RetrogeneDB ID: retro_atha_16

Retrocopy location

• Organism: Mouse-ear cress (Arabidopsis thaliana)
• Coordinates: 4:9341151..9342555(-)
• Located in intron of: None

Retrocopy information

• Ensembl ID: AT4G16580
• Aliases: None
• Status: KNOWN_PROTEIN_CODING

Parental gene information

• Parental gene symbol: None
• Ensembl ID: AT5G66720
• Aliases: None
• Description: None

Sequence

>retro_atha_16
ATGTTACCTGTGAGAGAAAGTCTTCAGAAACAAGTTAAGATTTTGATTGGATTAGGGAATTTAGGGTTTGGTGGTTATAG
AGGATTGTACACTAGATTTACTAACCCTAACGGGTTTTTAGAACCAGCTAGCTCTGATTTGTTGTTGATTAACGAAAGGA
GGAATCTTTCTGTTATTGGTGCTGTTTCTCGAACTTTCTCTGTTCCTTCTGTATCTGGTCCGGCCTTTCAGGTCTGTGGA
TATCACATTGATCTTTTGCTTTCGGATCCGTGTAAATCAATGGCGAGTTTAGGTTCTAAGTCTTTGTTTGTGGATCGTCA
TTCTGCTTCTCTTGTTTCAAAGCGTTTCACTGGTGGTATGGTATCTGGAGATGGTCCTAACCGTGGAAGAATCAGTATGA
GACTCAGAGGTAAAGATCACAATGAGAAGTCTACGATCTGTGCGTATTTTGCTTATAGAGGTGCTAAGAGATGGATTTAT
TTGAATCAGCAAAGAAGAGGAATGGGATTTAGAGGCTTGCATAGCTCACTCTCTAATCGCTTATCAGCTGGGAATGCGCC
TGATGTCTCTTTAGATAACTCTGTTACTGACGAACAGGTTAGAGATTCTTCGGATTCTGTAGCGGCTAAGCTATGTACTA
AGCCTCTGAAGCTTGTCTCGGGGTCGTGTTATCTACCGCATCCTGATAAAGAGGCCACTGGGGGAGAGGATGCACATTTT
ATCTGTGCTGAAGAGCAAGCATTAGGTGTGGCAGATGGTGTGGGGGGTTGGGCAGAGCTTGGTATTGATGCAGGTTACTA
TTCTCGGGAGCTTATGTCTAACTCAGTGAATGCAATCCAAGATGAGCCTAAAGGTTCGATTGATCCAGCCAGAGTATTGG
AAAAAGCTCATACTTGCACAAAGTCGCAAGGGTCTTCAACAGCTTGCATCATAGCCTTAACCAACCAGGGACTTCATGCA
ATCAATTTAGGCGACAGCGGGTTCATGGTTGTTCGTGAAGGGCATACGGTTTTCCGTTCCCCTGTTCAACAGCATGACTT
CAACTTCACCTATCAGCTGGAGAGTGGAAGAAACGGCGATTTGCCAAGCTCAGGTCAGGTTTTCACTGTTGCTGTCGCTC
CTGGAGACGTCATAATAGCTGGAACAGATGGGTTGTTTGACAACCTGTACAACAACGAGATCACAGCCATAGTGGTTCAC
GCTGTGAGAGCCAACATAGATCCCCAGGTAACAGCGCAGAAGATTGCAGCATTGGCGCGACAAAGAGCACAGGACAAAAA
CAGACAAACTCCATTCTCGACAGCAGCACAAGATGCTGGCTTCAGATACTACGGTGGTAAGCTTGATGACATTACAGTTG
TTGTCTCTTATGTGGCGGCTTCGAAAGAAGAAGGAAAACATTGA

Alignment

ORF - retro_atha_16 Open Reading Frame is conserved.

Retrocopy - Parental Gene Alignment summary:

• Percent Identity: 76. %
• Parental protein coverage: 60.83 %
• Number of stop codons detected: 0
• Number of frameshifts detected: 0

Retrocopy - Parental Gene Alignment:

Parental  TTSLKLVSGSCYLPHPEKEATGGEDAHFICDEEQAIGVADGVGGWAEVGVNAGLFSRELMSYSVSAIQEQ
          T..LKLVSGSCYLPHP.KEATGGEDAHFIC.EEQA.GVADGVGGWAE.G..AG..SRELMS.SV.AIQ..
Retrocopy TKPLKLVSGSCYLPHPDKEATGGEDAHFICAEEQALGVADGVGGWAELGIDAGYYSRELMSNSVNAIQDE

Parental  HKGSSIDPLVVLEKAHSQTKAKGSSTACIIVLKDKGLHAINLGDSGFTVVREGTTVFQSPVQQHGFNFTY
          .KGS.IDP..VLEKAH..TK..GSSTACII.L...GLHAINLGDSGF.VVREG.TVF.SPVQQH.FNFTY
Retrocopy PKGS-IDPARVLEKAHTCTKSQGSSTACIIALTNQGLHAINLGDSGFMVVREGHTVFRSPVQQHDFNFTY

Parental  QLESGNSADVPSSGQVFTIDVQSGDVIVAGTDGVYDNLYNEEITGVVVSSVRAGLDPKGTAQKIAELARQ
          QLESG...D.PSSGQVFT..V..GDVI.AGTDG..DNLYN.EIT..VV..VRA..DP..TAQKIA.LARQ
Retrocopy QLESGRNGDLPSSGQVFTVAVAPGDVIIAGTDGLFDNLYNNEITAIVVHAVRANIDPQVTAQKIAALARQ

Parental  RAVDKKRQSPFATAAQEAGYRYYGGKLDDITAVVSYVTSS
          RA.DK.RQ.PF.TAAQ.AG.RYYGGKLDDIT.VVSYV..S
Retrocopy RAQDKNRQTPFSTAAQDAGFRYYGGKLDDITVVVSYVAAS

Legend:

• *: Stop codon
• >: Forward frameshift by one nucleotide
• <: Reverse frameshift by one nucleotide

Expression

RNA-Seq

Arabidopsis thaliana was not studied using RNA-Seq expression data.

ChIP-Seq

Arabidopsis thaliana was not studied using ChIP-Seq data.

EST

Arabidopsis thaliana was not studied using EST data.

TSS

Arabidopsis thaliana was not studied using FANTOM5 data.

Lab

retro_atha_16 was not experimentally validated.

Homology

Retrocopy orthology:

Arabidopsis thaliana 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 3 parental genes, and 3 retrocopies.

Species	Parental gene accession	Retrocopies number
Arabidopsis thaliana	AT5G66720	1 retrocopy	retro_atha_16 ,
Brassica oleracea	Bo7g064600	1 retrocopy	retro_bole_4,
Brassica rapa	Bra012095	1 retrocopy	retro_brap_22,