RetrogeneDB ID: retro_atri_50

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00170:565521..565951(+)
• Located in intron of: None

Retrocopy information

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

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00028p00023590
• Aliases: None
• Description: None

Sequence

>retro_atri_50
ATGGATCCATCTTTTGCCCATGCCCCTTTTCCCATTGAAGAAGATGAATGAGATGAAAATAGTTTTGGGATTTCAAGCTT
GTGATTGGGACAAAAGGAGTTGAGTGAGCCGGATGAACCTACTACAAGTGATTCAAAGCCTTCATCTCTAAAGATAAACA
AGAAAGAGAAGATATACTTGGGTCCACACTGCGCTCCTCCCTCTCTCAGTAAGCAAGAAGAACTAAGTGCCTCAGGGCGA
AGCAACGACTCAAGAATAAACTTAAAGATGTTGATAATAAATTTTCTGGTGTTGGTATGGAAAACAAGGTCGAGCAGATT
TGAGAGATAGTTGGTGGGAGTAATAAGGTAAGTGCCGTTATGTCAAAGACTTCTCCTCGAGATTGGCTTGACCCCACTGC
CATGAGTCACAGTTTGAGAGGTCTTCTCAT

Alignment

ORF - retro_atri_50 Open Reading Frame is not conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 80.82 %
• Parental protein coverage: 100.0 %
• Number of stop codons detected: 3
• Number of frameshifts detected: 2

Retrocopy - Parental Gene Alignment:

Parental  MDPASAHAPSSIEDDEWDADGFVIPSLGLGQKDLSEPDEPTANDSKPSSPKINKEEKIYLGPHGAPPSLT
          MDP..AHAP..IE.DE.D...F.I.SL.LGQK.LSEPDEPT..DSKPSS.KINK.EKIYLGPH.APPSL.
Retrocopy MDPSFAHAPFPIEEDE*DENSFGISSL*LGQKELSEPDEPTTSDSKPSSLKINKKEKIYLGPHCAPPSLS

Parental  KQQELSASGR-KQRLKHKLKDADKKFSGVGRENKVEQIREIVGGGNKVSAVMSKTSPRDWLD-PHCHESQ
          KQ.ELSASGR.KQRLK.KLKD.D.KFSGVG.ENKVEQI.EIVGG.NKVSAVMSKTSPRDWLD.PHCHESQ
Retrocopy KQEELSASGR<KQRLKNKLKDVDNKFSGVGMENKVEQI*EIVGGSNKVSAVMSKTSPRDWLD<PHCHESQ

Parental  FERSSH
          FERSSH
Retrocopy FERSSH

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_50 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_s00028p00023590	1 retrocopy	retro_atri_50 ,