RetrogeneDB ID: retro_atri_20

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00012:3682138..3682622(-)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00057p00185220
• Aliases: None
• Description: None

Sequence

>retro_atri_20
TCTATTTTGTGGGTTCGGAACCTTCACCGCTACGTTCGCAATCGTGCTGGATTGGGCTCGGAGGCGTTAATAGAGCTTGA
AACAAAAAGGAGATTACTCAATATATTAAAAAAGAAGCAACAAAAGAATGCCGAAGCTGGCGCAATTCCAAGCTTCTACA
AAACAAACCAACAGAAGGGTCTATAAGTAACTAAGTTTAAAGATTGGCGAAGTCCAGGTTCTTGAAGAAGCAATCAGATT
TGTTGCTGAATGCTGATGATTTAGAAGCCATGTGGGTTTGCTTGCGCGAGAATTGCGTGATCGATGACTCCACAGGTACT
GAGAAGATGACCTATGAAGATTTTTGCCACATTGCATCTGTGTGTAGTGAGCAAATTGGTCCAAAATGTCGGCGCTTCTT
CAGTCCTTCAAATTTATGAAGTTTGAGAAGGATGAATCTGGAAGAATAGCTATTCTGCCAATTTACCTCTATGTGATGCC
CACG

Alignment

ORF - retro_atri_20 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 87.2 %
• Parental protein coverage: 78.26 %
• Number of stop codons detected: 2
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  SMLWVRNLRRYVRNRAGLGSEALMELETKRILLDIFKEKQQRNAEAGAIPSFYK-KKPTEGSISNRVQRL
          S.LWVRNL.RYVRNRAGLGSEAL.ELETKR.LL.I.K.KQQ.NAEAGAIPSFYK..KPTEGSISN.V.RL
Retrocopy SILWVRNLHRYVRNRAGLGSEALIELETKRRLLNILKKKQQKNAEAGAIPSFYK<NKPTEGSISN*V*RL

Parental  AKFRFLKKQSDLLLNADDLDAMWVCLREKCVVDDSTGTEKMNYEDFCRIASVCSEQIGPKCRRFFSPSN-
          AK.RFLKKQSDLLLNADDL.AMWVCLRE.CV.DDSTGTEKM.YEDFC.IASVCSEQIGPKCRRFFSPSN.
Retrocopy AKSRFLKKQSDLLLNADDLEAMWVCLRENCVIDDSTGTEKMTYEDFCHIASVCSEQIGPKCRRFFSPSN<

Parental  FMKFEKDESGRIAILPFYLYVMRT
          FMKFEKDESGRIAILP.YLYVM.T
Retrocopy FMKFEKDESGRIAILPIYLYVMPT

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_20 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_s00057p00185220	1 retrocopy	retro_atri_20 ,