RetrogeneDB ID: retro_dmel_17

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 3L:15465721..15466678(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: FBgn0036496
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: TBPH
• Ensembl ID: FBgn0025790
• Aliases: None
• Description: TAR DNA-binding protein-43 homolog [Source:FlyBase gene name;Acc:FBgn0025790]

Sequence

>retro_dmel_17
ATGGTTTTCGTTCACGTTTCGGAGAAGGAGGGCGACGAGCCCATCGAGCTGCCGGCTGAGGAGGATGGCACTTTGCTGCT
GTCCACACTGCAGGCGCAGTTTCCGGAATCTAGCGGTCTGCAGTACCGCAACGTGGACACGAAGGCGGTGCGTGGAGTTC
GCTCCAACGAGGGCCGACTGTATTCGCCCAGCGAAGAAACCGGCTGGGGCGAGTACCATTACTTTTGCGTCTTTCCCAAG
AAGAACAAGCGCCAGAGCGAAGATAACTTGGAAAACTCAACTGCCAAAACCAAGCGCACTGAGGCCCATCTGCGCTGCTT
TGATCTCATCGTGCTCGGCTTGTCCTATAACACCACCGAGCAGGATTTGCGTGAGTACTTCGAGACCTACGGCGATGTGG
TGAAGGCTGAGATCAAGAAGGACACCAGGTCGGGCCACTCCAAGGGTTTCGGGTTCGTGCGCTTCGGCTCTTACGATGTC
CAGATGCACGTACTCTCTAAGCGCCATTCAATTGATGGTCGCTGGTGCGAGGTTAAGGTGCCCGCCTCGAGGGGCATGGG
CAATCAGGAGCCTGGCAAGGTATTCGTCGGCCGCTGCACCGAGGACATAGAGGCGGATGACTTGCGCGAGTACTTCTCAA
AGTTTGGCGAAGTGATCGACGTGTTCATTCCCAAGCCCTTCAGGGCTTTTAGCTTTGTAACCTTTCTCGATCCGTATGTA
CCACGCGTCGTGTGCGGAGAGAAACACATAATCAAGGGAGTTTCGGTCCATGTGTCGACTGCTGACAAAAAGAACGTGCA
GAACAAAAACCAACTGTTCCAGACCAACAACTACAACAATTTGGACAACAACTTTAAGATGCAACCGGCCAACAACTTTA
GAATGCACCCAGCCAACAACTTTAGCATGCATTCATTTAATCCACATGGTTACCAAATGAATCGCGTCATGAACTAG

Alignment

ORF - retro_dmel_17 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 73.4 %
• Parental protein coverage: 58.38 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  MDFVQVSEEEGDEPIELPAEEDGTLLLSTLQAQFPGSCGLKYRNLDTKAVRGVRSNEGRLFPPSVESGWG
          M.FV.VSE.EGDEPIELPAEEDGTLLLSTLQAQFP.S.GL.YRN.DTKAVRGVRSNEGRL..PS.E.GWG
Retrocopy MVFVHVSEKEGDEPIELPAEEDGTLLLSTLQAQFPESSGLQYRNVDTKAVRGVRSNEGRLYSPSEETGWG

Parental  EYAYFCVFPKENKRKSDDNLENSTAKTKRIETRLRCTDLIVLGLPWKTTEESLREYFETYGEVLMAQIKK
          EY.YFCVFPK.NKR.S.DNLENSTAKTKR.E..LRC.DLIVLGL...TTE..LREYFETYG.V..A.IKK
Retrocopy EYHYFCVFPKKNKRQSEDNLENSTAKTKRTEAHLRCFDLIVLGLSYNTTEQDLREYFETYGDVVKAEIKK

Parental  DTKSGQSKGFGFVRFGSYDAQMRVLTNRHLIDGRWCEVKVPNSKGMGHQVPCKVFVGRCTEDINSDDLRE
          DT.SG.SKGFGFVRFGSYD.QM.VL..RH.IDGRWCEVKVP.S.GMG.Q.P.KVFVGRCTEDI..DDLRE
Retrocopy DTRSGHSKGFGFVRFGSYDVQMHVLSKRHSIDGRWCEVKVPASRGMGNQEPGKVFVGRCTEDIEADDLRE

Parental  YFSKFGEVTDVFIPRPFRAFSFVTFLDPDVAQSLCGEDHIIKGVSVHVSNAAPKAEQNRNQQVQSYNYNS
          YFSKFGEV.DVFIP.PFRAFSFVTFLDP.V....CGE.HIIKGVSVHVS.A..K..QN.NQ..Q..NYN.
Retrocopy YFSKFGEVIDVFIPKPFRAFSFVTFLDPYVPRVVCGEKHIIKGVSVHVSTADKKNVQNKNQLFQTNNYNN

Parental  A-NSFGMHSYHPQGN-HMNPGRNGHHRGNNQH
          ..N.F.M....P..N..M.P..N......N.H
Retrocopy LDNNFKM---QPANNFRMHPANNFSMHSFNPH

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_17 retrocopy.

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_17 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 11 parental genes, and 15 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000002381	2 retrocopies	retro_cjac_2457, retro_cjac_525,
Dasypus novemcinctus	ENSDNOG00000008531	1 retrocopy	retro_dnov_2262,
Homo sapiens	ENSG00000120948	2 retrocopies	retro_hsap_1209, retro_hsap_3637,
Macaca mulatta	ENSMMUG00000007456	1 retrocopy	retro_mmul_1847,
Mus musculus	ENSMUSG00000041459	1 retrocopy	retro_mmus_1958,
Nomascus leucogenys	ENSNLEG00000009512	2 retrocopies	retro_nleu_201, retro_nleu_819,
Pongo abelii	ENSPPYG00000001894	1 retrocopy	retro_pabe_1008,
Pan troglodytes	ENSPTRG00000000136	2 retrocopies	retro_ptro_2460, retro_ptro_828,
Sus scrofa	ENSSSCG00000023126	1 retrocopy	retro_sscr_652,
Tarsius syrichta	ENSTSYG00000004077	1 retrocopy	retro_tsyr_2004,
Drosophila melanogaster	FBgn0025790	1 retrocopy	retro_dmel_17 ,