RetrogeneDB ID: retro_atri_42

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00089:477745..478191(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00078p00099060
• Aliases: None
• Description: None

Sequence

>retro_atri_42
ATGGGTCAATTTCTCTATTGTTGTATTCAAGTGGATTAGTCAATTGTGGCTATTAAAGAGAGGTATGGGCGATTTGATGA
TGTGCTTGAGCCAGGTTGCCATTGCATGCCATGGTTTCTTGGTAGCGAGCTTGCTGGTCATCTCACGTTACGTTTGCAAC
AACTTGATGTTAGATGCGAAACAAAGACCAAGGATAATGTCTTTGTTAACGTAGTTGCTTCTATTTAGTATAGTGTGCTT
GTTGATAAGGCAAGCGATGCTTTATACAAGTTAAGCAATACAAGGACACAAATCCAAACATATGTTTTCGATGTGATCAG
GCAAGCGTTCCAAAGCTCAACTTGGATTATGTCTTTTAACAAAAGAATGATATTGCCAAGGCTATGGAAGATGAACTTGA
GAAGGCAATGTCTGCTTATGGATACCAGATAGTACAGGTTCTGATA

Alignment

ORF - retro_atri_42 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 77.33 %
• Parental protein coverage: 52.11 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 1

Retrocopy - Parental Gene Alignment:

Parental  MGQ-LFCCLQVDQSNVAIREQFGKFDDVLEPGCHFLPWCLGSQVAGYLTLRVQQLDVRCETKTKDNVFVT
          MGQ.L.CC.QVD.S.VAI.E..G.FDDVLEPGCH..PW.LGS..AG.LTLR.QQLDVRCETKTKDNVFV.
Retrocopy MGQFLYCCIQVD*SIVAIKERYGRFDDVLEPGCHCMPWFLGSELAGHLTLRLQQLDVRCETKTKDNVFVN

Parental  VVASIQYRALADKASDAFYKLSNTKNQIQAYVFDVIR-ASVPKLNLDDAFEQKNEIAKAVEEELEKAMSA
          VVASI.Y..L.DKASDA.YKLSNT..QIQ.YVFDVIR.ASVPKLNLD..F.QKN.IAKA.E.ELEKAMSA
Retrocopy VVASI*YSVLVDKASDALYKLSNTRTQIQTYVFDVIR<ASVPKLNLDYVF*QKNDIAKAMEDELEKAMSA

Parental  YGYEIVQTLI
          YGY.IVQ.LI
Retrocopy YGYQIVQVLI

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_42 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_s00078p00099060	1 retrocopy	retro_atri_42 ,