Dasypus novemcinctus	ENSDNOG00000007986	3 retrocopies	retro_dnov_2565, retro_dnov_525, retro_dnov_872,
Dipodomys ordii	ENSDORG00000010484	2 retrocopies	retro_dord_260, retro_dord_261,
Equus caballus	ENSECAG00000017228	1 retrocopy	retro_ecab_853,
Echinops telfairi	ENSETEG00000015721	1 retrocopy	retro_etel_2065,
Macropus eugenii	ENSMEUG00000005323	1 retrocopy	retro_meug_1748,
Myotis lucifugus	ENSMLUG00000010661	2 retrocopies	retro_mluc_15, retro_mluc_2217,
Mus musculus	ENSMUSG00000004455	5 retrocopies	retro_mmus_2274, retro_mmus_2968, retro_mmus_3418, retro_mmus_851, retro_mmus_925,
Oryctolagus cuniculus	ENSOCUG00000009275	2 retrocopies	retro_ocun_1232, retro_ocun_665,
Pan troglodytes	ENSPTRG00000005448	1 retrocopy	retro_ptro_2435,
Sorex araneus	ENSSARG00000000571	1 retrocopy	retro_sara_700,
Tupaia belangeri	ENSTBEG00000013852	4 retrocopies	retro_tbel_1710, retro_tbel_2116, retro_tbel_2311, retro_tbel_4450,
Vicugna pacos	ENSVPAG00000008411	1 retrocopy	retro_vpac_540,
Drosophila melanogaster	FBgn0003134	5 retrocopies	retro_dmel_21 , retro_dmel_37, retro_dmel_42, retro_dmel_48, retro_dmel_81,