RetrogeneDB ID: retro_dmel_75

Retrocopy location

• Organism: Fruit fly (Drosophila melanogaster)
• Coordinates: 2L:9013049..9013922(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: FBgn0032089
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: Rcd-1
• Ensembl ID: FBgn0031047
• Aliases: None
• Description: Required for cell differentiation 1 ortholog [Source:FlyBase gene name;Acc:FBgn0031047]

Sequence

>retro_dmel_75
ATGAGTGCGGAACCAAGTCCGGTAATGAGTCCCCAGCAGCAGGCCGAGCGGGAGAAGGTGTACCAGTTGATCATCGAGCT
GGCCTATCCTGCCACGCGGGAGACCGCTCTGCTGGAGCTGAGCAAGAACACCTATGCGGACCTGGCCCCCATGCTGTGGA
AAAGCGTCGGTACCACCTGCACCCTGCTGCAGGAGATCGTCAACATATACCCCATAATAACGACGCCCGTTTTGAAGGCC
AACCAGTCGAACCGCGTGTGCTACGCCCTGACTTTGCTACAGTGCGTCGCCTCGCATCCGGAGACTCGCCCGGCCTTCCT
GCGGGACCAGATACCGATGTACTTGTACCCCTTCTTGTCGACCACGTTCAAGAGCAGGCCCTTCGAGCAGCTGCGCCTGA
CCACGCTGGGCGTGATTAATGCTCTGGCCGAGACCGGTGATACGGAGGTCCTCATCTTCCTGATATGGAGCGAGGTCGTG
CCTCACTGTCTGACCAATATGGTCAGGGGATCGAAGCTGACCAAGATCGCGGCCACTTCAATCCTTGAGAAGATACTGCT
CGATGAGATGGGTCTGACGTACATTTGCGAGAACCACGATCGCTTCTCGCAGGTGGCCATCACCCTGGGCAAAATGGTCA
TCCATATGTTGAAGTTTCCATGCCTCCGGGTGCTGAAGCATGTGGTGCGCTGCTATCTACTACTTACGGAAAATGCGCGC
GCTCGCAGTGCACTTAGAGTGTGTCTGCCGGATCTGCTGCGTGACGGCACCTTCACGTCGCTCGTGCAACATGACACGTG
CACCAAGCAGTGGCTGCAGATGCTGCTCAAGAACCTGCAGACAAACGCCGTCAACCCAATGGGCTCCTCCTAG

Alignment

ORF - retro_dmel_75 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 69.12 %
• Parental protein coverage: 89.47 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QQQTEQEKVYQWINELAHPDTRETALLELSKKRETDLAPMLWNSFGTACALLQEIVNIYPSITPPTLTAH
          QQQ.E.EKVYQ.I.ELA.P.TRETALLELSK....DLAPMLW.S.GT.C.LLQEIVNIYP.IT.P.L.A.
Retrocopy QQQAEREKVYQLIIELAYPATRETALLELSKNTYADLAPMLWKSVGTTCTLLQEIVNIYPIITTPVLKAN

Parental  QSNRVCNALALLQCVASHPETRTAFLQAQIPLYLYPFLSTTSKTRPFEYLRLTSLGVIGALVKTDEQEVI
          QSNRVC.AL.LLQCVASHPETR.AFL..QIP.YLYPFLSTT.K.RPFE.LRLT.LGVI.AL..T...EV.
Retrocopy QSNRVCYALTLLQCVASHPETRPAFLRDQIPMYLYPFLSTTFKSRPFEQLRLTTLGVINALAETGDTEVL

Parental  TFLLTTEIVPLCLSIMDSGSELSKTVATFIIQKILLDESGLSYICQTYERFSHVAITLGKMVIQLAKDPC
          .FL...E.VP.CL..M..GS.L.K..AT.I..KILLDE.GL.YIC....RFS.VAITLGKMVI...K.PC
Retrocopy IFLIWSEVVPHCLTNMVRGSKLTKIAATSILEKILLDEMGLTYICENHDRFSQVAITLGKMVIHMLKFPC

Parental  ARLLKHVVRCYLRLSDNTRARKALGQCLPDQLRDGTFALCLQEDKSTKQWLQMLLKNLELGA
          .R.LKHVVRCYL.L..N.RAR.AL..CLPD.LRDGTF....Q.D..TKQWLQMLLKNL...A
Retrocopy LRVLKHVVRCYLLLTENARARSALRVCLPDLLRDGTFTSLVQHDTCTKQWLQMLLKNLQTNA

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_75 retrocopy.

TSS

Drosophila melanogaster was not studied using FANTOM5 data.

Lab

retro_dmel_75 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 2 parental genes, and 2 retrocopies.

Species	Parental gene accession	Retrocopies number
Callithrix jacchus	ENSCJAG00000011079	1 retrocopy	retro_cjac_2525,
Drosophila melanogaster	FBgn0031047	1 retrocopy	retro_dmel_75 ,