RetrogeneDB ID: retro_atri_40

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00087:2032142..2032875(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00096p00102520
• Aliases: None
• Description: None

Sequence

>retro_atri_40
GATCACAAGGAAAATAAAGCGGTTGTGGTGAATGGTCGTAGGACTGAAGATGGCCATGTAATTTCAACGACTATTGGAGG
CCGTAATGGCCAACCAAAATAGACAATCTCGTACATGGCAGAACATGTAGTAGGCCATGGTCCATTTAGTGAGGTCTTCC
GTGCTAAATGCCTGCAAACAGGTGAAGTGGTTGCTATAAAGAAGTTGTTGCAGGATAAAAGACACAAAAACAGAGAACTT
CAAGTTATGCACTTACTTGACCTCCCTAATGTGATTCGGCTGAACATTGTTTCTTTTCAACCACGGAGAAAGATGAAGTC
TACCTTAGTCTTGTAATGGAATATGTATCAAAGACTATGTACAAAGTTGCCAAGCACTACAGCAAAATGAGCCAATGGAT
GCCCCTTGTTTATGTGAAATTATATCCATATCAGATTTGTCGGTCGTTTGCTTACATTCATGGTGTTATTGGTGTCTGCC
ACCATGACATAAAGCCACAAAATTTATTGGTTAATCCCTACACTCATCAACTAAAGCTTTTGTGATTTTGGGAAGTGCAA
AAATGTTGGTAGCTGGTGAACATAATATTTCCTGCATCAGTTCCCGTTATGATAGAGCTCCGGAGTTGATCTTTGGAGCT
ACTGAATATACAATTGCAATTGACACGTGGTCTGTTGGTTGTGTATTAACTGTGCTGCCTCTGGGATAGCCTCTCTTCCT
TGGAGAAAGTGGA

Alignment

ORF - retro_atri_40 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 74.49 %
• Parental protein coverage: 68.54 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 3

Retrocopy - Parental Gene Alignment:

Parental  DDKEMEANVVDGNGTETGQIIVTTIGGRNGQPKQNISYMAERVVGHGSFGIVFQAKCLETGETVAIKKVL
          D.KE..A.VV.G..TE.G..I.TTIGGRNGQPK..ISYMAE.VVGHG.F..VF.AKCL.TGE.VAIKK.L
Retrocopy DHKENKAVVVNGRRTEDGHVISTTIGGRNGQPK*TISYMAEHVVGHGPFSEVFRAKCLQTGEVVAIKKLL

Parental  QDKRYKNRELQTMRLLDHPNIVSL-KHCFFSTTDKDELYLNLVMEYVPETVYRVAKHYSRMNQRMPFIYV
          QDKR.KNRELQ.M.LLD.PN...L..HCFFSTT.KDE.YL.LVMEYV..T.Y.VAKHYS.M.Q.MP..YV
Retrocopy QDKRHKNRELQVMHLLDLPNVIRL<EHCFFSTTEKDEVYLSLVMEYVSKTMYKVAKHYSKMSQWMPLVYV

Parental  KLYTYQICRALAYIHGGIGVCHRDIKPQNLLVNPHTHQLKL-CDF-GSAKVLVKGEPNISYICSRYYRAP
          KLY.YQICR..AYIHG.IGVCH.DIKPQNLLVNP.THQLKL.CDF.GSAK.LV.GE.NIS.I.SRY.RAP
Retrocopy KLYPYQICRSFAYIHGVIGVCHHDIKPQNLLVNPYTHQLKL>CDF>GSAKMLVAGEHNISCISSRYDRAP

Parental  ELIFGATEYTTAIDMWSVGCVLAELLLGSPLFPGESG
          ELIFGATEYT.AID.WSVGCVL..L.LG.PLF.GESG
Retrocopy ELIFGATEYTIAIDTWSVGCVLTVLPLG*PLFLGESG

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_40 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_s00096p00102520	1 retrocopy	retro_atri_40 ,