RetrogeneDB ID: retro_macu_24

Retrocopy location

• Organism: Wild banana (Musa acuminata)
• Coordinates: 10:28445343..28446538(-)
• Located in intron of: GSMUA_Achr10G23910_001

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GSMUA_Achr7G04260_001
• Aliases: None
• Description: None

Sequence

>retro_macu_24
ATTTTCATCATCAGGCTAGGCTATGGTGAAAGGAAGATTGTTGAGAAGTCACGTTCATCAAATTTCGTATCTTCAAGTGA
TGGATTCATAGAAAGCTCATTCGAAGACAAATCCTCAAGTAATTCCACGCAAGATATGGCACAACCTGTACCACCAACTT
CTACTTATTTTGGTAACAAAAGTATGCTTTCTGCTATTCCTGATGAAACTGCTAATGAAAAGTTTGTCAGTGATGAGGGT
ACACTTTGTTGGAATCTGTTGTTTTCAAGGCTATTTTTTTATGTGAAAAAAGATAGTGAGATCAATAATCCCATAAAAGC
ATGCATCCAGAGGACATTGTCAAATATGAGGACACCAAGTTATATTGGTGAAATCACATGTACTGGCTTAGATCTTGGTA
ACCTTCCACCTTATGTTCATAGAATGAGAGTTTTCCCTATGGACTTGAATGAAGTGTAGTCTAGTCTATGGAAGTTGATA
TTGAATACTCTGGTGGTATAATATTGGACATAGAGACAAGACTTGAAGTCCGTGAACCTGAATTGCAAAAAAGACATAAT
AAAAACAAATTTAGAATCAAATTCTGCTGGTGAGGTGAATTCTAATTTTCTTGATGGCATTGAGCATCATGGAAACTAGT
TGAAATCCTCAAGAAATTCAGCTGTTAGAATGGATAACAGAAATGATGTGGATAAAGCACATGGCCTTAGAAACTCAAAG
AGCACCAGTTGGACGTCAGGTTACGTGTCTAGATGGAAGGCTATCCTACATTCTCTCGCTGATCAAGTTTCACAGGTACC
ACTTTCTTTGGCAATACAAGTTGCTTCACTTCGTGGGACATTGCACTTACATATTAAGCCGCCGCCTTTTGATCAATTGT
GGTTTGGCTTCACAACAATGCTGGAATTAGATTGGAATTTGGACTCATCAGTTGGGGATTGAAAAATAACCAGCAGCCAT
ATTGCTTTGCTTTTTGGCAATCAGGTTAAAGCTGCAATTCGGGATAGTTTGGTGCTTCCTAACTAATGAAAGCATATGCA
TCCCATGGATGTTAGCTGAAAAGGATGATTGGATCCCAAGGAAAGTTGCACCATTCATATGGATCAACAATGACAGTATG
GACATGACAGGCCTTGAGCACACAGTGCCCCAAGATAGGGATAAGATTATTCAACTTGTAAGAGATAATCTCACA

Alignment

ORF - retro_macu_24 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.3 %
• Parental protein coverage: 52.33 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  LFLKRLAKKASKSGLESRQASF--SSSGYGERKI-DKSSSNSMQDMAQPVPPTSTHFGNKSMLSAIPDAA
          .F..RL.....K....SR...F..SS.G..E....DKSSSNS.QDMAQPVPPTST.FGNKSMLSAIPD..
Retrocopy IFIIRLGYGERKIVEKSRSSNFVSSSDGFIESSFEDKSSSNSTQDMAQPVPPTSTYFGNKSMLSAIPDET

Parental  ADEKFVSDEGTLCWNLLFSRLFFDAKKSSEINNLIKARIQRTLSNMRTTSYIGEITCTGLDLGNLPPYVH
          A.EKFVSDEGTLCWNLLFSRL....KK.SEINN.IKA.IQRTLSNMRT.SYIGEITCTGLDLGNLPPYVH
Retrocopy ANEKFVSDEGTLCWNLLFSRLXXXVKKDSEINNPIKACIQRTLSNMRTPSYIGEITCTGLDLGNLPPYVH

Parental  RMRV-FPMDL--NEVWSMEVDIEYSGGIILDIETRLEVREPELQK-DILKTSLESNSAGEVNSDFLEGIE
          RMRV.FP..L....V.SMEVDIEYSGGIILDIETRLEVREPELQK.DI.KT.LESNSAGEVNS.FL.GIE
Retrocopy RMRV<FPYGLE*SVV*SMEVDIEYSGGIILDIETRLEVREPELQK>DIIKTNLESNSAGEVNSNFLDGIE

Parental  HYGNQLKSSSNSTVGMDNRNEADKADGLRNSKSTSWTSGYVSRWKAILHSLADQVSQVPLSLAIRVASLR
          H.GN.LKSS.NS.V.MDNRN..DKA.GLRNSKSTSWTSGYVSRWKAILHSLADQVSQVPLSLAI.VASLR
Retrocopy HHGN*LKSSRNSAVRMDNRNDVDKAHGLRNSKSTSWTSGYVSRWKAILHSLADQVSQVPLSLAIQVASLR

Parental  GTLRLHIKPPPSDQLWFGFTTMPELDWNLDSSVGDRKITSSHIALLFGNRVKAAIRDSLVLPN-YESICI
          GTL.LHIKPPP.DQLWFGFTTM.ELDWNLDSSVGD.KITSSHIALLFGN.VKAAIRDSLVLPN..ESICI
Retrocopy GTLHLHIKPPPFDQLWFGFTTMLELDWNLDSSVGD*KITSSHIALLFGNQVKAAIRDSLVLPN>NESICI

Parental  PWMLAEKDDWIPRKLAPFIWINNDSMDMAGTELTVPQDREDKSKLDGSNKT
          PWMLAEKDDWIPRK.APFIWINNDSMDM.G.E.TVPQDR.....L...N.T
Retrocopy PWMLAEKDDWIPRKVAPFIWINNDSMDMTGLEHTVPQDRDKIIQLVRDNLT

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_24 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Musa acuminata	GSMUA_Achr7G04260_001	1 retrocopy	retro_macu_24 ,