RetrogeneDB ID: retro_macu_2

Retrocopy location

• Organism: Wild banana (Musa acuminata)
• Coordinates: 6:788228..789557(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: GSMUA_Achr6G01190_001
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GSMUA_Achr7G03380_001
• Aliases: None
• Description: None

Sequence

>retro_macu_2
ATGATCTCCTCCGTACATGCTCTGCTTCCGCCATCGTTATCGCCTCTTCCTTCTTCCTACCGTTACCACACAGAAACCCA
CCACCTGAGGCACGTAGCCGCCATTAGATTCCGCGCAGCTAGTATTTGTGGCCTCCCAAGTAAAACAATCCCCTTCTCGT
GCTTCTCCGTGCGTCAATCCGTCCTCCAGATCGGCCTCAAAAGAATCTCCGCAGGTCTCAGGCCCGTCGCTGCCGCAGCC
GCCGCCGCCGCCGGCGTCCCTGATCCGGATGGAGATCCGAATGCCTCACCTGCTCCTCAGTCGCAAGATCCAACGGGAGG
AGGATCGGAAGACGCCAGCTCTCATGATAGGAGCAGCCGCGACGGTGTCAAGAAGAAGAGCAATCCGAGACTGAATCTGG
CCATAGTGTTCGGCTTCTGGTACTTCCAAAACGTGGTGTTCAACATCTACAACAAGAAGGTGCTCAACGTCTTCCCTTAC
CCCTGGCTCCTCGCCTCCTTCCAGCTCCTTGCCGGCTCCCTCTGGATGTCCGCCCTCTGGCTCTCCGGCCTCCAGCCCTT
TCCCCGCCCTCTCGGCCGCCGCTTCTTCCTCGCCCTCCTCGGCCCCGCCCTGTTCCACACCGTCGGCCACATCTCCGCCT
GCGTCTCCTTCTCCAAAGTCGCCGTCTCCTTCACTCACGTTATCAAGGCCTCCGAGCCCGTCTTCTCCGTCCTCTTCTCT
GCCCTCCTCGGCGTCCGCCTCTACCCCCTCCCGGTTTGGCTCTCCGTCCTCCCCATCGTCGCCGGGTGCTCCCTGGCCGC
AGTCACCGAGGTCTCCTTCGACGCCCAGGGCCTCTGGGGCGCCCTCATCAGCAACGTCGGCTTCGTGTTCCGAAACATCT
ACTCCAAGAAGAGCCTGCAGGACTTCACGCACGTCAACGGTCTCAACCTCTACGGCTGGATCAGCATCGTCTCCCTTCTC
TACCTCTTCCCCGTCGCCATCTTCGTCGAGGGCTCCCAGTGGGTGGAGGGCTTCCGCAGGGCCTTGGTGGCGGTTCCCAC
CCCGTGGACCTTCTACTTTTGGGTGCTCTTGTCCGGGATCTTTTACCATCTCTACAACCAGTCGTCGTACCAGGCGCTCG
ACGAAATCAGCCCCTTGACCTTCTCTGTCGGCAACACCATGAAGCGAGTCGTGGTGATTGTGGCCTCCGTTTTGGCCTTC
AGGAATCCCATTAGGCCATTGAACGCCTTGGGGTCTGCTATCGCCATCTTCGGGACTTTCTTATATTCGCAGGCCACCAC
AATGGGCAACAAGAGCGGGAAGAATGATATCCCCGAGAGGAAGAGCTAA

Alignment

ORF - retro_macu_2 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 53.16 %
• Parental protein coverage: 79.39 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  DRSENIEISHQEARSAAGQKLRIGIYFATWWALNVVFNIYNKKVLNAFPYPWLTSTLSLATGSLMMLVSW
          D.S.....S...........L...I.F..W...NVVFNIYNKKVLN.FPYPWL.....L..GSL.M...W
Retrocopy DASSHDRSSRDGVKKKSNPRLNLAIVFGFWYFQNVVFNIYNKKVLNVFPYPWLLASFQLLAGSLWMSALW

Parental  ATGIAEAPET-DFEFWKALAPVAVAHTIGHVAATVSMSKVAVSFTHIIKSGEPAFSVLVSRLLLGETFPL
          ..G....P......F..AL...A..HT.GH..A.VS.SKVAVSFTH.IK..EP.FSVL.S.LL.....PL
Retrocopy LSGLQPFPRPLGRRFFLALLGPALFHTVGHISACVSFSKVAVSFTHVIKASEPVFSVLFSALLGVRLYPL

Parental  PVYLSLVPIIGGCALAAVTELNFNMTGFVGAMISNLAFVFRNIFSKKGMKG-KSVGGMNYYACLSILSLL
          PV.LS..PI..GC.LAAVTE..F...G..GA.ISN..FVFRNI.SKK.......V.G.N.Y...SI.SLL
Retrocopy PVWLSVLPIVAGCSLAAVTEVSFDAQGLWGALISNVGFVFRNIYSKKSLQDFTHVNGLNLYGWISIVSLL

Parental  ILTPFAIAIEGPQMWTAGWQKALSQIGP--HFVWWVAAQSVFYHLYNQVSYMSLDEISPLTFSIGNTMKR
          .L.P.AI..EG.Q.W..G...AL........F..WV.....FYHLYNQ.SY..LDEISPLTFS.GNTMKR
Retrocopy YLFPVAIFVEGSQ-WVEGFRRALVAVPTPWTFYFWVLLSGIFYHLYNQSSYQALDEISPLTFSVGNTMKR

Parental  ISVIVSSIIIFHTPVQPVNALGAAIAILGTFLYSQA
          ..VIV.S...F..P..P.NALG.AIAI.GTFLYSQA
Retrocopy VVVIVASVLAFRNPIRPLNALGSAIAIFGTFLYSQA

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_2 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 9 parental genes, and 9 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00062p00036220	1 retrocopy	retro_atri_14,
Brassica oleracea	Bo9g118840	1 retrocopy	retro_bole_30,
Musa acuminata	GSMUA_Achr7G03380_001	1 retrocopy	retro_macu_2 ,
Populus trichocarpa	POPTR_0001s44610	1 retrocopy	retro_ptri_19,
Physcomitrella patens	PP1S70_177V6	1 retrocopy	retro_ppat_10,
Arabidopsis lyrata	scaffold_802017.1	1 retrocopy	retro_alyr_24,
Solanum lycopersicum	Solyc07g064270.2	1 retrocopy	retro_slyc_32,
Theobroma cacao	TCM_030978	1 retrocopy	retro_tcac_18,
Vitis vinifera	VIT_10s0116g00760	1 retrocopy	retro_vvin_26,