RetrogeneDB ID: retro_macu_3

Retrocopy location

• Organism: Wild banana (Musa acuminata)
• Coordinates: 1:6184111..6185260(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GSMUA_Achr1G08040_001
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GSMUA_Achr10G05900_001
• Aliases: None
• Description: None

Sequence

>retro_macu_3
ATGGTGGAAACCCACATGCAGACCGGCACGACGAGGCGCGGCAGCAACCCCCGCCTCGAGTCTGCCGATCTCGTCGGCAT
CGACATCCCGCCGACCCCGCCGAGCGACGCCCGCCCCGGCGCTAAGCAGGCCACCTCCTTCCTCTCCCTCATCGTCCCCT
TCCTCCTCGCGTCCTCCTCCCATGCCCCCTCTTCCGGCGCTGCCGCTCCCGGCTCCTCTTCCTCCACCGTCGCCACCGCC
TTCGTCATCGGATCTTGGTACTTTTCCAACATCGGGGTGCTCCTGCTGAACAAGTACCTGCTCAGCATCTACGGCTATCG
CTACCCCGTCTTCCTCACGGCGCTCCACATGGCCTCCTGCTCCGCCTACAGCGCCGTTGCCCTGCGGTGGCTCTGCTTGG
TTCCCTTCCAGCCCGTCTCCTCCCGCAGGCAGCTGTTCAAGATCGCCGCCCTCGGCGCCATCTTCTGTTTCTCCGTCGTC
TGCGGCAACGCCTCCCTCCGGTTCCTGCCCGTCTCGTTCAATCAGGCCGTCGGCGCGACCACCCCCTTCTTCACGGCCAT
CTTCGCCCTCGCGATCACCTGCCGCCGCGAGCCCTCCGCCGTCTACGTCGCGCTGCTCCCCGTTGTCCTCGGCATCGTCC
TCGCCAGCAACAGCGAGCCCCTCTTCCACCCCCTGGGCTTCCTCCTCTGCCTCGGCTCCACCTCCGGTCGCGCTCTCAAG
TCCGTCGTCCAGGGAATCCTCCTCACCTCCGACTCCGAGAAGCTCAACTCCATGAACCTGCTCATGCACATGGCCCCCAT
CGCCGCCGCCATCCTGCTGCCCCTCTCCCTCTGGACCGAGCCCGGCGTCGTCCCCGCCACCGCCGCCAAGATCCGCGACG
ACCCCTACCTCGCCCTCCTCCTCTTCGCCAACGCCACCATCGCCTACCTCGTCAACCTCACCAACTTCCTCGTCACCAAG
CACACCAGCGCCCTCACCCTGCAGGTGCTCGGCAATGCCAAGGCCGCCGTCGCCGCCCTCGTCTCCGTTCTAATCTTCCG
TAATCCCGTGACGGTCATGGGTGTCACCGGCTTCGGCATCACCATCATCGGCGTCGTGCTGTACAGCGAAGCCACGAAGA
GGTCTAAGTCATCGTCTTCTTCTTCGTAG

Alignment

ORF - retro_macu_3 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 61.66 %
• Parental protein coverage: 99.37 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TKGNWSPPAVSGRLFTFGLVASWYSSNIGVLLLNKYLLSNYGFKYPIFLTMCHMAACSLLSYVAIAWLRV
          ..G...P...S....T.....SWY.SNIGVLLLNKYLLS.YG..YP.FLT..HMA.CS..S.VA..WL..
Retrocopy SSGAAAPGSSSSTVATAFVIGSWYFSNIGVLLLNKYLLSIYGYRYPVFLTALHMASCSAYSAVALRWLCL

Parental  VPMQTVRSRLQFLKIATLSLVFCGSVVSGNVSLKYLPVSFNQAVGATTPFFTAVFAYLMTVKREAWITYI
          VP.Q.V.SR.Q..KIA.L...FC.SVV.GN.SL..LPVSFNQAVGATTPFFTA.FA...T..RE....Y.
Retrocopy VPFQPVSSRRQLFKIAALGAIFCFSVVCGNASLRFLPVSFNQAVGATTPFFTAIFALAITCRREPSAVYV

Parental  TLIPVVTGVIIASGGEPSFHLFGFIMCVGATAARALKSVLQGILLSSEGEKLNSMNLLLYMAPIAVVLLL
          .L.PVV.G...AS..EP.FH..GF..C.G.T..RALKSV.QGILL.S..EKLNSMNLL..MAPIA...LL
Retrocopy ALLPVVLGIVLASNSEPLFHPLGFLLCLGSTSGRALKSVVQGILLTSDSEKLNSMNLLMHMAPIAAAILL

Parental  PATLVMEENVVGITMALAREDFKLIWYLLFNSTLAYFVNLTNFLVTKHTSALTLQVLGNAKGAVAVVVSI
          P..L..E..VV..T.A..R.D..L...L..N.T.AY.VNLTNFLVTKHTSALTLQVLGNAK.AVA..VS.
Retrocopy PLSLWTEPGVVPATAAKIRDDPYLALLLFANATIAYLVNLTNFLVTKHTSALTLQVLGNAKAAVAALVSV

Parental  LIFKNPVTVTGMLGYTVTVIGVILYSEAKKRSK
          LIF.NPVTV.G..G...T.IGV.LYSEA.KRSK
Retrocopy LIFRNPVTVMGVTGFGITIIGVVLYSEATKRSK

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Musa acuminata was not studied using RNA-Seq expression data.

ChIP-Seq

Musa acuminata was not studied using ChIP-Seq data.

EST

Musa acuminata was not studied using EST data.

TSS

Musa acuminata was not studied using FANTOM5 data.

Lab

retro_macu_3 was not experimentally validated.

Homology

Retrocopy orthology:

Musa acuminata 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
Amborella trichopoda	AMTR_s00080p00074790	1 retrocopy	retro_atri_6,
Musa acuminata	GSMUA_Achr10G05900_001	1 retrocopy	retro_macu_3 ,