RetrogeneDB ID: retro_atri_26

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00027:5886017..5886650(+)
• Located in intron of: AMTR_s00027p00244500

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00069p00126080
• Aliases: None
• Description: None

Sequence

>retro_atri_26
ATGATGAAAATCAGGGCATAGACCCCAGGACCCATGACGATGAATGGGAGCTCGAATGGCGGTGGCTCTGAAATAGTGGA
TTGGGAGAGGCCAAGAGGAATGCTTGTTCAGAAGAGGAGCCTAGGTTCTGATCATGCCTCTTCTACTCCAGCTCCCACCA
TTAGGGTAGAGTAAAATATGGAGCTTTGATGCATGAGATCCACATCAGTTCTCAAGCCACGTTTGGGGAGTTAAAGAAAT
TGCTTGCATCCAAGACAGTACTCCACACTCAAGACCAAAAGCTTCTCTTTAAAGACAAGGAGAGGGATTCTAATGCTTAT
TTGGACATGGCGGGAGTGAAGGACAAGTCAAAGATTGTGTTGATCGAAGATCCCACCAATTAGGAGAGAAGGTATATTGA
GATGCGAAAGAATGCAAATATGAAGAGAGCTTCAAAATACATTGCAAGGATCAGTTTAGAGGTGGATAAGCTTGCGGATC
AGGTTGCTTCTCTCGAATATTTTAATCTCCAAAGGTGGAAAAGTAGTTGAGAATGAGGTTTTGGGTTTGATTGAACTCTT
GATGAATCAGCTTCTCAAACTTGATGGCATTGTAGCTGATGGAGATGTCAAATTGCACAAAAGAACACAAATA

Alignment

ORF - retro_atri_26 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 86.92 %
• Parental protein coverage: 77.94 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MMRIRAKNPGPMTMNGSSNGGGSEIVDWELRPGGMLVQKRSLGIDQASSAPAPTIRV-RVKYGALMHEIH
          MM.IRA..PGPMTMNGSSNGGGSEIVDWE.RP.GMLVQKRSLG.D.ASS.PAPTIRV.RVKYGALMHEIH
Retrocopy MMKIRA*TPGPMTMNGSSNGGGSEIVDWE-RPRGMLVQKRSLGSDHASSTPAPTIRV<RVKYGALMHEIH

Parental  ISSQATFGELKKLLASETGLHTQDQKLLFKDKERDSNAYLDMAGVKDKSKIVLIEDPTSQERRYIEMRKN
          ISSQATFGELKKLLAS.T.LHTQDQKLLFKDKERDSNAYLDMAGVKDKSKIVLIEDPT..ERRYIEMRKN
Retrocopy ISSQATFGELKKLLASKTVLHTQDQKLLFKDKERDSNAYLDMAGVKDKSKIVLIEDPTN*ERRYIEMRKN

Parental  AKMERASKSIAEISLEVDKLAAQVASLE-SVISRGGKVAENEVLGLIELLMNQLLKLDGVVADGDVKLQR
          A.M.RASK.IA.ISLEVDKLA.QVASLE...IS.GGKV.ENEVLGLIELLMNQLLKLDG.VADGDVKL..
Retrocopy ANMKRASKYIARISLEVDKLADQVASLE>ILISKGGKVVENEVLGLIELLMNQLLKLDGIVADGDVKLHK

Parental  RIQV
          R.Q.
Retrocopy RTQI

Legend:

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

Expression

RNA-Seq

Amborella trichopoda was not studied using RNA-Seq expression data.

ChIP-Seq

Amborella trichopoda was not studied using ChIP-Seq data.

EST

Amborella trichopoda was not studied using EST data.

TSS

Amborella trichopoda was not studied using FANTOM5 data.

Lab

retro_atri_26 was not experimentally validated.

Homology

Retrocopy orthology:

Amborella trichopoda 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 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00069p00126080	3 retrocopies	retro_atri_24, retro_atri_26 , retro_atri_3,