RetrogeneDB ID: retro_atri_5

Retrocopy location

• Organism: Amborella (Amborella trichopoda)
• Coordinates: AmTr_v1.0_scaffold00023:296984..297587(+)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AMTR_s00023p00037680
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AMTR_s00107p00103680
• Aliases: None
• Description: None

Sequence

>retro_atri_5
ATGATCTGCCACAAGCAGGCCCACCTCCCTTCCCATCTCCCCCCCTGCACACCACCAATCCCCCAGCCCTCCCCCGACCT
CTCGGACTTGTTGCGCCGCTACCACAACCACCCTCTCCTCCCCAACCAATGCACCTCCACCGTGGTTCAGCCCATTGACG
CTCCCGTCTCCTCCGTCTGGTCTGTCGTCCGACGCTTCGACGAGCCTCAGACTTACAAGCACTTCATCCGGAGCTGCTCC
CTCCGTGCCGGCGACGGCACCTCTGTCGGCACCCTCCGCGAGGTCCGCGTCGTCTCCGGCCTTCCTGCGGCCTCCAGCAC
CGAGCGCCTGGAGATCCTCGACGACGAGCACCACATCATCAGCTTCCGGGTCATTGGAGGGGATCATAGGCTGGCGAATT
ATCGCTCCGTCACTACCCTCCACCCTGTGGCAAGGTCCAATGGTGAGGGCACCTTGGTAATTGAGTCCTACGTCGTAGAC
GTTCCACCGGGGAACACCAAGGAGGAGACGGTGACGTTTGTGGACACCATCGTCAAATGCAACCTGCAGTCCCTTGCTCA
GATCGCAGAGAGCCTCAATCATCGACAACGCCGCCGCCTCTGA

Alignment

ORF - retro_atri_5 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 56.02 %
• Parental protein coverage: 90.66 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  QRHHRHEIMENQCTSALVKHIKAPLQLVWSLVRRFDQPQKYKPFISRCVLVRGD-LEIGSVREVNVRSGL
          .R.H.H....NQCTS..V..I.AP...VWS.VRRFD.PQ.YK.FI..C.L..GD....G..REV.V.SGL
Retrocopy RRYHNHPLLPNQCTSTVVQPIDAPVSSVWSVVRRFDEPQTYKHFIRSCSLRAGDGTSVGTLREVRVVSGL

Parental  PATTSTERLELLDDNEHILSVKIVGGDHRLKNYSSLITLHPEIIEGRPGTMVIESFVVDVPDGNTTDETR
          PA..STERLE.LDD..HI.S....GGDHRL.NY.S..TLHP.......GT.VIES.VVDVP.GNT..ET.
Retrocopy PAASSTERLEILDDEHHIISFRVIGGDHRLANYRSVTTLHPVARSNGEGTLVIESYVVDVPPGNTKEETV

Parental  YFVEALIKCNLKSLADVSERLAIQDR
          .FV....KCNL.SLA...E.L....R
Retrocopy TFVDTIVKCNLQSLAQIAESLNHRQR

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_5 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 4 parental genes, and 4 retrocopies.

Species	Parental gene accession	Retrocopies number
Amborella trichopoda	AMTR_s00107p00103680	1 retrocopy	retro_atri_5 ,
Oryza brachyantha	OB05G16630	1 retrocopy	retro_obra_18,
Oryza barthii	OBART05G07210	1 retrocopy	retro_obar_15,
Prunus persica	PRUPE_ppa012114mg	1 retrocopy	retro_pper_8,