RetrogeneDB ID: retro_macu_90

Retrocopy location

• Organism: Wild banana (Musa acuminata)
• Coordinates: 9:33548967..33549402(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: GSMUA_Achr3G30150_001
• Aliases: None
• Description: None

Sequence

>retro_macu_90
TTGACCGGGAAGACCATCACCCTTGAGGTGGAGAGCTCGGACACCATCGACAATGTAAAGGCCAAGATTCAGGACAAGGA
GGGTATTCCCCCGGACCAGCAAAGGCTCATCTTTGCTGGCAAGCAGCTTGAGGATGGCCGCACCCTGGCAGATTACAACA
TTCAGAAGGAGTCTACCCTTCACCTTGTGCTGAGACTTAGGGGTGGCATGCAGATCTTTGTTAAGACGCTCACAGGGAAG
ACCATTACCTTGGAGGTGGAGAGTTCGGACACGATTGATAATGTCAAGGCAAAGATCCAGGACAAGGAGGGGATTCCACC
GGATCAGCAGAGGCTGATCTTTGCTGGGAAGCAGCTGGAGGACGGGCGCACCCTGGCAGATTACAACATTCAGAAGGAAT
CCACCCTTCACCTGGTGCTCCGCCTCCGCGGGGGT

Alignment

ORF - retro_macu_90 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.0 %
• Parental protein coverage: 92.36 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGM
          LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGM
Retrocopy LTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVLRLRGGM

Parental  MIKVKTLTGKEIEIDIEPTDTIDRIKERVEEKEGIPPVQQRLIYAGKQLADDKTAKEYNIEGGSVLHLVL
          .I.VKTLTGK.I....E..DTID..K.....KEGIPP.QQRLI.AGKQL.D..T...YNI...S.LHLVL
Retrocopy QIFVKTLTGKTITLEVESSDTIDNVKAKIQDKEGIPPDQQRLIFAGKQLEDGRTLADYNIQKESTLHLVL

Parental  ALRGG
          .LRGG
Retrocopy RLRGG

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_90 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 5 parental genes, and 8 retrocopies.

Species	Parental gene accession	Retrocopies number
Oryza sativa indica	BGIOSGA036765	1 retrocopy	retro_oind_26,
Musa acuminata	GSMUA_Achr3G30150_001	1 retrocopy	retro_macu_90 ,
Oryza glaberrima	ORGLA06G0191700	1 retrocopy	retro_ogla_18,
Oryza sativa japonica	OS06G0650100	1 retrocopy	retro_osat_51,
Triticum aestivum	Traes_5BL_8FFD203BD	4 retrocopies	retro_taes_156, retro_taes_160, retro_taes_166, retro_taes_45,