RetrogeneDB ID: retro_dmel_63

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 3R:16573990..16574740(-)
• Located in intron of: FBgn0259222

Retrocopy information

• Ensembl ID: FBgn0017557
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Pros28.1
• Ensembl ID: FBgn0004066
• Aliases: None
• Description: Proteasome 28kD subunit 1 [Source:FlyBase gene name;Acc:FBgn0004066]

Sequence

>retro_dmel_63
ATGTCCTCACGCTACGGTCGAGCTCTAACCATATTCTCGCCGGATGGCCACCTGTTGCAGGTGGAGTACGCCCAGGAAGC
TGTTCGAAAGGGCTCCACAGCGGTCGGCGTTCGTGGAGCCAATTGTGTGGTGCTGGGTGTGGAGAAGAGCTCGGTGTCCG
AGATGCAGGAGGATCGGACGGTGCGCAAGATCAGCATGCTCGATCGCCACGTGGCGTTGGCATTTGCCGGTCTCACGGCC
GATGCACGGATCCTTATAAATCGAGGGCAGGTCGAGTGCCAGAGCCATCGACTCAACTTCGAAAACCAGGTGACCCTCGA
GTACATCACCAGATACCTTGCCCAGCTCAAGCAGAAGTACACGCAGTGCAATGGACGTCGTCCTTTCGGTATATCGTGTC
TAATAGGAGGCATTGACGCCGATGGCTCTGCACGTCTCTTTCATACCGAACCATCCGGGATATTCCACGAGTACAAGGCG
ACCGCCACTGGGCGTTGGGCAAATACTGTGAGGGAGTTTTTTGAGAAGGCCTATAGCGATCATGAAGTGACAACCAAATG
TGATGCCATCAAACTAGCCATGCGTGCCCTTCTCGAAGTAACCCAGATGAGCCAGATGCGCCTGGAGGTGGCCGTATTGG
AGAATGGCAAGCCAATGAAAATGCTGGACAGTGTAGTAATTTCGGAAATAGTCAAGATCGTTCAGAACGAAAAGGAGCTC
CAAGCGAAGGCACATAAAATGAAGAGATGA

Alignment

ORF - retro_dmel_63 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 75.1 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MSSRYDRAVTIFSPDGHLLQVEYAQEAVRKGSTAVGVRGANCVVLGVEKKSVAQLQEDRKVRKICMLDNH
          MSSRY.RA.TIFSPDGHLLQVEYAQEAVRKGSTAVGVRGANCVVLGVEK.SV...QEDR.VRKI.MLD.H
Retrocopy MSSRYGRALTIFSPDGHLLQVEYAQEAVRKGSTAVGVRGANCVVLGVEKSSVSEMQEDRTVRKISMLDRH

Parental  VVMAFAGLTADARIMINRAQVECQSHRLNVEDPVTLEYITRFIAQLKQKYTQSNGRRPFGISCLIGGFDA
          V..AFAGLTADARI.INR.QVECQSHRLN.E..VTLEYITR..AQLKQKYTQ.NGRRPFGISCLIGG.DA
Retrocopy VALAFAGLTADARILINRGQVECQSHRLNFENQVTLEYITRYLAQLKQKYTQCNGRRPFGISCLIGGIDA

Parental  DGSAHLFQTEPSGIFYEYKANATGRSAKVVREFFEKSYREEEVANEHGAVKLAIRALLEVAQSGQNNLEV
          DGSA.LF.TEPSGIF.EYKA.ATGR.A..VREFFEK.Y...EV.....A.KLA.RALLEV.Q..Q..LEV
Retrocopy DGSARLFHTEPSGIFHEYKATATGRWANTVREFFEKAYSDHEVTTKCDAIKLAMRALLEVTQMSQMRLEV

Parental  AIMENGKPLKMLDTDVITDYVKIIEKEKEEELEKKKQKK
          A..ENGKP.KMLD..VI...VKI...EKE......K.K.
Retrocopy AVLENGKPMKMLDSVVISEIVKIVQNEKELQAKAHKMKR

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_63 retrocopy.

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_63 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 9 parental genes, and 10 retrocopies.

Species	Parental gene accession	Retrocopies number
Bos taurus	ENSBTAG00000005127	1 retrocopy	retro_btau_1356,
Callithrix jacchus	ENSCJAG00000014419	1 retrocopy	retro_cjac_426,
Felis catus	ENSFCAG00000003249	1 retrocopy	retro_fcat_1621,
Macropus eugenii	ENSMEUG00000013254	1 retrocopy	retro_meug_757,
Mus musculus	ENSMUSG00000027566	1 retrocopy	retro_mmus_407,
Rattus norvegicus	ENSRNOG00000008630	1 retrocopy	retro_rnor_2693,
Ictidomys tridecemlineatus	ENSSTOG00000012489	1 retrocopy	retro_itri_279,
Tupaia belangeri	ENSTBEG00000012281	2 retrocopies	retro_tbel_1048, retro_tbel_2392,
Drosophila melanogaster	FBgn0004066	1 retrocopy	retro_dmel_63 ,