RetrogeneDB ID: retro_atri_38

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00069:68874..69414(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00135p00066200
• Aliases: None
• Description: None

Sequence

>retro_atri_38
CAAGGTAAAGCTTGGATGATACAATTGTTATCAGTTACCTGTTTGTATCCGGCTGCTAAGATGGACATGGACGAAGATGA
TGTGCCATTATCTCTTCATTTACATGTTAGGGAAGCGAAATATGTATTCTAGTCTCGAACGATTTTGAGAACGGAGCTTC
TTGCACATAGCACCTTGAAGTGGAGAATGTAGTCTGTGACACCATTCTCTTTTGTTGATTACTTTCTTCATAAGATCAAT
GGCTCGATTCCTGGGCCCTGTGAGCTTGTCCCTGTAGATCAAGTGAAAAAATCTTAAGCACAATCAAAAGGACTGAGTTT
TTGGAGTTCAAACCTTTTGAGATTGCTGCAGCTGTAGCCGTATCTGTATCTGACAAATCCAAATCACTTGATTTCAACAA
CGCTCTTTCTTGTAGCCCCCATGTTGAAAATGGCAAGGTGTTGAGGTGCTATTGAACTTATTCAATAAATTTTGTTGATT
AAGAGCATTGGGTCAGTTTCATCAGGGCCTCGGAGTCCAATAAGGGTTCTTGATTCTCCA

Alignment

ORF - retro_atri_38 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 70.88 %
• Parental protein coverage: 51.74 %
• Number of stop codons detected: 4
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  QGKAWMIQLLSVACLSLAAKME--ETDVPLSLDLQVGEAKYVFESRTIQRMELLVLSNLKWRMQSVTPFS
          QGKAWMIQLLSV.CL..AAKM...E.DVPLSL.L.V.EAKYVF.SRTI.R.ELL..S.LKWRM.SVTPFS
Retrocopy QGKAWMIQLLSVTCLYPAAKMDMDEDDVPLSLHLHVREAKYVF*SRTILRTELLAHSTLKWRM*SVTPFS

Parental  FVDYFLHKINGD-DSWAPRAYLCRSSDIILTTIKGTEFLEFRPSEIAAAVAISVSEESKSLDFNNALACC
          FVDYFLHKING..DSWA..A..CRSS..IL.TIK.TEFLEF.P.EIAAAVA.SVS..SKSLDFNNAL.C.
Retrocopy FVDYFLHKINGS<DSWAL*ACPCRSSEKILSTIKRTEFLEFKPFEIAAAVAVSVSDKSKSLDFNNALSCS

Parental  PNVEKGKVLRCY-ELIQEIVLIKNQKLVKIAAGSVSSVPQSP
          P.VE.GKVLRCY.ELIQ.I.LIK....V.....S...V..SP
Retrocopy PHVENGKVLRCY>ELIQ*ILLIKSIGSVSSGPRSPIRVLDSP

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_38 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 1 retrocopy.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00135p00066200	1 retrocopy	retro_atri_38 ,