RetrogeneDB ID: retro_macu_75

Retrocopy location

• Organism: Wild banana (Musa acuminata)
• Coordinates: 8:10161792..10162235(+)
• Located in intron of: GSMUA_Achr8G13420_001

Retrocopy information

• Ensembl ID: None
• Aliases: None
• Status: NOVEL

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GSMUA_Achr6G25970_001
• Aliases: None
• Description: None

Sequence

>retro_macu_75
ATGGCGCCGAGTTTCAATCGCCTTGGGATGGCCACGAACATTCCATCGTCCGCATACAAGCCCTTGCATGAGTATTGAAT
TCGTTGAGTTAGCAATTCCCCTCACCTCTGTGAGCTTTGCATAACTCTTTCGGTTGTTGAACAACCCATTCCACTTTGCA
CGATCTCATCCTTTACCAAGTGCCTCGCTTGCCTTGAGCACCATCAAGTATGGTTGCCAACGTCGAGCCATAGCTCGAAC
TCAGCCATCCCAACCTTTATGCGCTATGCATTCTTCCCAGCTTGCTTGTCCTCATGGTGCCTGTTGTGCGAAGGGCTGAC
CATTCCTCTGGATGCTAATCTCATATGCTTGCTCCTCTGAGCGACTCTTTTTCTTTACATCTCCATGCCCGTTTCCCCCA
AACGGTCGCACGTGCTAGCTGCCTTCAACGCAGCCCCGCTAGG

Alignment

ORF - retro_macu_75 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 51.66 %
• Parental protein coverage: 77.2 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MASSFSLLGTATDSPSFAYKPLHEYLILQVSNSSHLCELCTTLKVAKQPIPPCMVLFFAKCPACLEHHQV
          MA.SF..LG.AT..PS.AYKPLHEY.I..VSNS.HLCELC.TL.V..QPIP.C....F.KC.ACLEHHQV
Retrocopy MAPSFNRLGMATNIPSSAYKPLHEY*IR*VSNSPHLCELCITLSVVEQPIPLCTISSFTKCLACLEHHQV

Parental  WLPMLSYCSNSTIITFVSYVSFLVPSLL-VFVVPITRRGANTSDFNRHSGARLG-ARARRDEARAPRFMS
          WLP..S..SNS.I.TF..Y..F..P..L.V..VP..RR....S....H..A.L.........AR.P....
Retrocopy WLPTSSHSSNSAIPTFMRYAFF--PACL<VLMVPVVRRADHSSGC*SHMLAPLSDSFSLHLHARFPQTVA

Parental  RRLASKRAPPR
          R.....R.P.R
Retrocopy RASCLQRSPAR

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_75 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 1 parental gene, and 33 retrocopies.

Species	Parental gene accession	Retrocopies number
Musa acuminata	GSMUA_Achr6G25970_001	33 retrocopies	retro_macu_103, retro_macu_104, retro_macu_105, retro_macu_107, retro_macu_12, retro_macu_15, retro_macu_37, retro_macu_38, retro_macu_39, retro_macu_40, retro_macu_42, retro_macu_48, retro_macu_55, retro_macu_56, retro_macu_57, retro_macu_59, retro_macu_63, retro_macu_64, retro_macu_66, retro_macu_72, retro_macu_75 , retro_macu_76, retro_macu_77, retro_macu_79, retro_macu_80, retro_macu_83, retro_macu_84, retro_macu_86, retro_macu_88, retro_macu_9, retro_macu_91, retro_macu_93, retro_macu_96,